From e029db8882ac8c97fb945ada4f81db483ea07fc6 Mon Sep 17 00:00:00 2001 From: giang-trinh Date: Mon, 24 Apr 2023 12:21:27 +0200 Subject: [PATCH 01/12] Preprocessing SSF same as in mtsNFVS --- nfvsmotifs/SuccessionDiagram.py | 22 +++---- nfvsmotifs/motif_avoidant.py | 110 +++++++++++++++++++++----------- 2 files changed, 82 insertions(+), 50 deletions(-) diff --git a/nfvsmotifs/SuccessionDiagram.py b/nfvsmotifs/SuccessionDiagram.py index cc0aaddb..aad228af 100644 --- a/nfvsmotifs/SuccessionDiagram.py +++ b/nfvsmotifs/SuccessionDiagram.py @@ -357,18 +357,16 @@ def expand_attractors(self, node_id: int) -> list[dict[str, int]]: if DEBUG: print(f"[id={node_id};children={len(child_spaces)}] Candidates: {len(candidate_seeds)}") - if len(candidate_seeds) == 1 and len(child_spaces) == 0: - # If this is a (non-strict) minimal trap and there is only one seed, - # the seed must be valid. - attractors = candidate_seeds - else: - attractors = detect_motif_avoidant_attractors( - self.network, - self.petri_net, - candidate_seeds, - terminal_restriction_space, - max_iterations=1000 - ) + is_in_an_mts = len(child_spaces) == 0 + attractors = detect_motif_avoidant_attractors( + self.network, + self.petri_net, + candidate_seeds, + terminal_restriction_space, + max_iterations=1000, + ensure_subspace=node_space, + is_in_an_mts=is_in_an_mts + ) if len(attractors) > 0: self.attractors[node_id] = attractors diff --git a/nfvsmotifs/motif_avoidant.py b/nfvsmotifs/motif_avoidant.py index e3649968..8cf69b35 100644 --- a/nfvsmotifs/motif_avoidant.py +++ b/nfvsmotifs/motif_avoidant.py @@ -45,7 +45,9 @@ def detect_motif_avoidant_attractors( if len(candidates) == 1 and is_in_an_mts: return candidates - candidates = _preprocess_candidates(network, candidates, terminal_restriction_space, max_iterations, ensure_subspace=ensure_subspace) + candidates = _preprocess_candidates(network, candidates, terminal_restriction_space, max_iterations, ensure_subspace=ensure_subspace,is_in_an_mts=is_in_an_mts) + + print(f"Candidates (after): {len(candidates)}") if len(candidates) == 0: return [] @@ -60,7 +62,8 @@ def _preprocess_candidates( candidates: list[dict[str, int]], terminal_restriction_space: BinaryDecisionDiagram, max_iterations: int, - ensure_subspace: dict[str, int] = {} + ensure_subspace: dict[str, int] = {}, + is_in_an_mts: bool = False ) -> list[dict[str, int]]: """ A fast but incomplete method for eliminating spurious attractor candidates. @@ -93,47 +96,78 @@ def _preprocess_candidates( function_bdd = expr2bdd(aeon_to_pyeda(function_expression)) update_functions[var_name] = function_bdd - symbolic_candidates = state_list_to_bdd(candidates) - filtered_candidates = [] - for state in candidates: - state_bdd = state_to_bdd(state) - - # Remove state from the symbolic set. If we can prove that is - # is not an attractor, we will put it back. - symbolic_candidates = symbolic_candidates & ~state_bdd - simulation = state.copy() # A copy of the state that we can overwrite. - is_valid_candidate = True + if is_in_an_mts == False: + symbolic_candidates = state_list_to_bdd(candidates) + filtered_candidates = [] + for state in candidates: + state_bdd = state_to_bdd(state) + + # Remove state from the symbolic set. If we can prove that is + # is not an attractor, we will put it back. + symbolic_candidates = symbolic_candidates & ~state_bdd + + simulation = state.copy() # A copy of the state that we can overwrite. + is_valid_candidate = True + for _ in range(max_iterations): + # Advance all variables by one step in random order. + random.shuffle(variables) + for var in variables: + step = function_eval(update_functions[var], simulation) + assert step is not None + simulation[var] = step + + if function_is_true(symbolic_candidates, simulation): + # The state can reach some other state in the candidate + # set. This does not mean it cannot be an attractor, but + # it means it is sufficient to keep considering the other + # candidate. + is_valid_candidate = False + break + + if not function_is_true(terminal_restriction_space, simulation): + # The state can reach some other state outside of the + # terminal restriction space, which means it cannot be + # a motif avoidant attractor in this subspace. + is_valid_candidate = False + break + + if is_valid_candidate: + # If we cannot rule out the candidate, we can put it back + # into candidate set. + symbolic_candidates = symbolic_candidates | state_bdd + filtered_candidates.append(state) + + return filtered_candidates + else: + filtered_candidates = [] for _ in range(max_iterations): - # Advance all variables by one step in random order. random.shuffle(variables) - for var in variables: - step = function_eval(update_functions[var], simulation) - assert step is not None - simulation[var] = step - - if function_is_true(symbolic_candidates, simulation): - # The state can reach some other state in the candidate - # set. This does not mean it cannot be an attractor, but - # it means it is sufficient to keep considering the other - # candidate. - is_valid_candidate = False - break + symbolic_candidates = state_list_to_bdd(candidates) + filtered_candidates = [] + + for state in candidates: + state_bdd = state_to_bdd(state) + symbolic_candidates = symbolic_candidates & ~state_bdd + + simulation = state.copy() + for var in variables: + step = function_eval(update_functions[var], simulation) + assert step is not None + simulation[var] = step - if not function_is_true(terminal_restriction_space, simulation): - # The state can reach some other state outside of the - # terminal restriction space, which means it cannot be - # a motif avoidant attractor in this subspace. - is_valid_candidate = False + if not function_is_true(symbolic_candidates, simulation): + #symbolic_candidates = symbolic_candidates | state_bdd + symbolic_candidates = symbolic_candidates | state_to_bdd(simulation) + filtered_candidates.append(simulation) + + if len(filtered_candidates) <= 1: break - if is_valid_candidate: - # If we cannot rule out the candidate, we can put it back - # into candidate set. - symbolic_candidates = symbolic_candidates | state_bdd - filtered_candidates.append(state) - - return filtered_candidates + candidates = filtered_candidates.copy() + + return filtered_candidates + def _filter_candidates( @@ -144,7 +178,7 @@ def _filter_candidates( """ Filter candidate states using reachability procedure in Pint. """ - + print("Run _filter_candidates") avoid_states = ~terminal_restriction_space | state_list_to_bdd(candidates) filtered_candidates = [] From 2de9b05a77381a3bd3c87a9c859c4fd00e2848c6 Mon Sep 17 00:00:00 2001 From: giang-trinh Date: Mon, 24 Apr 2023 19:18:22 +0200 Subject: [PATCH 02/12] Heuristics for setting retained set --- nfvsmotifs/SuccessionDiagram.py | 24 ++++++++++++++++++++++-- nfvsmotifs/motif_avoidant.py | 4 +++- 2 files changed, 25 insertions(+), 3 deletions(-) diff --git a/nfvsmotifs/SuccessionDiagram.py b/nfvsmotifs/SuccessionDiagram.py index aad228af..675ea848 100644 --- a/nfvsmotifs/SuccessionDiagram.py +++ b/nfvsmotifs/SuccessionDiagram.py @@ -8,6 +8,8 @@ import networkx as nx # type: ignore +import random # type: ignore + from nfvsmotifs.petri_net_translation import network_to_petrinet from nfvsmotifs.interaction_graph_utils import find_minimum_NFVS, feedback_vertex_set from nfvsmotifs.trappist_core import trappist, compute_fixed_point_reduced_STG @@ -15,6 +17,7 @@ from nfvsmotifs.motif_avoidant import detect_motif_avoidant_attractors from nfvsmotifs.state_utils import state_list_to_bdd from nfvsmotifs.terminal_restriction_space import get_terminal_restriction_space +from nfvsmotifs.pyeda_utils import aeon_to_pyeda # Enables helpful "progress" messages. DEBUG = False @@ -306,7 +309,24 @@ def expand_attractors(self, node_id: int) -> list[dict[str, int]]: retained_set = node_space.copy() for x in self.nfvs: if x not in retained_set: - retained_set[x] = 0 + """Set all nodes to 0""" + #retained_set[x] = 0 + + """Set nodes to values based on the majority of satisfying values of functions""" + fx = self.network.get_update_function(x) + fx = aeon_to_pyeda(fx) + n_input = len(list(fx.support)) + n_poss_sat = pow(2, n_input - 1) + + n_sat = fx.satisfy_count() + + if n_sat > n_poss_sat: + retained_set[x] = 1 + elif n_sat < n_poss_sat: + retained_set[x] = 0 + else: + retained_set[x] = random.randint(0, 1) + child_spaces = [self.node_space(child) for child in self.G.successors(node_id)] @@ -317,7 +337,7 @@ def expand_attractors(self, node_id: int) -> list[dict[str, int]]: return [retained_set] # old code - # terminal_restriction_space = ~state_list_to_bdd(child_spaces) + #terminal_restriction_space = ~state_list_to_bdd(child_spaces) # new code that should be the same as before terminal_restriction_space = get_terminal_restriction_space(child_spaces, diff --git a/nfvsmotifs/motif_avoidant.py b/nfvsmotifs/motif_avoidant.py index 8cf69b35..81586c97 100644 --- a/nfvsmotifs/motif_avoidant.py +++ b/nfvsmotifs/motif_avoidant.py @@ -92,7 +92,7 @@ def _preprocess_candidates( continue var_name = network.get_variable_name(var) variables.append(var_name) - function_expression = network.get_update_function(var) + function_expression = network.get_update_function(var) function_bdd = expr2bdd(aeon_to_pyeda(function_expression)) update_functions[var_name] = function_bdd @@ -101,6 +101,7 @@ def _preprocess_candidates( symbolic_candidates = state_list_to_bdd(candidates) filtered_candidates = [] for state in candidates: + print("Run outside mts") state_bdd = state_to_bdd(state) # Remove state from the symbolic set. If we can prove that is @@ -142,6 +143,7 @@ def _preprocess_candidates( else: filtered_candidates = [] for _ in range(max_iterations): + print("Run inside mts") random.shuffle(variables) symbolic_candidates = state_list_to_bdd(candidates) filtered_candidates = [] From 9d7fa56439de2401bfe2a29f0f04e7c8747a1822 Mon Sep 17 00:00:00 2001 From: giang-trinh Date: Tue, 25 Apr 2023 22:36:15 +0200 Subject: [PATCH 03/12] Add Jordan's code for ruling out BDDs --- nfvsmotifs/motif_avoidant.py | 43 ++++++++++++++++++++++-------------- nfvsmotifs/state_utils.py | 27 +++++++++++++++++++++- 2 files changed, 53 insertions(+), 17 deletions(-) diff --git a/nfvsmotifs/motif_avoidant.py b/nfvsmotifs/motif_avoidant.py index 81586c97..a73dc07f 100644 --- a/nfvsmotifs/motif_avoidant.py +++ b/nfvsmotifs/motif_avoidant.py @@ -1,5 +1,6 @@ from __future__ import annotations +from copy import deepcopy import random from functools import reduce from networkx import DiGraph # type:ignore @@ -9,7 +10,7 @@ from nfvsmotifs.petri_net_translation import place_to_variable from nfvsmotifs.pyeda_utils import aeon_to_pyeda -from nfvsmotifs.state_utils import state_to_bdd, state_list_to_bdd, function_eval, function_is_true +from nfvsmotifs.state_utils import dnf_function_is_true, remove_state_from_dnf, state_to_bdd, state_list_to_bdd, function_eval, function_is_true from typing import TYPE_CHECKING if TYPE_CHECKING: @@ -96,17 +97,21 @@ def _preprocess_candidates( function_bdd = expr2bdd(aeon_to_pyeda(function_expression)) update_functions[var_name] = function_bdd - + print("Finish loading functions") if is_in_an_mts == False: - symbolic_candidates = state_list_to_bdd(candidates) + #symbolic_candidates = state_list_to_bdd(candidates) + symbolic_candidates = deepcopy(candidates) filtered_candidates = [] + i = 1 for state in candidates: - print("Run outside mts") - state_bdd = state_to_bdd(state) + print(f"Run outside mts - {i}") + i += 1 + #state_bdd = state_to_bdd(state) # Remove state from the symbolic set. If we can prove that is # is not an attractor, we will put it back. - symbolic_candidates = symbolic_candidates & ~state_bdd + #symbolic_candidates = symbolic_candidates & ~state_bdd + symbolic_candidates = remove_state_from_dnf(symbolic_candidates, state) simulation = state.copy() # A copy of the state that we can overwrite. is_valid_candidate = True @@ -118,7 +123,8 @@ def _preprocess_candidates( assert step is not None simulation[var] = step - if function_is_true(symbolic_candidates, simulation): + #if function_is_true(symbolic_candidates, simulation): + if dnf_function_is_true(symbolic_candidates, simulation): # The state can reach some other state in the candidate # set. This does not mean it cannot be an attractor, but # it means it is sufficient to keep considering the other @@ -136,21 +142,24 @@ def _preprocess_candidates( if is_valid_candidate: # If we cannot rule out the candidate, we can put it back # into candidate set. - symbolic_candidates = symbolic_candidates | state_bdd + #symbolic_candidates = symbolic_candidates | state_bdd + symbolic_candidates.append(state) filtered_candidates.append(state) return filtered_candidates else: filtered_candidates = [] - for _ in range(max_iterations): - print("Run inside mts") + for i in range(max_iterations): + print(f"Run inside mts - {i + 1}") random.shuffle(variables) - symbolic_candidates = state_list_to_bdd(candidates) + #symbolic_candidates = state_list_to_bdd(candidates) + symbolic_candidates = deepcopy(candidates) filtered_candidates = [] for state in candidates: - state_bdd = state_to_bdd(state) - symbolic_candidates = symbolic_candidates & ~state_bdd + #state_bdd = state_to_bdd(state) + #symbolic_candidates = symbolic_candidates & ~state_bdd + symbolic_candidates = remove_state_from_dnf(symbolic_candidates, state) simulation = state.copy() for var in variables: @@ -158,15 +167,17 @@ def _preprocess_candidates( assert step is not None simulation[var] = step - if not function_is_true(symbolic_candidates, simulation): + #if not function_is_true(symbolic_candidates, simulation): + if not dnf_function_is_true(symbolic_candidates, simulation): #symbolic_candidates = symbolic_candidates | state_bdd - symbolic_candidates = symbolic_candidates | state_to_bdd(simulation) + #symbolic_candidates = symbolic_candidates | state_to_bdd(simulation) + symbolic_candidates.append(simulation) filtered_candidates.append(simulation) if len(filtered_candidates) <= 1: break - candidates = filtered_candidates.copy() + candidates = deepcopy(filtered_candidates) return filtered_candidates diff --git a/nfvsmotifs/state_utils.py b/nfvsmotifs/state_utils.py index 8c1a4491..20959be7 100644 --- a/nfvsmotifs/state_utils.py +++ b/nfvsmotifs/state_utils.py @@ -77,4 +77,29 @@ def function_is_true(f: BinaryDecisionDiagram, state: dict[str, int]) -> bool: return False return function_restrict(f, state).is_one() - \ No newline at end of file + + +def dnf_function_is_true(dnf: list[dict[str, int]], state: dict[str, int]) -> bool: + """ + Returns `True` if the given DNF function evaluates to `1` for the given + state (or space). + """ + if len(dnf) == 0: + return False + + for conjunction in dnf: + if conjunction.items() <= state.items(): + return True + return False + +def remove_state_from_dnf(dnf: list[dict[str, int]], state: dict[str, int]) -> list[dict[str, int]]: + """ + Removes all conjunctions that are True in the state + """ + modified_dnf = [] + for conjunction in dnf: + if conjunction.items() <= state.items(): + pass + else: + modified_dnf.append(conjunction) + return modified_dnf \ No newline at end of file From f847dea9cba742d9ed6f12169e9701cddf78d2ed Mon Sep 17 00:00:00 2001 From: giang-trinh Date: Tue, 16 May 2023 16:59:38 +0200 Subject: [PATCH 04/12] New heuristic for setting retained_set --- nfvsmotifs/SuccessionDiagram.py | 81 +++++--- nfvsmotifs/motif_avoidant.py | 6 +- test.bnet | 25 +++ test/A_model.bnet | 75 ++++++++ test/CASCADE1.bnet | 66 +++++++ test/CASCADE2.bnet | 141 ++++++++++++++ test/CASCADE3.bnet | 177 ++++++++++++++++++ test/Cell-Cycle-2019.bnet | 88 +++++++++ test/Drosophila.bnet | 59 ++++++ test/EMT.bnet | 75 ++++++++ test/EMT_Mechanosensing.bnet | 136 ++++++++++++++ ...ion_CIP_Migration_CellCycle_Apoptosis.bnet | 121 ++++++++++++ test/SEGMENT-POLARITY-6-CELL.bnet | 103 ++++++++++ test/T-CELL-RECEPTOR-SIGNALING.bnet | 50 +++++ ..._083]__[SIGNALING-IN-PROSTATE-CANCER].bnet | 117 ++++++++++++ ...id_075]__[INFLAMMATORY-BOWEL-DISEASE].bnet | 47 +++++ ...60]__[id_085]__[T-LGL-SIGNALING-2008].bnet | 58 ++++++ ...d_014]__[T-LGL-SURVIVAL-NETWORK-2008].bnet | 59 ++++++ test/[var_62]__[id_145]__[MELANOGENESIS].bnet | 53 ++++++ ...LING-PATHWAY-FOR-BUTHANOL-PRODUCTION].bnet | 58 ++++++ ...1]__[COLITIS-ASSOCIATED-COLON-CANCER].bnet | 67 +++++++ .../[var_86]__[id_019]__[IL-6-SIGNALING].bnet | 56 ++++++ test/ascidian_embryo_validation.bnet | 48 +++++ test/flobak_2015.bnet | 66 +++++++ test/fumia_2013.bnet | 85 +++++++++ test/steinway_2015.bnet | 69 +++++++ 26 files changed, 1962 insertions(+), 24 deletions(-) create mode 100644 test.bnet create mode 100644 test/A_model.bnet create mode 100644 test/CASCADE1.bnet create mode 100644 test/CASCADE2.bnet create mode 100755 test/CASCADE3.bnet create mode 100644 test/Cell-Cycle-2019.bnet create mode 100644 test/Drosophila.bnet create mode 100644 test/EMT.bnet create mode 100644 test/EMT_Mechanosensing.bnet create mode 100644 test/Regan2020_Adhesion_CIP_Migration_CellCycle_Apoptosis.bnet create mode 100644 test/SEGMENT-POLARITY-6-CELL.bnet create mode 100755 test/T-CELL-RECEPTOR-SIGNALING.bnet create mode 100644 test/[var_133]__[id_083]__[SIGNALING-IN-PROSTATE-CANCER].bnet create mode 100644 test/[var_47]__[id_075]__[INFLAMMATORY-BOWEL-DISEASE].bnet create mode 100644 test/[var_60]__[id_085]__[T-LGL-SIGNALING-2008].bnet create mode 100644 test/[var_61]__[id_014]__[T-LGL-SURVIVAL-NETWORK-2008].bnet create mode 100644 test/[var_62]__[id_145]__[MELANOGENESIS].bnet create mode 100644 test/[var_66]__[id_077]__[SIGNALING-PATHWAY-FOR-BUTHANOL-PRODUCTION].bnet create mode 100644 test/[var_70]__[id_051]__[COLITIS-ASSOCIATED-COLON-CANCER].bnet create mode 100644 test/[var_86]__[id_019]__[IL-6-SIGNALING].bnet create mode 100644 test/ascidian_embryo_validation.bnet create mode 100644 test/flobak_2015.bnet create mode 100644 test/fumia_2013.bnet create mode 100644 test/steinway_2015.bnet diff --git a/nfvsmotifs/SuccessionDiagram.py b/nfvsmotifs/SuccessionDiagram.py index 675ea848..8a187901 100644 --- a/nfvsmotifs/SuccessionDiagram.py +++ b/nfvsmotifs/SuccessionDiagram.py @@ -29,7 +29,10 @@ def __init__(self, network: BooleanNetwork): # A Petri net representation of the original Boolean network. self.petri_net = network_to_petrinet(network) # Negative feedback vertex set. - self.nfvs = feedback_vertex_set(network, parity="negative")#find_minimum_NFVS(network) + self.nfvs = feedback_vertex_set(network, parity="negative") + #self.nfvs = find_minimum_NFVS(network) + print(f"|U-| = {len(self.nfvs)}") + #print(self.nfvs) # A directed acyclic graph representing the succession diagram. self.G = nx.DiGraph() # A dictionary used for uniqueness checks on the nodes of the succession diagram. @@ -307,29 +310,65 @@ def expand_attractors(self, node_id: int) -> list[dict[str, int]]: # the space is a trap and this will remove the corresponding unnecessary # Petri net transitions. retained_set = node_space.copy() - for x in self.nfvs: - if x not in retained_set: - """Set all nodes to 0""" - #retained_set[x] = 0 - - """Set nodes to values based on the majority of satisfying values of functions""" - fx = self.network.get_update_function(x) - fx = aeon_to_pyeda(fx) - n_input = len(list(fx.support)) - n_poss_sat = pow(2, n_input - 1) - - n_sat = fx.satisfy_count() - - if n_sat > n_poss_sat: - retained_set[x] = 1 - elif n_sat < n_poss_sat: - retained_set[x] = 0 - else: - retained_set[x] = random.randint(0, 1) - child_spaces = [self.node_space(child) for child in self.G.successors(node_id)] + # find the child space least common with NFVS + if (len(child_spaces) > 0): + least_common_child_space = child_spaces[0] + least_common_nodes = len(set(least_common_child_space) & set(self.nfvs)) + for child_space in child_spaces: + common_nodes = len(set(child_space) & set(self.nfvs)) + if (common_nodes < least_common_nodes): + least_common_nodes = common_nodes + least_common_child_space = child_space + + for x in self.nfvs: + if x not in retained_set: + if x in least_common_child_space: + retained_set[x] = least_common_child_space[x] + else: + """Set nodes to values based on the majority of satisfying values of functions""" + fx = self.network.get_update_function(x) + fx = aeon_to_pyeda(fx) + n_input = len(list(fx.support)) + n_poss_sat = pow(2, n_input - 1) + + n_sat = fx.satisfy_count() + + if n_sat > n_poss_sat: + retained_set[x] = 1 + elif n_sat < n_poss_sat: + retained_set[x] = 0 + else: + #retained_set[x] = random.randint(0, 1) + retained_set[x] = 0 + #retained_set[x] = 1 + else: + for x in self.nfvs: + if x not in retained_set: + """Set all nodes to 0""" + #retained_set[x] = 0 + + """Set nodes to values based on the majority of satisfying values of functions""" + fx = self.network.get_update_function(x) + fx = aeon_to_pyeda(fx) + n_input = len(list(fx.support)) + n_poss_sat = pow(2, n_input - 1) + + n_sat = fx.satisfy_count() + + if n_sat > n_poss_sat: + retained_set[x] = 1 + elif n_sat < n_poss_sat: + retained_set[x] = 0 + else: + #retained_set[x] = random.randint(0, 1) + retained_set[x] = 0 + #retained_set[x] = 1 + + + if len(retained_set) == self.network.num_vars() and len(child_spaces) == 0: # There is only a single attractor remaining here, # and its "seed" is the retain set. diff --git a/nfvsmotifs/motif_avoidant.py b/nfvsmotifs/motif_avoidant.py index a73dc07f..2f142547 100644 --- a/nfvsmotifs/motif_avoidant.py +++ b/nfvsmotifs/motif_avoidant.py @@ -97,14 +97,14 @@ def _preprocess_candidates( function_bdd = expr2bdd(aeon_to_pyeda(function_expression)) update_functions[var_name] = function_bdd - print("Finish loading functions") + #print("Finish loading functions") if is_in_an_mts == False: #symbolic_candidates = state_list_to_bdd(candidates) symbolic_candidates = deepcopy(candidates) filtered_candidates = [] i = 1 for state in candidates: - print(f"Run outside mts - {i}") + #print(f"Run outside mts - {i}") i += 1 #state_bdd = state_to_bdd(state) @@ -150,7 +150,7 @@ def _preprocess_candidates( else: filtered_candidates = [] for i in range(max_iterations): - print(f"Run inside mts - {i + 1}") + #print(f"Run inside mts - {i + 1}") random.shuffle(variables) #symbolic_candidates = state_list_to_bdd(candidates) symbolic_candidates = deepcopy(candidates) diff --git a/test.bnet b/test.bnet new file mode 100644 index 00000000..46ac2e68 --- /dev/null +++ b/test.bnet @@ -0,0 +1,25 @@ +targets, fact|s +A, (!A & !B) | C +B, (!A & !B) | C +C, A & B + +#A, !E | (A & B & C) +#B, !F | (A & B & C) +#C, !D | (A & B & C) +#D, A +#E, B +#F, C + +#A, !E | (G & B & C) +#B, !F | (A & H & C) +#C, !D | (A & B & I) +#D, A +#E, B +#F, C +#G, A +#H, B +#I, C + +#A, !A | !B +#B, !A | !B +#C, A & B diff --git a/test/A_model.bnet b/test/A_model.bnet new file mode 100644 index 00000000..50b4300b --- /dev/null +++ b/test/A_model.bnet @@ -0,0 +1,75 @@ +targets, factors +a_secretase, (CREB|s_NMDAR)&(!ROCK|!Cholesterol) +Ab, ((APP&BACE1)&(Sortilin|PICALM|Cholesterol))&!Autophagy +ABCA7, SREBP2 +AKT, (s_NMDAR&PI3K)&(!PTEN|!PP2A)&!CASP3 +APOE4, APOE4 +Apoer2, Reelin&!APOE4 +Apoptosis, CASP3 +APP, ERK&(!(a_secretase&(Sortilin|LRP6))|!SORL1|!(Dab1&Apoer2)|!(Dab1&Fyn)) +ATM, ROS +Autophagy, (ULK1&LC3&p62&LAMP2&beclin1)&!(Cholesterol&ROS) +BACE1, (STAT3|Cholesterol)&!PGC1a +BAD, !AKT&PP2B +BAX, ((Bim&PUMA)&p53)&!AKT&!Bcl2 +Bcl2, !BAD&(!p53|!JNK|!Bim) +BDNF, (CREB|PGC1a)&Sortilin +beclin1, (ROCK|JNK)&(!Bcl2|!CASP3) +Bim, EGR1|FOXO +Ca_ion, e_NMDAR +CASP2, p53 +CASP3, BAX&Bim +Cdk5, Ca_ion|EGR1 +Cholesterol, !CYP46A1&(SREBP2&HMGCR)|(!LPL|!ABCA7) +CIP2A, Ab +CLU, p53|EGR1 +CREB, (ERK&Jacob&s_NMDAR)|!(Jacob&e_NMDAR) +CYP46A1, !APP&Ca_ion +Dab1, Apoer2&!Fyn +Dkk1, Ab&(CLU|PICALM) +DLK, APOE4 +e_NMDAR, (Ab&Fyn)|PTEN +EGR1, JNK +ERK, !(pTau&PP2A)&((s_NMDAR&!STEP)|MKK7) +FOXO, JNK&!AKT +Fyn, ((Apoer2&Dab1)|mGluR)&!STEP +GSK3beta, (Ca_ion|PP2A)&!(AKT|LRP6) +Jacob, (s_NMDAR&ERK)|e_NMDAR +JNK, MKK7|Vangl2 +LAMP2, PIP2|TFEB +LC3, PIP2|TFEB|!PICALM +LPL, SREBP2&!SORL1 +LRP6, !APOE4|!Dkk1 +MAPT, e_NMDAR&!CREB +MDM2, p53&(!ATM&!CASP2|!GSK3beta) +mGluR, Ab +MKK7, DLK|e_NMDAR +mTOR, (AKT|ERK|Cholesterol)&!SIRT1 +p38, !STEP +p53, (p38|ATM)&!MDM2 +p62, PIP2|TFEB|!PICALM +PGC1a, (CREB|SIRT1)&p38 +PI3K, Dab1|s_NMDAR|BDNF +PICALM, !Ca_ion&!CASP3 +PIP2, !synj1 +PP2A, (!mGluR|!GSK3beta)&!APOE4&!CIP2A +PP2B, mGluR|Ca_ion +PTEN, ROCK +PUMA, !s_NMDAR&(FOXO|p53) +Reelin, !Apoptosis +RhoA, CASP2|Vangl2 +ROCK, RhoA|!SIRT1 +ROS, (Ca_ion|Ab)&!PGC1a +s_NMDAR, (Fyn|BDNF)&!STEP&!pTau +SORL1, !ROCK|BDNF +Sortilin, ROCK +SREBP2, (!Cholesterol|!APP|!ABCA7)|AKT +STAT3, Cdk5 +STEP, (PP2B)&(!s_NMDAR|!e_NMDAR) +synj1, APOE4|(!Cdk5&PP2B) +pTau, (MAPT&(GSK3beta|Cdk5|ERK))&!PP2A&!Autophagy +TFEB, (!APOE4|!mTOR)&PP2B +ULK1, !mTOR +Vangl2, Dkk1 +SIRT1, (!APOE4|!ROS) +HMGCR, BDNF|SREBP2 diff --git a/test/CASCADE1.bnet b/test/CASCADE1.bnet new file mode 100644 index 00000000..25674edf --- /dev/null +++ b/test/CASCADE1.bnet @@ -0,0 +1,66 @@ +targets, factors +AKT1S1, !AKT_f +AKT_f, !mTORC2_c&PDPK1|mTORC2_c +AXIN1, !LRP_f +BTRC, !GSK3_f&!AXIN1&CK1_f|!GSK3_f&AXIN1|GSK3_f +CHUK, AKT_f +CK1_f, !LRP_f +CTNNB1, !BTRC&CHUK +DKK_f, DKK_g +DKK_g, !MYC&TCF7_f +DUSP1, !MAPK14&MSK_f|MAPK14 +DUSP6, !ERK_f&mTORC1_c|ERK_f +DVL_f, FZD_f +EGR1, !TCF7_f +ERK_f, MEK_f&!DUSP6 +FOXO_f, !AKT_f&!NLK +FZD_f, !SFRP1 +GAB_f, GRB2&!ERK_f +GRAP2, !MAPK14 +GRB2, SHC1 +GSK3_f, !DVL_f&!MAPK14&!AKT_f&!ERK_f&!RSK_f&!S6K_f&!LRP_f +IKBKB, MAP3K7&!TP53 +IRS1, !ERK_f&!S6K_f&!IKBKB +JNK_f, !MAP2K4&MAP2K7&!DUSP1|MAP2K4&!DUSP1 +KRAS, !SOS1&PTPN11|SOS1 +LEF, CTNNB1 +LRP_f, !JNK_f&!MAPK14&!ERK_f&FZD_f&!DKK_f|!JNK_f&!MAPK14&ERK_f&!DKK_f|!JNK_f&MAPK14&!DKK_f|JNK_f&!DKK_f +MAP2K3, !MAP3K7&MAP3K5|MAP3K7 +MAP2K4, !MAP3K4&!MAP3K11&!MAP3K7&GRAP2|!MAP3K4&!MAP3K11&MAP3K7|!MAP3K4&MAP3K11|MAP3K4 +MAP2K7, !MAP3K7&GRAP2|MAP3K7 +MAP3K11, RAC_f +MAP3K4, RAC_f +MAP3K5, !AKT_f +MAP3K7, TAB_f +MAP3K8, IKBKB +MAPK14, !MAP2K4&!DUSP1&MAP2K3|MAP2K4&!DUSP1 +MDM2, !AKT_f&!S6K_f&MDM2_g|AKT_f&!S6K_f +MDM2_g, !TP53&NFKB_f|TP53 +MEK_f, !ERK_f&!RAF_f&MAP3K8|!ERK_f&RAF_f +MMP_f, LEF +MSK_f, !MAPK14&ERK_f|MAPK14 +MYC, TCF7_f +NFKB_f, !MSK_f&!IKBKB&CHUK|!MSK_f&IKBKB|MSK_f +NLK, MAP3K7 +PDPK1, !PTEN&PIK3CA +PIK3CA, !KRAS&!GAB_f&IRS1|!KRAS&GAB_f|KRAS +PTEN, PTEN_g&!GSK3_f +PTEN_g, EGR1 +PTPN11, GAB_f +RAC_f, !mTORC2_c&DVL_f|mTORC2_c +RAF_f, !AKT_f&!ERK_f&KRAS&!RHEB +RHEB, !TSC_f +RSK_f, !ERK_f&PDPK1|ERK_f +RTPK_f, !MAPK14&!RTPK_g&!MEK_f&MMP_f|!MAPK14&RTPK_g&!MEK_f +RTPK_g, FOXO_f +S6K_f, !mTORC1_c&PDPK1|mTORC1_c +SFRP1, SFRP1_g +SFRP1_g, !MYC +SHC1, RTPK_f&!PTEN +SOS1, GRB2&!ERK_f +TAB_f, !MAPK14 +TCF7_f, !NLK&CTNNB1 +TP53, MAPK14&!MDM2 +TSC_f, !AKT_f&!ERK_f&!RSK_f&!IKBKB&GSK3_f +mTORC1_c, !RHEB&RSK_f&!AKT1S1|RHEB&!AKT1S1 +mTORC2_c, !S6K_f&TSC_f diff --git a/test/CASCADE2.bnet b/test/CASCADE2.bnet new file mode 100644 index 00000000..67e93f4a --- /dev/null +++ b/test/CASCADE2.bnet @@ -0,0 +1,141 @@ +targets, factors +ACVR1, BMPR2 +AKT1S1, !AKT_f +AKT_f, !mTORC2_c&!PDPK1&!PPP1CA&ILK|!mTORC2_c&PDPK1&!PPP1CA|mTORC2_c&!PPP1CA +AP1_c, !SMAD4&!SMAD3&!ATF2&!FOS&JUN|!SMAD4&!SMAD3&!ATF2&FOS|!SMAD4&!SMAD3&ATF2|!SMAD4&SMAD3|SMAD4 +ARHGAP24, ROCK1 +ATF2, !MAPK14&!JNK_f&ERK_f|!MAPK14&JNK_f|MAPK14 +AXIN1, !LRP_f&GSK3_f&!PPP1CA&!PPM1A +BAD, !AKT_f&!RSK_f +BAX, TP53 +BCL2, !BAD +BMPR2, !SMURF1&!SMURF2 +BTRC, !LRP_f&!CK1_f&!AXIN1&GSK3_f|!LRP_f&!CK1_f&AXIN1|!LRP_f&CK1_f +CASP3, !CASP8&CASP9|CASP8 +CASP8, !CFLAR +CASP9, !CYCS&PPP1CA|CYCS +CBPp300_c, !TP53&!CREBBP&EP300|!TP53&CREBBP +CCND1, !TCF7_f&!RSK_f&STAT3|!TCF7_f&RSK_f|TCF7_f +CDC42, SRC&!ARHGAP24 +CFLAR, AKT_f&!ITCH +CFL_f, !LIMK2&LIMK1|LIMK2 +CHUK, !AKT_f&!PRKCA&TRAF6|!AKT_f&PRKCA|AKT_f +CK1_f, !LRP_f +CREBBP, CHUK +CSK, PRKACA +CTNNB1, CHUK&!BTRC +CYCS, !BCL2&BAX +DAAM1, DVL_f +DKK_f, DKK_g +DKK_g, TCF7_f&!MYC +DUSP1, !SKP2&!MAPK14&!DUSP1_g&MSK_f|!SKP2&!MAPK14&DUSP1_g|!SKP2&MAPK14 +DUSP1_g, !MAPK14&ERK_f|MAPK14 +DUSP6, !mTORC1_c&ERK_f|mTORC1_c +DVL_f, !FZD_f&SMAD1&!ITCH|FZD_f&!ITCH +EGR1, !TCF7_f +EP300, AKT_f&!PRKCD&!SKI +ERK_f, MEK_f&!PPP1CA&!DUSP6 +FOS, !ERK_f&!RSK_f&SRF|!ERK_f&RSK_f|ERK_f +FOXO_f, !CK1_f&!AKT_f&!NLK +FZD_f, !SFRP1 +GAB_f, !ERK_f&GRB2 +GRAP2, !MAPK14 +GRB2, SHC1 +GSK3_f, !DVL_f&!AKT_f&!MAPK14&!ERK_f&!RSK_f&!S6K_f +IKBKB, !TP53&!PLK1&MAP3K7&!PPM1A +ILK, PAK1 +ILR_f, !LIF&AP1_c|LIF +IRAK1, ILR_f&!SOCS1 +IRS1, !ERK_f&!S6K_f&!IKBKB +ITCH, JNK_f +JAK_f, ILR_f&!SOCS1&!PTPN6 +JNK_f, !DUSP1&!MAP2K4&!MAP2K7&PAK1|!DUSP1&!MAP2K4&MAP2K7|!DUSP1&MAP2K4 +JUN, !GSK3_f&JNK_f +KRAS, !PTPN11&SOS1|PTPN11 +LEF1, CTNNB1 +LIF, RAF_f +LIMK1, !RAC_f&ROCK1|RAC_f +LIMK2, !PRKCD&ROCK1 +LRP_f, !DKK_f&!FZD_f&!MAPK14&!JNK_f&ERK_f|!DKK_f&!FZD_f&!MAPK14&JNK_f|!DKK_f&!FZD_f&MAPK14|!DKK_f&FZD_f +MAP2K3, !MAP3K5&MAP3K7|MAP3K5 +MAP2K4, !GRAP2&!MAP3K7&!MAP3K11&MAP3K4|!GRAP2&!MAP3K7&MAP3K11|!GRAP2&MAP3K7|GRAP2 +MAP2K7, !GRAP2&!MAP3K7&MAPK8IP3|!GRAP2&MAP3K7|GRAP2 +MAP3K11, RAC_f +MAP3K4, RAC_f +MAP3K5, !AKT_f +MAP3K7, TAB_f +MAP3K8, IKBKB +MAPK14, !DUSP1&!MAP2K4&MAP2K3|!DUSP1&MAP2K4 +MAPK8IP3, ROCK1 +MAPKAPK2, MAPK14 +MDM2, !AKT_f&!PPP1CA&!S6K_f&!MDM2_g&MAPKAPK2|!AKT_f&!PPP1CA&!S6K_f&MDM2_g|!AKT_f&PPP1CA&!S6K_f|AKT_f&!S6K_f +MDM2_g, !TP53&NFKB_f|TP53 +MEK_f, !RAF_f&!ERK_f&MAP3K8|RAF_f&!ERK_f +MMP_f, !LEF1&STAT3|LEF1 +MSK_f, !MAPK14&ERK_f|MAPK14 +MYC, !TCF7_f&!GSK3_f&!PLK1&STAT3|!TCF7_f&!GSK3_f&PLK1|TCF7_f&!GSK3_f +NFKB_f, !CHUK&!REL_f&!IKBKB&MSK_f|!CHUK&!REL_f&IKBKB|!CHUK&REL_f|CHUK +NLK, MAP3K7 +PAK1, !RAC_f&CDC42|RAC_f +PARD6A, !TGFBR2&TGFBR1|TGFBR2 +PDPK1, !PTEN&PIK3CA +PIAS1, MAPKAPK2 +PIK3CA, !IRS1&!KRAS&GAB_f|!IRS1&KRAS|IRS1 +PLCG1, SYK +PLK1, !PDPK1&MAPKAPK2|PDPK1 +PPM1A, PTEN +PPP1CA, SMAD7&!RTPK_f +PRKACA, !NFKB_f&FOS|NFKB_f +PRKCA, PLCG1 +PRKCD, !PDPK1&CASP3|PDPK1 +PTEN, !SRC&!CBPp300_c&!PTEN_g&!GSK3_f&ROCK1|!SRC&!CBPp300_c&PTEN_g&!GSK3_f +PTEN_g, EGR1 +PTPN11, GAB_f +PTPN6, SRC +RAC_f, !DVL_f&!mTORC2_c&!VAV1&!ARHGAP24&TIAM1|!DVL_f&!mTORC2_c&VAV1&!ARHGAP24|!DVL_f&mTORC2_c&!ARHGAP24|DVL_f&!ARHGAP24 +RAF_f, !AKT_f&!RHEB&KRAS&!ERK_f +REL_f, !CBPp300_c&!STAT1&!IKBKB&MSK_f|!CBPp300_c&!STAT1&IKBKB|CBPp300_c&!STAT1 +RHEB, !TSC_f +RHOA, !RAC_f&!SMURF1&!PARD6A&DAAM1&!RND3 +RND3, ROCK1 +ROCK1, !CASP3&RHOA|CASP3 +RSK_f, !PDPK1&ERK_f|PDPK1 +RTPK_f, !MMP_f&!MEK_f&RTPK_g&!MAPK14|MMP_f&!MEK_f&!MAPK14 +RTPK_g, FOXO_f +S6K_f, !PDPK1&mTORC1_c|PDPK1 +SFRP1, SFRP1_g +SFRP1_g, !MYC +SHC1, !SRC&!ILR_f&!RTPK_f&!PTEN&TGFBR1|!SRC&!ILR_f&RTPK_f&!PTEN|!SRC&ILR_f&!PTEN|SRC&!PTEN +SKI, !AKT_f +SKP2, !CCND1&!ERK_f&EP300|!CCND1&ERK_f|CCND1 +SMAD1, !SMAD6&!GSK3_f&!ERK_f&!SKI&ACVR1&!SMURF1&!PPM1A +SMAD2, !CBPp300_c&!ERK_f&!SKI&!ACVR1&!TGFBR1&!SMURF2&!PPM1A&ITCH|!CBPp300_c&!ERK_f&!SKI&!ACVR1&TGFBR1&!SMURF2&!PPM1A|!CBPp300_c&!ERK_f&!SKI&ACVR1&!SMURF2&!PPM1A|!CBPp300_c&ERK_f&!SKI&!SMURF2&!PPM1A|CBPp300_c&!SKI&!SMURF2&!PPM1A +SMAD3, !SMAD7&!SMAD6&!GSK3_f&!AKT_f&!MAPK14&!JNK_f&!ERK_f&!SKI&!ACVR1&TGFBR1&!PPM1A|!SMAD7&!SMAD6&!GSK3_f&!AKT_f&!MAPK14&!JNK_f&!ERK_f&!SKI&ACVR1&!PPM1A|!SMAD7&!SMAD6&!GSK3_f&!AKT_f&!MAPK14&JNK_f&!ERK_f&!SKI&!PPM1A|!SMAD7&!SMAD6&!GSK3_f&!AKT_f&MAPK14&!ERK_f&!SKI&!PPM1A +SMAD4, !SMAD7&!SMAD6&!ERK_f&!PIAS1&!SMAD2&!SKI&!SMAD3&!SMAD5&SMAD1&!SMURF1|!SMAD7&!SMAD6&!ERK_f&!PIAS1&!SMAD2&!SKI&!SMAD3&SMAD5&!SMURF1|!SMAD7&!SMAD6&!ERK_f&!PIAS1&!SMAD2&!SKI&SMAD3&!SMURF1|!SMAD7&!SMAD6&!ERK_f&!PIAS1&SMAD2&!SKI&!SMURF1|!SMAD7&!SMAD6&!ERK_f&PIAS1&!SKI&!SMURF1|!SMAD7&!SMAD6&ERK_f&!SKI&!SMURF1 +SMAD5, !SKI&ACVR1&!SMURF2 +SMAD6, SMAD6_g +SMAD6_g, !SMAD2&!SMAD4&SMAD3|!SMAD2&SMAD4|SMAD2 +SMAD7, !AXIN1&!EP300&!SMAD7_g&SMURF1&!SMURF2&!ITCH|!AXIN1&!EP300&SMAD7_g&!SMURF2&!ITCH|!AXIN1&EP300&!SMURF2&!ITCH +SMAD7_g, !SMAD2&!SMAD4&SMAD3|!SMAD2&SMAD4|SMAD2 +SMURF1, SMAD7 +SMURF2, SMAD7 +SOCS1, SOCS1_g +SOCS1_g, STAT1 +SOS1, !ERK_f&!PLCG1&GRB2|!ERK_f&PLCG1 +SRC, !CSK&RTPK_f +SRF, !RSK_f&!MAPKAPK2&CFL_f|!RSK_f&MAPKAPK2|RSK_f +STAT1, !SRC&!JAK_f&!MAPK14&!PRKCD&IKBKB&!PIAS1|!SRC&!JAK_f&!MAPK14&PRKCD&!PIAS1|!SRC&!JAK_f&MAPK14&!PIAS1|!SRC&JAK_f&!PIAS1|SRC&!PIAS1 +STAT3, !SRC&!IRAK1&!JAK_f&!mTORC1_c&!MAPK14&!JNK_f&!ERK_f&!PPP1CA&PRKCD|!SRC&!IRAK1&!JAK_f&!mTORC1_c&!MAPK14&!JNK_f&ERK_f&!PPP1CA|!SRC&!IRAK1&!JAK_f&!mTORC1_c&!MAPK14&JNK_f&!PPP1CA|!SRC&!IRAK1&!JAK_f&!mTORC1_c&MAPK14&!PPP1CA|!SRC&!IRAK1&!JAK_f&mTORC1_c&!PPP1CA|!SRC&!IRAK1&JAK_f&!PPP1CA|!SRC&IRAK1&!PPP1CA|SRC&!PPP1CA +SYK, ILR_f +TAB_f, !MAPK14&TRAF6 +TCF7_f, CTNNB1&!NLK +TGFB1, !NFKB_f&!FOS&JUN|!NFKB_f&FOS|NFKB_f +TGFBR1, TGFBR2&!SMAD7&!SMAD6&!SMURF1&!SMURF2 +TGFBR2, TGFB1&!SMURF1&!SMURF2 +TIAM1, !ROCK1 +TP53, !MDM2&!MAPK14&!PRKCD&!EP300&PIAS1|!MDM2&!MAPK14&!PRKCD&EP300|!MDM2&!MAPK14&PRKCD|!MDM2&MAPK14 +TRAF6, !IRAK1&TGFBR1|IRAK1 +TSC_f, GSK3_f&!AKT_f&!ERK_f&!RSK_f&!IKBKB +VAV1, SYK +mTORC1_c, !RHEB&RSK_f&!AKT1S1|RHEB&!AKT1S1 +mTORC2_c, !PIK3CA&!S6K_f&TSC_f|PIK3CA&!S6K_f diff --git a/test/CASCADE3.bnet b/test/CASCADE3.bnet new file mode 100755 index 00000000..8d0cec3e --- /dev/null +++ b/test/CASCADE3.bnet @@ -0,0 +1,177 @@ +targets, factors +ABL1, (ATM & !RB1) +ACVR1, BMPR2 +ADAM17, ERK_f +AKT1S1, !AKT_f +AKT_f, (!ATM & ((!PDPK1 & (!PHLPP1 & (!PPP1CA & mTORC2_c))) | (PDPK1 & (!PHLPP1 & !PPP1CA)))) +AP1_c, ((!FOS & SMAD4) | FOS) +APAF1, CYCS +APC, ((!AXIN1 & (!DVL_f & (GSK3_f & !PRKACA))) | (AXIN1 & (!DVL_f & !PRKACA))) +ARHGAP24, ROCK1 +ATF2, ((!ERK_f & MAPK14) | ERK_f) +ATM, ((!ATR & BRCA1) | ATR) +ATR, ((!ABL1 & CDKN2A) | ABL1) +AURKA, PAK1 +AURKB, (!ATM & CHEK1) +AXIN1, (!AURKA & (GSK3_f & (!LRP_f & (!PPM1A & !PPP1CA)))) +BAD, (!AKT_f & (!PAK1 & (!RAF_f & !RSK_f))) +BAK1, (!BCL2 & ((!BID & (!MCL1 & TP53)) | (BID & !MCL1))) +BAX, ((!BID & (!MCL1 & TP53)) | (BID & !MCL1)) +BBC3, TP53 +BCL2, (!BAD & (!BBC3 & (!BID & (CREB1 & !TP53)))) +BID, ((!CASP8 & CSNK1A1) | CASP8) +BIRC_f, (!AURKB & (!DIABLO & (STAT3 & !TP53))) +BMPR2, (!SMURF1 & !SMURF2) +BRCA1, ((!AKT_f & (!CCND1 & CHEK2)) | (AKT_f & !CCND1)) +BTRC, ((!AXIN1 & (GSK3_f & !LRP_f)) | (AXIN1 & !LRP_f)) +BUB1, ATM +CASP3, (!BIRC_f & ((!CASP8 & (CASP9 & !XIAP)) | (CASP8 & !XIAP))) +CASP8, (!CFLAR & (DD_f & !SRC)) +CASP9, (!BIRC_f & (PPP1CA & !XIAP)) +CBPp300_c, (EP300 & !TP53) +CCNB1, !CDKN1A +CCND1, (!CDKN2A & (!CHUK & (!GSK3_f & ((!RSK_f & STAT3) | RSK_f)))) +CCNE1, ((!CDC25A & (!CDKN1A & (!CDKN1B & (E2F1 & !TGFB1)))) | (CDC25A & (!CDKN1A & (!CDKN1B & !TGFB1)))) +CDC25A, (!CHEK1 & (!CHEK2 & (!CSNK1A1 & (!GSK3_f & (MYC & !SMAD3))))) +CDC42, (!ARHGAP24 & SRC) +CDH1, (!SNAI_f & !TWIST1) +CDKN1A, (!AKT_f & ((!BRCA1 & (!MDM2 & (!MYC & (!SKP2 & TP53)))) | (BRCA1 & (!MDM2 & (!MYC & !SKP2))))) +CDKN1B, (!AKT_f & (!MYC & TGFB1)) +CDKN2A, !MYC +CFLAR, ((!AKT_f & (!ITCH & MAPK14)) | (AKT_f & !ITCH)) +CFL_f, ((!LIMK1 & LIMK2) | LIMK1) +CHEK1, (!AKT_f & ATR) +CHEK2, ((!ATR & PLK1) | ATR) +CHUK, ((!AKT_f & TRAF6) | AKT_f) +CREB1, ((!AKT_f & (!ATM & (!ATR & SMAD2))) | (AKT_f & (!ATM & !ATR))) +CREBBP, CHUK +CSK, PRKACA +CSNK1A1, !LRP_f +CSNK1_f, ((!AXIN1 & DVL_f) | AXIN1) +CTNNB1, (!APC & (!BTRC & ((!CHUK & (!CSNK1A1 & (!CSNK1_f & YAP_TAZ))) | (CHUK & (!CSNK1A1 & !CSNK1_f))))) +CYCS, ((!BAK1 & (BAX & !BCL2)) | (BAK1 & !BCL2)) +DAAM1, DVL_f +DD_f, (AURKA & (!CSNK1A1 & !MAP2K7)) +DIABLO, ((!BAK1 & (BAX & (!BCL2 & !BIRC_f))) | (BAK1 & (!BCL2 & !BIRC_f))) +DKK_f, (!MYC & TCF7_f) +DUSP1, ((!ERK_f & (MSK_f & !SKP2)) | (ERK_f & !SKP2)) +DUSP6, ((!ERK_f & mTORC1_c) | ERK_f) +DVL_f, ((!FZD_f & (!ITCH & (SMAD1 & !YAP_TAZ))) | (FZD_f & (!ITCH & !YAP_TAZ))) +E2F1, (!HES1 & !RB1) +EGR1, (NFKB_f & !TCF7_f) +EP300, (AKT_f & (!PRKCD & !SKI)) +ERK_f, (!DUSP6 & (MEK_f & !PPP1CA)) +FOS, ((!ERK_f & SRF) | ERK_f) +FOXO_f, (!AKT_f & (!CREB1 & (!CSNK1A1 & (DUSP6 & (!IKBKB & !NLK))))) +FZD_f, !SFRP1 +GAB_f, (!ERK_f & GRB2) +GLI_f, (!CSNK1A1 & (!GSK3_f & (!PRKACA & !SUFU))) +GRB2, ((!RTPK_f & SHC1) | RTPK_f) +GSK3_f, (!AKT_f & (CSNK1A1 & (!DVL_f & (!ERK_f & (!MAPK14 & (!RSK_f & !S6K_f)))))) +HES1, ((!NOTCH1 & REL_f) | NOTCH1) +IKBKB, (DD_f & (!PLK1 & (!PPM1A & !TP53))) +ILK, (PAK1 & !TWIST1) +ILR_f, ((!AP1_c & LIF) | AP1_c) +IRAK1, (ILR_f & !SOCS1) +IRS1, (!ERK_f & (!IKBKB & !S6K_f)) +ITCH, JNK_f +JAK_f, (ILR_f & (!PTPN6 & !SOCS1)) +JNK_f, (!DUSP1 & ((!MAP2K4 & MAP2K7) | MAP2K4)) +JUN, (!GSK3_f & JNK_f) +KRAS, ((!PTPN11 & SOS1) | PTPN11) +LATS_f, ((!AURKA & MOB1_f) | AURKA) +LEF1, (!CSNK1_f & CTNNB1) +LIF, RAF_f +LIMK1, ((!RAC_f & ROCK1) | RAC_f) +LIMK2, (!PRKCD & ROCK1) +LRP_f, (!DKK_f & ((!ERK_f & FZD_f) | ERK_f)) +MAP2K3, ((!MAP3K5 & MAP3K7) | MAP3K5) +MAP2K4, ((!MAP3K11 & MAP3K4) | MAP3K11) +MAP2K7, ((!MAP3K7 & MAPK8IP3) | MAP3K7) +MAP3K11, RAC_f +MAP3K4, RAC_f +MAP3K5, !AKT_f +MAP3K7, ((!TAB_f & TRAF6) | TAB_f) +MAP3K8, IKBKB +MAPK14, (!DUSP1 & ((!MAP2K3 & MAP2K4) | MAP2K3)) +MAPK8IP3, ROCK1 +MAPKAPK2, MAPK14 +MCL1, (!BBC3 & ((!ERK_f & (!GSK3_f & JNK_f)) | (ERK_f & !GSK3_f))) +MDM2, (!ABL1 & ((!AKT_f & (!ATM & (!ATR & (!CDKN2A & (!CSNK1_f & (!S6K_f & TP53)))))) | (AKT_f & (!ATM & (!ATR & (!CDKN2A & (!CSNK1_f & !S6K_f))))))) +MEK_f, (!ERK_f & RAF_f) +MMP_f, ((!LEF1 & STAT3) | LEF1) +MOB1_f, STK_f +MSK_f, ((!ERK_f & MAPK14) | ERK_f) +MYC, (!GSK3_f & ((!PLK1 & STAT3) | PLK1)) +NFKB_f, (!CHEK1 & ((!IKBKB & MSK_f) | IKBKB)) +NLK, MAP3K7 +NOTCH1, ADAM17 +PAK1, ((!CDC42 & RAC_f) | CDC42) +PARD6A, ((!TGFBR1 & TGFBR2) | TGFBR1) +PDPK1, (PIK3CA & !PTEN) +PHLPP1, !GSK3_f +PIAS1, MAPKAPK2 +PIK3CA, ((!GAB_f & KRAS) | GAB_f) +PLCG1, SYK +PLK1, ((!MAPKAPK2 & PDPK1) | MAPKAPK2) +PPM1A, PTEN +PPP1CA, (!RTPK_f & SMAD7) +PRKACA, ((!FOS & NFKB_f) | FOS) +PRKCA, ((!PARD6A & (!PHLPP1 & PLCG1)) | (PARD6A & !PHLPP1)) +PRKCD, ((!CASP3 & PDPK1) | CASP3) +PRKDC, ((!ATM & ATR) | ATM) +PTCH1, GLI_f +PTEN, (!CBPp300_c & (!GSK3_f & (ROCK1 & !SRC))) +PTPN11, GAB_f +PTPN6, (!PRKCA & SRC) +RAC_f, (!ARHGAP24 & ((!PIK3CA & TIAM1) | PIK3CA)) +RAF_f, (!AKT_f & (!ERK_f & (KRAS & !RHEB))) +RB1, (!CCND1 & (!CCNE1 & ((!CHEK1 & CHEK2) | CHEK1))) +RBPJ, !HES1 +REL_f, ((!IKBKB & (PRKCA & !STAT1)) | (IKBKB & !STAT1)) +RHEB, !TSC_f +RHOA, (DAAM1 & (!PARD6A & (!RAC_f & (!RND3 & !SMURF1)))) +RND3, ROCK1 +ROCK1, ((!CASP3 & RHOA) | CASP3) +RSK_f, ((!ERK_f & PDPK1) | ERK_f) +RTPK_f, ((!FOXO_f & (!MAPK14 & (!MEK_f & MMP_f))) | (FOXO_f & (!MAPK14 & !MEK_f))) +S6K_f, ((!PDPK1 & (!PHLPP1 & mTORC1_c)) | (PDPK1 & !PHLPP1)) +SFRP1, !MYC +SHC1, (!PTEN & ((!SRC & TGFBR1) | SRC)) +SKI, !AKT_f +SKP2, ((!EP300 & ERK_f) | EP300) +SMAD1, ((!ACVR1 & (!ERK_f & (!GSK3_f & (!PPM1A & (!SKI & (!SMAD6 & (!SMURF1 & YAP_TAZ))))))) | (ACVR1 & (!ERK_f & (!GSK3_f & (!PPM1A & (!SKI & (!SMAD6 & !SMURF1))))))) +SMAD2, ((!ACVR1 & (!PPM1A & (!SKI & (!SMURF2 & TGFBR1)))) | (ACVR1 & (!PPM1A & (!SKI & !SMURF2)))) +SMAD3, ((!ACVR1 & (!AKT_f & (!ERK_f & (!GSK3_f & (!PPM1A & (!SKI & (!SMAD6 & (!SMAD7 & TGFBR1)))))))) | (ACVR1 & (!AKT_f & (!ERK_f & (!GSK3_f & (!PPM1A & (!SKI & (!SMAD6 & !SMAD7)))))))) +SMAD4, (!SKI & ((!SMAD2 & (SMAD5 & (!SMAD6 & (!SMAD7 & !SMURF1)))) | (SMAD2 & (!SMAD6 & (!SMAD7 & !SMURF1))))) +SMAD5, (ACVR1 & (!SKI & !SMURF2)) +SMAD6, ((!SMAD2 & SMAD4) | SMAD2) +SMAD7, (!AXIN1 & (!ITCH & ((!SMAD2 & (SMAD4 & !SMURF2)) | (SMAD2 & !SMURF2)))) +SMO, (CSNK1A1 & !PTCH1) +SMURF1, SMAD7 +SMURF2, SMAD7 +SNAI_f, (!GSK3_f & ((!LATS_f & PAK1) | LATS_f)) +SOCS1, STAT1 +SOS1, (!ERK_f & PLCG1) +SRC, (!CSK & ((!PRKACA & RTPK_f) | PRKACA)) +SRF, ((!CFL_f & RSK_f) | CFL_f) +STAT1, ((!IKBKB & (!PIAS1 & SRC)) | (IKBKB & !PIAS1)) +STAT3, ((!IRAK1 & (!PPP1CA & SRC)) | (IRAK1 & !PPP1CA)) +STK_f, (!AKT_f & (PHLPP1 & !RAF_f)) +SUFU, !SMO +SYK, (!CHEK1 & ILR_f) +TAB_f, (!MAPK14 & TRAF6) +TCF7_f, (CTNNB1 & !NLK) +TGFB1, ((!FOS & NFKB_f) | FOS) +TGFBR1, (!SMAD6 & (!SMAD7 & (!SMURF1 & (!SMURF2 & TGFBR2)))) +TGFBR2, (!SMURF1 & (!SMURF2 & TGFB1)) +TIAM1, !ROCK1 +TP53, (!AURKB & (EP300 & !MDM2)) +TRAF6, ((!IRAK1 & TGFBR1) | IRAK1) +TSC_f, (!AKT_f & (!ERK_f & (GSK3_f & (!IKBKB & !RSK_f)))) +TWIST1, ((!ERK_f & JNK_f) | ERK_f) +VAV1, SYK +XIAP, ((!AKT_f & (BIRC_f & !DIABLO)) | (AKT_f & !DIABLO)) +YAP_TAZ, (!BTRC & (!CSNK1_f & !LATS_f)) +mTORC1_c, (!AKT1S1 & ((!RHEB & RSK_f) | RHEB)) +mTORC2_c, ((!PIK3CA & (!S6K_f & TSC_f)) | (PIK3CA & !S6K_f)) diff --git a/test/Cell-Cycle-2019.bnet b/test/Cell-Cycle-2019.bnet new file mode 100644 index 00000000..5da20366 --- /dev/null +++ b/test/Cell-Cycle-2019.bnet @@ -0,0 +1,88 @@ +targets, factors +GF, GF|GF_High +RTK, !CAD&(GF_High|GF) +Grb2, RTK&GF_High +Ras, Grb2&SOS +RAF, !Casp3&Ras +mTORC2, PIP3|!S6K +PI3K, Ras|RTK +PIP3, PI3K_H|PI3K +PDK1, PI3K&PIP3 +AKT_B, !Casp3&PIP3&(PDK1|mTORC2) +p110_H, (FoxO3&!NeddL4)|(p110_H&(FoxO3|!NeddL4)) +PI3K_H, p110_H&RTK&PI3K&Ras +AKT_H, AKT_B&p110_H&PI3K_H&Ras&PIP3&PDK1&mTORC2 +FoxO3, !(AKT_B|AKT_H|ERK)|(!(AKT_H&(Plk1|Plk1_H|AKT_B|ERK))&!(Plk1&Plk1_H&ERK)) +PLCgamma, RTK&Grb2&p110_H&PI3K_H&PIP3 +NeddL4, Ca2&IP3 +FoxO1, !Plk1&!AKT_H +p21_mRNA, (FoxO1&FoxO3)|(!Myc&(FoxO1|FoxO3)) +TSC2, !AKT_H|!(AKT_B|ERK) +PRAS40, !AKT_H&(!mTORC1|!AKT_B) +Rheb, !TSC2&DAG +mTORC1, !Casp3&((Rheb&!PRAS40)|E2F1|(CyclinB&Cdk1&GSK3)) +S6K, !Casp3&mTORC1 +eIF4E, !Casp3&mTORC1 +GSK3, !AKT_H&!(S6K&ERK) +p21, p21_mRNA&!Casp3&!CyclinE +pRB, !Casp3&!CyclinD1&!CyclinA&(p27Kip1|!CyclinE) +p27Kip1, !Casp3&!CyclinD1&!(Cdk1&CyclinB)&((!CyclinE&(FoxO3&FoxO1))|(!CyclinA&(FoxO3|FoxO1))|(!CyclinE&!CyclinA)) +Myc, (ERK&(eIF4E|!GSK3))|(E2F1&!pRB&(eIF4E|ERK|!GSK3)) +CyclinD1, !CHK1&((!p21&((!GSK3&(Myc|E2F1))|(Myc&CyclinD1)|(Myc&E2F1)|(E2F1&CyclinD1)))|(!pRB&E2F1&((Myc&CyclinD1)|(Myc&!GSK3)|(CyclinD1&!GSK3)))) +E2F1, !(CAD|CyclinA|pRB)&(E2F1|Myc) +CyclinE, E2F1&Cdc6&Pre_RC&!(pRB|p27Kip1|CHK1|Casp3) +ORC, E2F1|(Pre_RC&Cdt1&Cdc6) +Cdc6, !Casp3&!(f4N_DNA&CyclinA)&((E2F1&ORC&!Plk1)|(Pre_RC&ORC&Cdc6&Cdt1)) +Cdt1, !geminin&ORC&Cdc6&!(CyclinE&CyclinA&Cdc25A)&((Pre_RC&(E2F1|Myc))|(E2F1&(Myc|!pRB))) +Pre_RC, ORC&Cdc6&Cdt1&!(Replication&f4N_DNA) +geminin, E2F1&!Cdh1&!(pAPC&Cdc20) +CyclinA_mRNA, !CAD&((E2F1&!pRB)|FoxM1) +Emi1, (E2F1|!pRB|!p21)&!(Plk1&CyclinB&Cdk1&(U_Kinetochores|A_Kinetochores)) +FoxM1, (Myc&CyclinE)|(CyclinA&Cdc25A&Cdc25B)|(Plk1&CyclinB&Cdk1) +Cdc25A, ((FoxM1&E2F1&!pRB)|(!Cdh1&(FoxM1|(E2F1&!pRB))))&(!(GSK3|CHK1)|CyclinE|CyclinA|(CyclinB&Cdk1)) +CyclinA, CyclinA_mRNA&!pAPC&((Cdc25A&(!Cdh1|Emi1))|(CyclinA&((!Cdh1&(Emi1|!UbcH10))|(Emi1&!UbcH10)))) +Wee1, !Casp3&!(Cdk1&CyclinB)&(Replication|CHK1)&(CHK1|!(Cdk1&CyclinA&Plk1)) +UbcH10, !Cdh1|(UbcH10&(Cdc20|CyclinA|CyclinB)) +CyclinB, (FoxM1|(FoxO3&CyclinB))&!(Cdh1|(pAPC&Cdc20)) +Cdc25B, FoxM1&f4N_DNA +Plk1, !Cdh1&(FoxM1|Plk1_H)&((CyclinB&Cdk1)|(CyclinA&!Wee1&Cdc25A)) +Cdc25C, f4N_DNA&Plk1&((Cdc25B&!CHK1)|(CyclinB&Cdk1)) +Cdk1, CyclinB&Cdc25C&(!CHK1|(!Wee1&Cdk1)) +pAPC, (CyclinB&Cdk1&Plk1)|(CyclinB&Cdk1&pAPC)|(pAPC&Cdc20) +Cdc20, pAPC&!Emi1&!Cdh1&(!Mad2|(!CyclinA&!(CyclinB&Cdk1))) +Cdh1, !(CyclinB&Cdk1)&!(CyclinA&(Emi1|Cdc25A)) +Replication, !CAD&Pre_RC&((E2F1&CyclinE&Cdc25A)|(Replication&CyclinA&Cdc25A&(E2F1|!f4N_DNA))) +f4N_DNA, !CAD&((Replication&((Pre_RC&CyclinA)|f4N_DNA))|(f4N_DNA&!Ect2)) +U_Kinetochores, f4N_DNA&!Cdh1&!A_Kinetochores&((CyclinB&Cdk1)|U_Kinetochores) +Mad2, U_Kinetochores&!A_Kinetochores +A_Kinetochores, f4N_DNA&!Cdh1&!(pAPC&Cdc20)&(A_Kinetochores|(U_Kinetochores&Plk1&CyclinB&Cdk1)) +Plk1_H, Plk1&FoxM1&(Plk1_H|FoxO3|FoxO1) +Ect2, f4N_DNA&Plk1_H&Cdh1&!U_Kinetochores&!A_Kinetochores +Casp8, DR4_5|Casp3 +Casp2, Casp3|(U_Kinetochores&Mad2&!(CyclinB&Cdk1)) +MCL_1, !Casp3&!Casp2&(!GSK3|(AKT_B&(ERK|!E2F1)))&(!(Cdk1&CyclinB&U_Kinetochores)) +BCLXL, !Casp3&(BCL2|!BAD)&(!U_Kinetochores|(Plk1&(!(CyclinB&Cdk1)|(BCL2&MCL_1)))|((BCL2&MCL_1)&!(CyclinB&Cdk1))) +BCL2, !(Casp3|BAD|BIM|BIK)&(!U_Kinetochores|(MCL_1&BCLXL)|(Plk1&(BCLXL|MCL_1|!(Cdk1&CyclinB)))) +BAD, Casp3|!(AKT_H|AKT_B|ERK|S6K)|(Casp8&(!(AKT_B&ERK&S6K)&!(AKT_H&(AKT_B|ERK)))) +BIK, !(MCL_1|BCLXL|BCL2) +BIM, FoxO3&GSK3&!(ERK|MCL_1|BCLXL|BCL2) +BID, Casp8|(Casp2&!(BCL2|BCLXL|MCL_1)) +BAK, (BID&(BIM|BIK|!(BCL2&BCLXL&MCL_1)))|((BIM|BIK)&!(BCLXL|MCL_1)) +BAX, (BIM&((BID|BIK)|!(BCL2&BCLXL&MCL_1)))|((BID|BIK)&!(BCL2|BCLXL)) +Cyto_C, BAX|BAK +SMAC, BAX|BAK +IAPs, !SMAC|AKT_H +Casp9, Casp3|(!IAPs&Cyto_C) +Casp3, (Casp9&Casp8)|(Casp3&(Casp9|Casp8))|(!IAPs&(Casp9|Casp8|Casp3)) +CAD, Casp3&Casp9 +ATR, Replication +CHK1, ATR +Ca2, IP3 +DAG, PLCgamma +DR4_5, Trail +ERK, MEK&!BIK +GF_High, GF_High +IP3, PLCgamma +MEK, RAF +SOS, Grb2 +Trail, Trail diff --git a/test/Drosophila.bnet b/test/Drosophila.bnet new file mode 100644 index 00000000..ebeaa1e6 --- /dev/null +++ b/test/Drosophila.bnet @@ -0,0 +1,59 @@ +targets, factors +# 52 nodes +# 124 interactions +# taken from +# Vega, M. R. (2014, May). Analyzing toys models of Arabidopsis & Drosphila using Z3 SMT-LIB. In Independent Component Analyses, Compressive Sampling, Wavelets, Neural Net, Biosystems, & Nanoengineering XII (Vol. 9118, p. 911813). International Society f| Optics & Photonics. + +wg1, (CIA1 & SLP1 & ! (CIR1)) | (wg1 & SLP1 & ! (CIR1)) | (wg1 & CIA1 & ! (CIR1)) +wg2, (CIA2 & SLP2 & ! (CIR2)) | (wg2 & SLP2 & ! (CIR2)) | (wg2 & CIA2 & ! (CIR2)) +wg3, (CIA3 & SLP3 & ! (CIR3)) | (wg3 & SLP3 & ! (CIR3)) | (wg3 & CIA3 & ! (CIR3)) +wg4, (CIA4 & SLP4 & ! (CIR4)) | (wg4 & SLP4 & ! (CIR4)) | (wg4 & CIA4 & ! (CIR4)) +WG1, (wg1) +WG2, (wg2) +WG3, (wg3) +WG4, (wg4) +en1, (WG2 & ! (SLP1)) +en2, (WG3 & ! (SLP2)) | (WG1 & ! (SLP2)) +en3, (WG4 & ! (SLP3)) | (WG2 & ! (SLP3)) +en4, (WG3 & ! (SLP4)) +EN1, (en1) +EN2, (en2) +EN3, (en3) +EN4, (en4) +hh1, (EN1 & ! (CIR1)) +hh2, (EN2 & ! (CIR2)) +hh3, (EN3 & ! (CIR3)) +hh4, (EN4 & ! (CIR4)) +HH1, (hh1) +HH2, (hh2) +HH3, (hh3) +HH4, (hh4) +ptc1, (CIA1 & ! (EN1) & ! (CIR1)) +ptc2, (CIA2 & ! (EN2) & ! (CIR2)) +ptc3, (CIA3 & ! (EN3) & ! (CIR3)) +ptc4, (CIA4 & ! (EN4) & ! (CIR4)) +PTC1, (PTC1 & ! (HH2)) | (ptc1) +PTC2, (PTC2 & ! (HH1) & ! (HH3)) | (ptc2) +PTC3, (PTC3 & ! (HH2) & ! (HH4)) | (ptc3) +PTC4, (PTC4 & ! (HH3)) | (ptc4) +ci1, (! (EN1)) +ci2, (! (EN2)) +ci3, (! (EN3)) +ci4, (! (EN4)) +CI1, (ci1) +CI2, (ci2) +CI3, (ci3) +CI4, (ci4) +CIA1, (CI1 & hh2) | (CI1 & HH2) | (CI1 & ! (PTC1)) +CIA2, (CI2 & hh3) | (CI2 & hh1) | (CI2 & HH3) | (CI2 & HH1) | (CI2 & ! (PTC2)) +CIA3, (CI3 & hh4) | (CI3 & hh2) | (CI3 & HH4) | (CI3 & HH2) | (CI3 & ! (PTC3)) +CIA4, (CI4 & hh3) | (CI4 & HH3) | (CI4 & ! (PTC4)) +CIR1, (CI1 & PTC1 & ! (HH2) & ! (hh2)) +CIR2, (CI2 & PTC2 & ! (HH1) & ! (HH3) & ! (hh1) & ! (hh3)) +CIR3, (CI3 & PTC3 & ! (HH2) & ! (HH4) & ! (hh2) & ! (hh4)) +CIR4, (CI4 & PTC4 & ! (HH3) & ! (hh3)) +# External +SLP1, SLP1 +SLP2, SLP2 +SLP3, SLP3 +SLP4, SLP4 diff --git a/test/EMT.bnet b/test/EMT.bnet new file mode 100644 index 00000000..b498f496 --- /dev/null +++ b/test/EMT.bnet @@ -0,0 +1,75 @@ +# n = 69 +# max SCC = 51 +# Parity and time reversal elucidate both decision-making in empirical models and attractor scaling in critical Boolean networks + +targets, factors +EGF, EGF +FGF, FGF +HGF, HGF +Goosecoid, Goosecoid +Hypoxia, Hypoxia +IGF1, IGF1 +PDGF, PDGF +CHD1L, CHD1L + +AKT, ILK | PI3K +Dest_compl, (GSK3B & AXIN2 & Bcatenin_nuc) | (GSK3B & Dest_compl) +AXIN2, AXIN2 | TCF_LEF +Bcatenin_memb, Ecadherin & ! Bcatenin_nuc +Bcatenin_nuc, ! Dest_compl & ! Bcatenin_memb & (! SUFU | ! Ecadherin) +BTrCP, ! Csn +CD44, TCF_LEF +CDC42, TGFBR | CHD1L +cfos, ERK +cMet, HGF | CD44 +Csl, NOTCH_ic +Csn, NFKB +DELTA, RAS +DSH, Frizzled +Ecadherin, Bcatenin_memb & (! SNAI1 | ! HEY1 | ! ZEB1 | ! ZEB2 | ! FOXC2 | ! TWIST1 | ! SNAI2) +EGFR, EGF +EGR1, cfos +EMT, ! Ecadherin +ERK, MEK +FGFR, FGF +FOXC2, Goosecoid | SNAI1 | TWIST1 +Frizzled, Wnt +FUS, SMO +GLI, TCF_LEF | ! SUFU +GSK3B, ! DSH & ! AKT & (! Csn | ! ERK | ! Dest_compl) +HEY1, Csl | SMAD +HIF1A, Hypoxia +IGF1R, IGF1 +IKKA, AKT +ILK, SMAD +Jagged, TCF_LEF | SMAD +LIV1, STAT +LOXL23, HIF1A +MEK, RAF | ! RKIP +miR200, ! SNAI1 & ! ZEB1 & ! ZEB2 +NFKB, IKKA +NOTCH, DELTA | Jagged +NOTCH_ic, NOTCH +PAK1, CDC42 +Patched, ! SHH +PDGFR, PDGF +PI3K, RAS +RAF, RAS +RAS, SOS_GRB2 | SRC | ! GSK3B | TCF_LEF +RKIP, ! ERK | ! SNAI1 +SHH, SMAD | GLI +SNAI2, ERK | Bcatenin_nuc | SNAI2 | TWIST1 +SMAD, (ERK | TGFBR) & (ZEB1 | ! ZEB2) +SMO, ! Patched +SNAI1, GLI | LOXL23 | SMAD | LIV1 | PAK1 | Csl | EGR1 | Goosecoid | ! BTrCP | ! GSK3B +SOS_GRB2, (PDGFR | cMet | TGFBR | FGFR | IGF1R | EGFR) & ! ERK +SRC, PDGFR | EGFR | FGFR | cMet | IGF1R +STAT, SRC +SUFU, ! FUS +TCF_LEF, Bcatenin_nuc +TGFB, Goosecoid | SNAI1 | TWIST1 | GLI +TGFBR, TGFB +TWIST1, NFKB | HIF1A | TCF_LEF | Goosecoid | SNAI1 +Wnt, GLI +ZEB1, (HIF1A | SNAI1 | Goosecoid) & ! miR200 +ZEB2, (HIF1A | SNAI1 | Goosecoid) & ! miR200 diff --git a/test/EMT_Mechanosensing.bnet b/test/EMT_Mechanosensing.bnet new file mode 100644 index 00000000..f2537ef6 --- /dev/null +++ b/test/EMT_Mechanosensing.bnet @@ -0,0 +1,136 @@ +targets, factors +CellDensity_High, CellDensity_High +CellDensity_Low, CellDensity_Low|CellDensity_High +Stiff_ECM, Stiff_ECM +ECM, ECM|Stiff_ECM +GF, GF|GF_High +GF_High, GF_High +RTK, (!CAD)&(GF_High|GF) +Shc, (RTK&GF_High)&(FAK|Src) +Grb2, RTK&Shc +SOS, Grb2 +Ras, ((Grb2&SOS)&Src)&((IQGAP1_LeadingE|(!Merlin))|N_bcatenin_H) +RAF, ((!Casp3)&Ras)&(!SPRY2) +MEK, RAF +ERK, (MEK&(!BIK))&(FocalAdhesions|N_bcatenin_H) +mTORC2, PIP3|(!S6K) +PI3K, (FAK|Src)&(Ras|RTK) +PIP3, PI3K_H|PI3K +PDK1, PI3K&PIP3 +AKT_B, ((!Casp3)&PIP3)&(PDK1|mTORC2) +p110_H, YAP&((FoxO3&(!Nedd4L))|(p110_H&(FoxO3|(!Nedd4L)))) +PI3K_H, ((((!PTEN_c)&p110_H)&RTK)&PI3K)&Ras +AKT_H, (((((AKT_B&p110_H)&PI3K_H)&PIP3)&PDK1)&mTORC2)&(Ras|PAK1) +FoxO3, (!((AKT_B|AKT_H)|ERK))|((!(AKT_H&(((Plk1|Plk1_H)|AKT_B)|ERK)))&(!((Plk1&Plk1_H)&ERK))) +PLCgamma, ((((RTK&Grb2)&GF_High)&p110_H)&PI3K_H)&PIP3 +IP3, PLCgamma +Ca2p, IP3 +Nedd4L, Ca2p&IP3 +FoxO1, (!Plk1)&(!AKT_H) +p21_mRNA, ((FoxO1&FoxO3)|((!Myc)&(FoxO1|FoxO3)))&(!ZEB1_H) +TSC2, (!AKT_H)|(!(AKT_B|ERK)) +PRAS40, (!AKT_H)&((!mTORC1)|(!AKT_B)) +DAG, PLCgamma +Rheb, (!TSC2)&DAG +mTORC1, (!Casp3)&((((Rheb&(!PRAS40))&(!Merlin))|E2F1)|((CyclinB&Cdk1)&GSK3)) +S6K, (!Casp3)&mTORC1 +eIF4E, mTORC1&(!Casp3) +GSK3, (!AKT_H)&(!(S6K&ERK)) +Integrin, ECM +FAK, ((!Casp3)&(!(Cdk1&CyclinB)))&Integrin +Src, (Integrin&(RTK|FAK))|(Cdk1&CyclinB) +Nectin3, CellDensity_Low|CellDensity_High +Necl5, FocalAdhesions|(!(Nectin3&CellDensity_High)) +SPRY2, ((!Necl5)&RTK)&Src +J_Ecadherin, (!Casp3)&(Nectin3&(Ecadherin_mRNA_H|Ecadherin_mRNA)) +J_bcatenin, (!Casp3)&J_Ecadherin +J_acatenin, J_bcatenin +FocalAdhesions, ((Integrin&FAK)&ECM)&(Stiff_ECM|((YAP&Rac1)&IQGAP1_LeadingE)) +Stress_Fibers, ((!CellDensity_High)&Stiff_ECM)&FocalAdhesions +YAP, (FocalAdhesions&Stress_Fibers)&(!((((ApicalBasal_Pol&J_acatenin)&AMOT)&Merlin)&Lats1_2)) +TRIO, YAP +WT1, YAP +TAZ, Stress_Fibers&(!((((ApicalBasal_Pol&J_acatenin)&AMOT)&Merlin)&Lats1_2)) +Ecadherin_mRNA_H, Ecadherin_mRNA&(!(YAP&WT1)) +ApicalBasal_Pol, (ECM&((((CellDensity_High&Nectin3)&J_Ecadherin)&J_bcatenin)&J_acatenin))&(Ecadherin_mRNA_H|(!Horizontal_Pol)) +Mst1_2, ApicalBasal_Pol +Lats1_2, Mst1_2&Merlin +AMOT, Lats1_2&Merlin +miR_29c, YAP +PTEN_c, (!miR_29c)&((S6K&(!(ERK&GSK3)))|((!ERK)&(!GSK3))) +Merlin, ((J_bcatenin&J_acatenin)&(!PAK1))&(!AKT_H) +IQGAP1_LeadingE, ((!CellDensity_High)&FocalAdhesions)&((Horizontal_Pol|Rac1)|Grb2) +Horizontal_Pol, (((((!ApicalBasal_Pol)&ECM)&IQGAP1_LeadingE)&FocalAdhesions)&TAZ)&FAK +Rac1, (!Casp3)&((((FocalAdhesions&Necl5)&Horizontal_Pol)&TRIO)&(((!(miR_200&miR_34))&(!((Merlin&Nectin3)&J_Ecadherin)))|Stiff_ECM)) +PAK1, Rac1 +IKKa, AKT_H +NfkB, IKKa|PAK1 +c_Myb, NfkB|E2F1 +N_bcatenin, (!Casp3)&(!(ApicalBasal_Pol&GSK3)) +SNAI1, (((((ZEB1_H&ZEB1)&(!miR_34))&(!GSK3))|((NfkB&(ZEB1_H|ZEB1))&(!(miR_34&GSK3))))|(((NfkB|PAK1)&ZEB1_H)&ZEB1))|(PAK1&(((!GSK3)|NfkB)|((ZEB1_H|ZEB1)&(!miR_34)))) +LEF1, ((ZEB1&(!miR_200))|ZEB1_H)|NfkB +SNAI2, Twist&((SNAI2|N_bcatenin)|(N_bcatenin_H&LEF1)) +Twist, (!Casp3)&(SNAI1&(NfkB|(!miR_34))) +miR_34, (!SNAI1)|(!(ZEB1|ZEB1_H)) +miR_200, p21|((!((Twist&ZEB1_H)&SNAI1))&(!(((Twist&SNAI1)&ZEB1)&(!(miR_200|c_Myb))))) +ZEB1_H, ZEB1&((N_bcatenin_H&LEF1)&(SNAI2|(!miR_200))) +ZEB1, SNAI2|(b_catenin_TCF4&(!miR_200)) +N_bcatenin_H, (((N_bcatenin&(!miR_34))&(!J_acatenin))&(!(miR_200&GSK3)))&(!((CyclinE|CyclinA)&GSK3)) +Ecadherin_mRNA, !((((ZEB1_H&ZEB1)&SNAI1)&SNAI2)&Twist) +b_catenin_TCF4, (N_bcatenin_H&SNAI1)&SNAI2 +p21, (p21_mRNA&(!Casp3))&(!CyclinE) +pRB, (((!Casp3)&(!CyclinD1))&(!CyclinA))&(p27Kip1|(!CyclinE)) +p27Kip1, (((!Casp3)&(!CyclinD1))&(!(Cdk1&CyclinB)))&((((!((CyclinA&Necl5)&CyclinE))&(FoxO3&FoxO1))|(((!CyclinA)|(!(Necl5|CyclinE)))&(FoxO3|FoxO1)))|((!CyclinA)&(!(Necl5&CyclinE)))) +Myc, ((ERK&YAP)|((ERK|YAP)&(eIF4E&(!GSK3))))|((E2F1&(!pRB))&((eIF4E|ERK)|(!GSK3))) +CyclinD1, (!CHK1)&(((!p21)&((((!GSK3)&YAP)&(Myc|E2F1))|(((CyclinD1&YAP)&(Myc|E2F1))|(Myc&E2F1))))|(((!pRB)&E2F1)&(((Myc&CyclinD1)|(Myc&(!GSK3)))|((YAP&CyclinD1)&(!GSK3))))) +E2F1, (!((CAD|CyclinA)|pRB))&((YAP&(E2F1|Myc))|(E2F1&Myc)) +CyclinE, ((E2F1&Cdc6)&Pre_RC)&(!(((pRB|p27Kip1)|CHK1)|Casp3)) +ORC, E2F1|((Pre_RC&Cdt1)&Cdc6) +Cdc6, ((!Casp3)&(!(f4N_DNA&CyclinA)))&(((E2F1&ORC)&(!Plk1))|(((Pre_RC&ORC)&Cdc6)&Cdt1)) +Cdt1, ((((!geminin)&ORC)&Cdc6)&(!((CyclinE&CyclinA)&Cdc25A)))&((Pre_RC&(E2F1|Myc))|(E2F1&(Myc|(!pRB)))) +Pre_RC, ((ORC&Cdc6)&Cdt1)&(!(Replication&f4N_DNA)) +geminin, (E2F1&(!Cdh1))&(!(pAPC&Cdc20)) +CyclinA_mRNA, (!CAD)&((E2F1&(!pRB))|FoxM1) +Emi1, ((E2F1|(!pRB))|(!p21))&(!(((Plk1&CyclinB)&Cdk1)&(U_Kinetochores|A_Kinetochores))) +FoxM1, (((Myc|YAP)&CyclinE)|((CyclinA&Cdc25A)&Cdc25B))|((Plk1&CyclinB)&Cdk1) +Cdc25A, (((FoxM1&E2F1)&(!pRB))|((!Cdh1)&(FoxM1|(E2F1&(!pRB)))))&((((!(GSK3|CHK1))|CyclinE)|CyclinA)|(CyclinB&Cdk1)) +Wee1, (((!Casp3)&(Replication|CHK1))&(!(Cdk1&CyclinB)))&(CHK1|(!((Cdk1&CyclinA)&Plk1))) +Cdc25B, FoxM1&f4N_DNA +Plk1, ((!Cdh1)&(FoxM1|Plk1_H))&((CyclinB&Cdk1)|((CyclinA&(!Wee1))&Cdc25A)) +CyclinA, (CyclinA_mRNA&(!pAPC))&((Cdc25A&((!Cdh1)|Emi1))|(CyclinA&(((!Cdh1)&(Emi1|(!UbcH10)))|(Emi1&(!UbcH10))))) +Cdc25C, (f4N_DNA&Plk1)&((Cdc25B&(!CHK1))|(CyclinB&Cdk1)) +CyclinB, (FoxM1|(FoxO3&CyclinB))&(!(Cdh1|(pAPC&Cdc20))) +UbcH10, (!Cdh1)|(UbcH10&((Cdc20|CyclinA)|CyclinB)) +Cdk1, (CyclinB&Cdc25C)&((!CHK1)|((!Wee1)&Cdk1)) +pAPC, (((CyclinB&Cdk1)&Plk1)|((CyclinB&Cdk1)&pAPC))|(pAPC&Cdc20) +Cdc20, ((pAPC&(!Emi1))&(!Cdh1))&((!Mad2)|((!CyclinA)&(!(CyclinB&Cdk1)))) +Cdh1, (!(CyclinB&Cdk1))&(!(CyclinA&(Emi1|Cdc25A))) +Replication, ((!CAD)&Pre_RC)&(((E2F1&CyclinE)&Cdc25A)|(((Replication&CyclinA)&Cdc25A)&(E2F1|(!f4N_DNA)))) +ATR, Replication +CHK1, ATR +f4N_DNA, (!CAD)&((Replication&((Pre_RC&CyclinA)|f4N_DNA))|(f4N_DNA&(!Cytokinesis))) +Mad2, U_Kinetochores&(!A_Kinetochores) +U_Kinetochores, ((f4N_DNA&(!Cdh1))&(!A_Kinetochores))&((CyclinB&Cdk1)|U_Kinetochores) +A_Kinetochores, ((f4N_DNA&(!Cdh1))&(!(pAPC&Cdc20)))&(A_Kinetochores|((((U_Kinetochores&Src)&Plk1)&CyclinB)&Cdk1)) +Plk1_H, (Plk1&FoxM1)&((Plk1_H|FoxO3)|FoxO1) +Ect2, (((f4N_DNA&Plk1_H)&Cdh1)&(!U_Kinetochores))&(!A_Kinetochores) +Cytokinesis, (Ect2&FAK)&Src +Trail, Trail +DR4_5, Trail +Casp8, DR4_5|Casp3 +Casp2, Casp3|((U_Kinetochores&Mad2)&(!(CyclinB&Cdk1))) +MCL_1, (((!Casp3)&(!Casp2))&((!GSK3)|(AKT_B&(ERK|(!E2F1)))))&(!((Cdk1&CyclinB)&U_Kinetochores)) +BCLXL, ((!Casp3)&(BCL2&(!BAD)))&(((!U_Kinetochores)|(Plk1&((!(CyclinB&Cdk1))|(BCL2&MCL_1))))|((BCL2&MCL_1)&(!(CyclinB&Cdk1)))) +BCL2, (!(((Casp3|BAD)|BIM)|BIK))&(((!U_Kinetochores)|(MCL_1&BCLXL))|(Plk1&((BCLXL|MCL_1)|(!(Cdk1&CyclinB))))) +BAD, (Casp3|(!(((AKT_H|AKT_B)|ERK)|S6K)))|(Casp8&((!((AKT_B&ERK)&S6K))&(!(AKT_H&(AKT_B|ERK))))) +BIK, !((MCL_1|BCLXL)|BCL2) +BIM, FoxO3&(GSK3&(!(((ERK|MCL_1)|BCLXL)|BCL2))) +BID, Casp8|(Casp2&(!((BCL2|BCLXL)|MCL_1))) +BAK, (BID&((BIM|BIK)|(!((BCL2&BCLXL)&MCL_1))))|((BIM|BIK)&(!(BCLXL|MCL_1))) +BAX, (BIM&((BID|BIK)|(!((BCL2&BCLXL)&MCL_1))))|((BID|BIK)&(!(BCL2|BCLXL))) +Cyto_C, BAX|BAK +SMAC, BAX|BAK +IAPs, (!SMAC)|AKT_H +Casp9, Casp3|((!IAPs)&Cyto_C) +Casp3, ((Casp9&Casp8)|(Casp3&(Casp9|Casp8)))|((!IAPs)&((Casp9|Casp8)|Casp3)) +CAD, Casp3&Casp9 diff --git a/test/Regan2020_Adhesion_CIP_Migration_CellCycle_Apoptosis.bnet b/test/Regan2020_Adhesion_CIP_Migration_CellCycle_Apoptosis.bnet new file mode 100644 index 00000000..d2af63b6 --- /dev/null +++ b/test/Regan2020_Adhesion_CIP_Migration_CellCycle_Apoptosis.bnet @@ -0,0 +1,121 @@ +targets, factors +CellDensity_High, CellDensity_High +CellDensity_Low, CellDensity_Low|CellDensity_High +Stiff_ECM, Stiff_ECM +ECM, ECM|Stiff_ECM +GF_High, GF_High +GF, GF|GF_High +RTK, !CAD&(GF_High|GF) +Shc, RTK&GF_High&(FAK|Src) +Grb2, Shc&RTK +SOS, Grb2 +Ras, Grb2&SOS&Src&(IQGAP1_LeadingE|(!Merlin)) +RAF, !Casp3&Ras&(!SPRY2) +MEK, RAF +ERK, MEK&!BIK +mTORC2, PIP3|!S6K +PI3K, (FAK|Src)&(Ras|RTK) +PIP3, PI3K_H|PI3K +PDK1, PI3K&PIP3 +AKT_B, !Casp3&PIP3&(PDK1|mTORC2) +p110_H, YAP&((FoxO3&!Nedd4L)|(p110_H&(FoxO3|!Nedd4L))) +PI3K_H, (!PTEN_c)&p110_H&RTK&PI3K&Ras +AKT_H, AKT_B&p110_H&PI3K_H&PIP3&PDK1&mTORC2&(Ras|PAK1) +FoxO3, !(AKT_B|AKT_H|ERK)|(!(AKT_H&(Plk1|Plk1_H|AKT_B|ERK))&!(Plk1&Plk1_H&ERK)) +PLCgamma, RTK&Grb2&p110_H&PI3K_H&PIP3 +IP3, PLCgamma +Ca2p, IP3 +Nedd4L, Ca2p&IP3 +FoxO1, !Plk1&!AKT_H +p21_mRNA, (FoxO1&FoxO3)|(!Myc&(FoxO1|FoxO3)) +TSC2, !AKT_H|!(AKT_B|ERK) +PRAS40, !AKT_H&(!mTORC1|!AKT_B) +DAG, PLCgamma +Rheb, !TSC2&DAG +mTORC1, !Casp3&((Rheb&!PRAS40&!Merlin)|E2F1|(CyclinB&Cdk1&GSK3)) +S6K, !Casp3&mTORC1 +eIF4E, !Casp3&mTORC1 +GSK3, !AKT_H&!(S6K&ERK) +Integrin, ECM +FAK, !Casp3&!(Cdk1&CyclinB)&Integrin +Src, (Integrin&(RTK|FAK))|(Cdk1&CyclinB) +Nectin3, CellDensity_Low|CellDensity_High +Necl5, FocalAdhesions|!(Nectin3&CellDensity_High) +SPRY2, !Necl5 +J_Ecadherin, !Casp3&Nectin3 +J_bcatenin, !Casp3&J_Ecadherin +J_acatenin, J_bcatenin +FocalAdhesions, Integrin&FAK&ECM&(Stiff_ECM|(YAP&Rac1&IQGAP1_LeadingE)) +Stress_Fibers, !CellDensity_High&Stiff_ECM&FocalAdhesions +YAP, FocalAdhesions&Stress_Fibers&!(ApicalBasal_Pol&J_acatenin&AMOT&Merlin&Lats1_2) +TRIO, YAP +WT1, YAP +TAZ, Stress_Fibers&!(ApicalBasal_Pol&J_acatenin&AMOT&Merlin&Lats1_2) +Ecadherin_mRNA_H, !(YAP&WT1) +ApicalBasal_Pol, CellDensity_High&Nectin3&J_Ecadherin&J_bcatenin&J_acatenin&(Ecadherin_mRNA_H|!Horizontal_Pol) +Mst1_2, ApicalBasal_Pol +Lats1_2, Mst1_2&Merlin +AMOT, Lats1_2&Merlin +Merlin, J_bcatenin&J_acatenin&(!PAK1)&(!AKT_H) +IQGAP1_LeadingE, !CellDensity_High&FocalAdhesions&(Horizontal_Pol|Rac1|Grb2) +Horizontal_Pol, !ApicalBasal_Pol&ECM&IQGAP1_LeadingE&FocalAdhesions&TAZ&FAK +Rac1, !Casp3&Stiff_ECM&FocalAdhesions&Necl5&Horizontal_Pol&TRIO +PAK1, Rac1 +miR_29c, YAP +PTEN_c, !miR_29c&((S6K&!(ERK&GSK3))|(!ERK&!GSK3)) +p21, p21_mRNA&!Casp3&!CyclinE +pRB, !Casp3&!CyclinD1&!CyclinA&(p27Kip1|!CyclinE) +p27Kip1, !Casp3&!CyclinD1&!(Cdk1&CyclinB)&((!(CyclinA&Necl5&CyclinE)&(FoxO3&FoxO1))|((!CyclinA|!(Necl5|CyclinE))&(FoxO3|FoxO1))|(!CyclinA&!(Necl5&CyclinE))) +Myc, (ERK&YAP)|((ERK|YAP)&(eIF4E&!GSK3))|(E2F1&(!pRB)&(eIF4E|ERK|!GSK3)) +CyclinD1, !CHK1&((!p21&((!GSK3&YAP&(Myc|E2F1))|(CyclinD1&YAP&(Myc|E2F1)|(Myc&E2F1))))|(!pRB&E2F1&((Myc&CyclinD1)|(Myc&!GSK3)|(YAP&CyclinD1&!GSK3)))) +E2F1, !(CAD|CyclinA|pRB)&((YAP&(E2F1|Myc))|(E2F1&Myc)) +CyclinE, E2F1&Cdc6&Pre_RC&!(pRB|p27Kip1|CHK1|Casp3) +ORC, E2F1|(Pre_RC&Cdt1&Cdc6) +Cdc6, !Casp3&!(f4N_DNA&CyclinA)&((E2F1&ORC&!Plk1)|(Pre_RC&ORC&Cdc6&Cdt1)) +Cdt1, !geminin&ORC&Cdc6&!(CyclinE&CyclinA&Cdc25A)&((Pre_RC&(E2F1|Myc))|(E2F1&(Myc|!pRB))) +Pre_RC, ORC&Cdc6&Cdt1&!(Replication&f4N_DNA) +geminin, E2F1&!Cdh1&!(pAPC&Cdc20) +CyclinA_mRNA, !CAD&((E2F1&!pRB)|FoxM1) +Emi1, (E2F1|!pRB|!p21)&!(Plk1&CyclinB&Cdk1&(U_Kinetochores|A_Kinetochores)) +FoxM1, ((Myc|YAP)&CyclinE)|(CyclinA&Cdc25A&Cdc25B)|(Plk1&CyclinB&Cdk1) +Cdc25A, ((FoxM1&E2F1&!pRB)|(!Cdh1&(FoxM1|(E2F1&!pRB))))&(!(GSK3|CHK1)|CyclinE|CyclinA|(CyclinB&Cdk1)) +CyclinA, CyclinA_mRNA&!pAPC&((Cdc25A&(!Cdh1|Emi1))|(CyclinA&((!Cdh1&(Emi1|!UbcH10))|(Emi1&!UbcH10)))) +Wee1, !Casp3&!(Cdk1&CyclinB)&(Replication|CHK1)&(CHK1|!(Cdk1&CyclinA&Plk1)) +UbcH10, !Cdh1|(UbcH10&(Cdc20|CyclinA|CyclinB)) +CyclinB, (FoxM1|(FoxO3&CyclinB))&!(Cdh1|(pAPC&Cdc20)) +Cdc25B, FoxM1&f4N_DNA +Plk1, !Cdh1&(FoxM1|Plk1_H)&((CyclinB&Cdk1)|(CyclinA&!Wee1&Cdc25A)) +Cdc25C, f4N_DNA&Plk1&((Cdc25B&!CHK1)|(CyclinB&Cdk1)) +Cdk1, CyclinB&Cdc25C&(!CHK1|(!Wee1&Cdk1)) +pAPC, (CyclinB&Cdk1&Plk1)|(CyclinB&Cdk1&pAPC)|(pAPC&Cdc20) +Cdc20, pAPC&!Emi1&!Cdh1&(!Mad2|(!CyclinA&!(CyclinB&Cdk1))) +Cdh1, !(CyclinB&Cdk1)&!(CyclinA&(Emi1|Cdc25A)) +Replication, !CAD&Pre_RC&((E2F1&CyclinE&Cdc25A)|(Replication&CyclinA&Cdc25A&(E2F1|!f4N_DNA))) +ATR, Replication +CHK1, ATR +f4N_DNA, !CAD&((Replication&((Pre_RC&CyclinA)|f4N_DNA))|(f4N_DNA&!Cytokinesis)) +U_Kinetochores, f4N_DNA&!Cdh1&!A_Kinetochores&((CyclinB&Cdk1)|U_Kinetochores) +Mad2, U_Kinetochores&!A_Kinetochores +A_Kinetochores, f4N_DNA&!Cdh1&!(pAPC&Cdc20)&(A_Kinetochores|(U_Kinetochores&Src&Plk1&CyclinB&Cdk1)) +Plk1_H, Plk1&FoxM1&(Plk1_H|FoxO3|FoxO1) +Ect2, f4N_DNA&Plk1_H&Cdh1&!U_Kinetochores&!A_Kinetochores +Cytokinesis, Ect2&FAK&Src +Trail, Trail +DR4_5, Trail +Casp8, DR4_5|Casp3 +Casp2, Casp3|(U_Kinetochores&Mad2&!(CyclinB&Cdk1)) +MCL_1, !Casp3&!Casp2&(!GSK3|(AKT_B&(ERK|!E2F1)))&(!(Cdk1&CyclinB&U_Kinetochores)) +BCLXL, !Casp3&(BCL2|!BAD)&(!U_Kinetochores|(Plk1&(!(CyclinB&Cdk1)|(BCL2&MCL_1)))|((BCL2&MCL_1)&!(CyclinB&Cdk1))) +BCL2, !(Casp3|BAD|BIM|BIK)&(!U_Kinetochores|(MCL_1&BCLXL)|(Plk1&(BCLXL|MCL_1|!(Cdk1&CyclinB)))) +BAD, Casp3|!(AKT_H|AKT_B|ERK|S6K)|(Casp8&(!(AKT_B&ERK&S6K)&!(AKT_H&(AKT_B|ERK)))) +BIK, !(MCL_1|BCLXL|BCL2) +BIM, FoxO3&GSK3&!(ERK|MCL_1|BCLXL|BCL2) +BID, Casp8|(Casp2&!(BCL2|BCLXL|MCL_1)) +BAK, (BID&(BIM|BIK|!(BCL2&BCLXL&MCL_1)))|((BIM|BIK)&!(BCLXL|MCL_1)) +BAX, (BIM&((BID|BIK)|!(BCL2&BCLXL&MCL_1)))|((BID|BIK)&!(BCL2|BCLXL)) +Cyto_C, BAX|BAK +SMAC, BAX|BAK +IAPs, !SMAC|AKT_H +Casp9, Casp3|(!IAPs&Cyto_C) +Casp3, (Casp9&Casp8)|(Casp3&(Casp9|Casp8))|(!IAPs&(Casp9|Casp8|Casp3)) +CAD, Casp3&Casp9 diff --git a/test/SEGMENT-POLARITY-6-CELL.bnet b/test/SEGMENT-POLARITY-6-CELL.bnet new file mode 100644 index 00000000..67971bed --- /dev/null +++ b/test/SEGMENT-POLARITY-6-CELL.bnet @@ -0,0 +1,103 @@ +targets, factors +v_Ci1, !v_En1 +v_Ci2, !v_En2 +v_Ci3, !v_En3 +v_Ci4, !v_En4 +v_Ci5, !v_En5 +v_Ci6, !v_En6 +v_Ciact1_b1, ((((((((!v_Dsh1&!v_Ci1)&v_Ciact1_b1)&v_Ciact1_b2)|(((!v_Dsh1&v_Ci1)&!v_Ciact1_b1)&!v_Pka1_b1))|((((!v_Dsh1&v_Ci1)&v_Ciact1_b1)&!v_Ciact1_b2)&!v_Pka1_b1))|(((!v_Dsh1&v_Ci1)&v_Ciact1_b1)&v_Ciact1_b2))|(((v_Dsh1&!v_Ci1)&v_Ciact1_b1)&v_Ciact1_b2))|(v_Dsh1&v_Ci1)) +v_Ciact1_b2, (((v_Dsh1&v_Ci1)&v_Ciact1_b1)&!v_Pka1_b1) +v_Ciact2_b1, ((((((((!v_Dsh2&!v_Ci2)&v_Ciact2_b1)&v_Ciact2_b2)|(((!v_Dsh2&v_Ci2)&!v_Ciact2_b1)&!v_Pka2_b1))|((((!v_Dsh2&v_Ci2)&v_Ciact2_b1)&!v_Ciact2_b2)&!v_Pka2_b1))|(((!v_Dsh2&v_Ci2)&v_Ciact2_b1)&v_Ciact2_b2))|(((v_Dsh2&!v_Ci2)&v_Ciact2_b1)&v_Ciact2_b2))|(v_Dsh2&v_Ci2)) +v_Ciact2_b2, (((v_Dsh2&v_Ci2)&v_Ciact2_b1)&!v_Pka2_b1) +v_Ciact3_b1, ((((((((!v_Dsh3&!v_Ci3)&v_Ciact3_b1)&v_Ciact3_b2)|(((!v_Dsh3&v_Ci3)&!v_Ciact3_b1)&!v_Pka3_b1))|((((!v_Dsh3&v_Ci3)&v_Ciact3_b1)&!v_Ciact3_b2)&!v_Pka3_b1))|(((!v_Dsh3&v_Ci3)&v_Ciact3_b1)&v_Ciact3_b2))|(((v_Dsh3&!v_Ci3)&v_Ciact3_b1)&v_Ciact3_b2))|(v_Dsh3&v_Ci3)) +v_Ciact3_b2, (((v_Dsh3&v_Ci3)&v_Ciact3_b1)&!v_Pka3_b1) +v_Ciact4_b1, ((((((((!v_Dsh4&!v_Ci4)&v_Ciact4_b1)&v_Ciact4_b2)|(((!v_Dsh4&v_Ci4)&!v_Ciact4_b1)&!v_Pka4_b1))|((((!v_Dsh4&v_Ci4)&v_Ciact4_b1)&!v_Ciact4_b2)&!v_Pka4_b1))|(((!v_Dsh4&v_Ci4)&v_Ciact4_b1)&v_Ciact4_b2))|(((v_Dsh4&!v_Ci4)&v_Ciact4_b1)&v_Ciact4_b2))|(v_Dsh4&v_Ci4)) +v_Ciact4_b2, (((v_Dsh4&v_Ci4)&v_Ciact4_b1)&!v_Pka4_b1) +v_Ciact5_b1, ((((((((!v_Dsh5&!v_Ci5)&v_Ciact5_b1)&v_Ciact5_b2)|(((!v_Dsh5&v_Ci5)&!v_Ciact5_b1)&!v_Pka5_b1))|((((!v_Dsh5&v_Ci5)&v_Ciact5_b1)&!v_Ciact5_b2)&!v_Pka5_b1))|(((!v_Dsh5&v_Ci5)&v_Ciact5_b1)&v_Ciact5_b2))|(((v_Dsh5&!v_Ci5)&v_Ciact5_b1)&v_Ciact5_b2))|(v_Dsh5&v_Ci5)) +v_Ciact5_b2, (((v_Dsh5&v_Ci5)&v_Ciact5_b1)&!v_Pka5_b1) +v_Ciact6_b1, ((((((((!v_Dsh6&!v_Ci6)&v_Ciact6_b1)&v_Ciact6_b2)|(((!v_Dsh6&v_Ci6)&!v_Ciact6_b1)&!v_Pka6_b1))|((((!v_Dsh6&v_Ci6)&v_Ciact6_b1)&!v_Ciact6_b2)&!v_Pka6_b1))|(((!v_Dsh6&v_Ci6)&v_Ciact6_b1)&v_Ciact6_b2))|(((v_Dsh6&!v_Ci6)&v_Ciact6_b1)&v_Ciact6_b2))|(v_Dsh6&v_Ci6)) +v_Ciact6_b2, (((v_Dsh6&v_Ci6)&v_Ciact6_b1)&!v_Pka6_b1) +v_Cirep1, (((!v_Dsh1&v_Ci1)&v_Pka1_b1)&v_Pka1_b2) +v_Cirep2, (((!v_Dsh2&v_Ci2)&v_Pka2_b1)&v_Pka2_b2) +v_Cirep3, (((!v_Dsh3&v_Ci3)&v_Pka3_b1)&v_Pka3_b2) +v_Cirep4, (((!v_Dsh4&v_Ci4)&v_Pka4_b1)&v_Pka4_b2) +v_Cirep5, (((!v_Dsh5&v_Ci5)&v_Pka5_b1)&v_Pka5_b2) +v_Cirep6, (((!v_Dsh6&v_Ci6)&v_Pka6_b1)&v_Pka6_b2) +v_Dsh1, v_Fz1 +v_Dsh2, v_Fz2 +v_Dsh3, v_Fz3 +v_Dsh4, v_Fz4 +v_Dsh5, v_Fz5 +v_Dsh6, v_Fz6 +v_En1, (v_Dsh1&!v_Slp1) +v_En2, (v_Dsh2&!v_Slp2) +v_En3, (v_Dsh3&!v_Slp3) +v_En4, (v_Dsh4&!v_Slp4) +v_En5, (v_Dsh5&!v_Slp5) +v_En6, (v_Dsh6&!v_Slp6) +v_Fz1, (((!v_Wg1_b1&v_Wg2_b1)&v_Wg2_b2)|v_Wg1_b1) +v_Fz2, (((((((!v_Wg1_b1&!v_Wg2_b1)&v_Wg3_b1)&v_Wg3_b2)|(!v_Wg1_b1&v_Wg2_b1))|((((v_Wg1_b1&!v_Wg1_b2)&!v_Wg2_b1)&v_Wg3_b1)&v_Wg3_b2))|((v_Wg1_b1&!v_Wg1_b2)&v_Wg2_b1))|(v_Wg1_b1&v_Wg1_b2)) +v_Fz3, (((((((!v_Wg2_b1&!v_Wg3_b1)&v_Wg4_b1)&v_Wg4_b2)|(!v_Wg2_b1&v_Wg3_b1))|((((v_Wg2_b1&!v_Wg2_b2)&!v_Wg3_b1)&v_Wg4_b1)&v_Wg4_b2))|((v_Wg2_b1&!v_Wg2_b2)&v_Wg3_b1))|(v_Wg2_b1&v_Wg2_b2)) +v_Fz4, (((((((!v_Wg3_b1&!v_Wg4_b1)&v_Wg5_b1)&v_Wg5_b2)|(!v_Wg3_b1&v_Wg4_b1))|((((v_Wg3_b1&!v_Wg3_b2)&!v_Wg4_b1)&v_Wg5_b1)&v_Wg5_b2))|((v_Wg3_b1&!v_Wg3_b2)&v_Wg4_b1))|(v_Wg3_b1&v_Wg3_b2)) +v_Fz5, (((((((!v_Wg4_b1&!v_Wg5_b1)&v_Wg6_b1)&v_Wg6_b2)|(!v_Wg4_b1&v_Wg5_b1))|((((v_Wg4_b1&!v_Wg4_b2)&!v_Wg5_b1)&v_Wg6_b1)&v_Wg6_b2))|((v_Wg4_b1&!v_Wg4_b2)&v_Wg5_b1))|(v_Wg4_b1&v_Wg4_b2)) +v_Fz6, (((!v_Wg5_b1&v_Wg6_b1)|((v_Wg5_b1&!v_Wg5_b2)&v_Wg6_b1))|(v_Wg5_b1&v_Wg5_b2)) +v_Hh1, (v_En1&!v_Cirep1) +v_Hh2, (v_En2&!v_Cirep2) +v_Hh3, (v_En3&!v_Cirep3) +v_Hh4, (v_En4&!v_Cirep4) +v_Hh5, (v_En5&!v_Cirep5) +v_Hh6, (v_En6&!v_Cirep6) +v_Nkd1_b1, (((!v_Nkd1_b1&!v_En1)|((v_Nkd1_b1&!v_Nkd1_b2)&!v_En1))|(v_Nkd1_b1&v_Nkd1_b2)) +v_Nkd1_b2, ((v_Dsh1&v_Nkd1_b1)&!v_En1) +v_Nkd2_b1, (((!v_Nkd2_b1&!v_En2)|((v_Nkd2_b1&!v_Nkd2_b2)&!v_En2))|(v_Nkd2_b1&v_Nkd2_b2)) +v_Nkd2_b2, ((v_Dsh2&v_Nkd2_b1)&!v_En2) +v_Nkd3_b1, (((!v_Nkd3_b1&!v_En3)|((v_Nkd3_b1&!v_Nkd3_b2)&!v_En3))|(v_Nkd3_b1&v_Nkd3_b2)) +v_Nkd3_b2, ((v_Dsh3&v_Nkd3_b1)&!v_En3) +v_Nkd4_b1, (((!v_Nkd4_b1&!v_En4)|((v_Nkd4_b1&!v_Nkd4_b2)&!v_En4))|(v_Nkd4_b1&v_Nkd4_b2)) +v_Nkd4_b2, ((v_Dsh4&v_Nkd4_b1)&!v_En4) +v_Nkd5_b1, (((!v_Nkd5_b1&!v_En5)|((v_Nkd5_b1&!v_Nkd5_b2)&!v_En5))|(v_Nkd5_b1&v_Nkd5_b2)) +v_Nkd5_b2, ((v_Dsh5&v_Nkd5_b1)&!v_En5) +v_Nkd6_b1, (((!v_Nkd6_b1&!v_En6)|((v_Nkd6_b1&!v_Nkd6_b2)&!v_En6))|(v_Nkd6_b1&v_Nkd6_b2)) +v_Nkd6_b2, ((v_Dsh6&v_Nkd6_b1)&!v_En6) +v_Pka1_b1, (((!v_Pka1_b1&v_Ptc1_b1)|((v_Pka1_b1&!v_Pka1_b2)&v_Ptc1_b1))|(v_Pka1_b1&v_Pka1_b2)) +v_Pka1_b2, (v_Pka1_b1&v_Ptc1_b1) +v_Pka2_b1, (((!v_Pka2_b1&v_Ptc2_b1)|((v_Pka2_b1&!v_Pka2_b2)&v_Ptc2_b1))|(v_Pka2_b1&v_Pka2_b2)) +v_Pka2_b2, (v_Pka2_b1&v_Ptc2_b1) +v_Pka3_b1, (((!v_Pka3_b1&v_Ptc3_b1)|((v_Pka3_b1&!v_Pka3_b2)&v_Ptc3_b1))|(v_Pka3_b1&v_Pka3_b2)) +v_Pka3_b2, (v_Pka3_b1&v_Ptc3_b1) +v_Pka4_b1, (((!v_Pka4_b1&v_Ptc4_b1)|((v_Pka4_b1&!v_Pka4_b2)&v_Ptc4_b1))|(v_Pka4_b1&v_Pka4_b2)) +v_Pka4_b2, (v_Pka4_b1&v_Ptc4_b1) +v_Pka5_b1, (((!v_Pka5_b1&v_Ptc5_b1)|((v_Pka5_b1&!v_Pka5_b2)&v_Ptc5_b1))|(v_Pka5_b1&v_Pka5_b2)) +v_Pka5_b2, (v_Pka5_b1&v_Ptc5_b1) +v_Pka6_b1, (((!v_Pka6_b1&v_Ptc6_b1)|((v_Pka6_b1&!v_Pka6_b2)&v_Ptc6_b1))|(v_Pka6_b1&v_Pka6_b2)) +v_Pka6_b2, (v_Pka6_b1&v_Ptc6_b1) +v_Ptc1_b1, (((((!v_En1&!v_Ptc1_b1)&!v_Hh2)|(((!v_En1&v_Ptc1_b1)&!v_Ptc1_b2)&!v_Hh2))|((!v_En1&v_Ptc1_b1)&v_Ptc1_b2))|((v_En1&v_Ptc1_b1)&v_Ptc1_b2)) +v_Ptc1_b2, (((!v_En1&v_Ciact1_b1)&v_Ptc1_b1)&!v_Hh2) +v_Ptc2_b1, (((((((!v_Hh1&!v_En2)&!v_Ptc2_b1)&!v_Hh3)|((((!v_Hh1&!v_En2)&v_Ptc2_b1)&!v_Ptc2_b2)&!v_Hh3))|(((!v_Hh1&!v_En2)&v_Ptc2_b1)&v_Ptc2_b2))|(((!v_Hh1&v_En2)&v_Ptc2_b1)&v_Ptc2_b2))|((v_Hh1&v_Ptc2_b1)&v_Ptc2_b2)) +v_Ptc2_b2, ((((!v_Hh1&!v_En2)&v_Ciact2_b1)&v_Ptc2_b1)&!v_Hh3) +v_Ptc3_b1, (((((((!v_Hh2&!v_En3)&!v_Ptc3_b1)&!v_Hh4)|((((!v_Hh2&!v_En3)&v_Ptc3_b1)&!v_Ptc3_b2)&!v_Hh4))|(((!v_Hh2&!v_En3)&v_Ptc3_b1)&v_Ptc3_b2))|(((!v_Hh2&v_En3)&v_Ptc3_b1)&v_Ptc3_b2))|((v_Hh2&v_Ptc3_b1)&v_Ptc3_b2)) +v_Ptc3_b2, ((((!v_Hh2&!v_En3)&v_Ciact3_b1)&v_Ptc3_b1)&!v_Hh4) +v_Ptc4_b1, (((((((!v_Hh3&!v_En4)&!v_Ptc4_b1)&!v_Hh5)|((((!v_Hh3&!v_En4)&v_Ptc4_b1)&!v_Ptc4_b2)&!v_Hh5))|(((!v_Hh3&!v_En4)&v_Ptc4_b1)&v_Ptc4_b2))|(((!v_Hh3&v_En4)&v_Ptc4_b1)&v_Ptc4_b2))|((v_Hh3&v_Ptc4_b1)&v_Ptc4_b2)) +v_Ptc4_b2, ((((!v_Hh3&!v_En4)&v_Ciact4_b1)&v_Ptc4_b1)&!v_Hh5) +v_Ptc5_b1, (((((((!v_Hh4&!v_En5)&!v_Ptc5_b1)&!v_Hh6)|((((!v_Hh4&!v_En5)&v_Ptc5_b1)&!v_Ptc5_b2)&!v_Hh6))|(((!v_Hh4&!v_En5)&v_Ptc5_b1)&v_Ptc5_b2))|(((!v_Hh4&v_En5)&v_Ptc5_b1)&v_Ptc5_b2))|((v_Hh4&v_Ptc5_b1)&v_Ptc5_b2)) +v_Ptc5_b2, ((((!v_Hh4&!v_En5)&v_Ciact5_b1)&v_Ptc5_b1)&!v_Hh6) +v_Ptc6_b1, (((!v_Hh5&!v_En6)|(((!v_Hh5&v_En6)&v_Ptc6_b1)&v_Ptc6_b2))|((v_Hh5&v_Ptc6_b1)&v_Ptc6_b2)) +v_Ptc6_b2, (((!v_Hh5&!v_En6)&v_Ciact6_b1)&v_Ptc6_b1) +v_Slp1, (v_Dsh1&!v_En1) +v_Slp2, (v_Dsh2&!v_En2) +v_Slp3, (v_Dsh3&!v_En3) +v_Slp4, (v_Dsh4&!v_En4) +v_Slp5, (v_Dsh5&!v_En5) +v_Slp6, (v_Dsh6&!v_En6) +v_Wg1_b1, ((((((((((!v_Wg1_b1&v_Slp1)&!v_Nkd1_b1)&!v_En1)&v_Ciact1_b1)|(((((!v_Wg1_b1&v_Slp1)&v_Nkd1_b1)&!v_Nkd1_b2)&!v_En1)&v_Ciact1_b1))|((((((!v_Wg1_b1&v_Slp1)&v_Nkd1_b1)&v_Nkd1_b2)&!v_En1)&v_Ciact1_b1)&v_Ciact1_b2))|(((((v_Wg1_b1&!v_Wg1_b2)&v_Slp1)&!v_Nkd1_b1)&!v_En1)&v_Ciact1_b1))|((((((v_Wg1_b1&!v_Wg1_b2)&v_Slp1)&v_Nkd1_b1)&!v_Nkd1_b2)&!v_En1)&v_Ciact1_b1))|(((((((v_Wg1_b1&!v_Wg1_b2)&v_Slp1)&v_Nkd1_b1)&v_Nkd1_b2)&!v_En1)&v_Ciact1_b1)&v_Ciact1_b2))|(v_Wg1_b1&v_Wg1_b2)) +v_Wg1_b2, ((((v_Wg1_b1&v_Slp1)&!v_En1)&v_Ciact1_b1)&v_Ciact1_b2) +v_Wg2_b1, ((((((((((!v_Wg2_b1&v_Slp2)&!v_Nkd2_b1)&!v_En2)&v_Ciact2_b1)|(((((!v_Wg2_b1&v_Slp2)&v_Nkd2_b1)&!v_Nkd2_b2)&!v_En2)&v_Ciact2_b1))|((((((!v_Wg2_b1&v_Slp2)&v_Nkd2_b1)&v_Nkd2_b2)&!v_En2)&v_Ciact2_b1)&v_Ciact2_b2))|(((((v_Wg2_b1&!v_Wg2_b2)&v_Slp2)&!v_Nkd2_b1)&!v_En2)&v_Ciact2_b1))|((((((v_Wg2_b1&!v_Wg2_b2)&v_Slp2)&v_Nkd2_b1)&!v_Nkd2_b2)&!v_En2)&v_Ciact2_b1))|(((((((v_Wg2_b1&!v_Wg2_b2)&v_Slp2)&v_Nkd2_b1)&v_Nkd2_b2)&!v_En2)&v_Ciact2_b1)&v_Ciact2_b2))|(v_Wg2_b1&v_Wg2_b2)) +v_Wg2_b2, ((((v_Wg2_b1&v_Slp2)&!v_En2)&v_Ciact2_b1)&v_Ciact2_b2) +v_Wg3_b1, ((((((((((!v_Wg3_b1&v_Slp3)&!v_Nkd3_b1)&!v_En3)&v_Ciact3_b1)|(((((!v_Wg3_b1&v_Slp3)&v_Nkd3_b1)&!v_Nkd3_b2)&!v_En3)&v_Ciact3_b1))|((((((!v_Wg3_b1&v_Slp3)&v_Nkd3_b1)&v_Nkd3_b2)&!v_En3)&v_Ciact3_b1)&v_Ciact3_b2))|(((((v_Wg3_b1&!v_Wg3_b2)&v_Slp3)&!v_Nkd3_b1)&!v_En3)&v_Ciact3_b1))|((((((v_Wg3_b1&!v_Wg3_b2)&v_Slp3)&v_Nkd3_b1)&!v_Nkd3_b2)&!v_En3)&v_Ciact3_b1))|(((((((v_Wg3_b1&!v_Wg3_b2)&v_Slp3)&v_Nkd3_b1)&v_Nkd3_b2)&!v_En3)&v_Ciact3_b1)&v_Ciact3_b2))|(v_Wg3_b1&v_Wg3_b2)) +v_Wg3_b2, ((((v_Wg3_b1&v_Slp3)&!v_En3)&v_Ciact3_b1)&v_Ciact3_b2) +v_Wg4_b1, ((((((((((!v_Wg4_b1&v_Slp4)&!v_Nkd4_b1)&!v_En4)&v_Ciact4_b1)|(((((!v_Wg4_b1&v_Slp4)&v_Nkd4_b1)&!v_Nkd4_b2)&!v_En4)&v_Ciact4_b1))|((((((!v_Wg4_b1&v_Slp4)&v_Nkd4_b1)&v_Nkd4_b2)&!v_En4)&v_Ciact4_b1)&v_Ciact4_b2))|(((((v_Wg4_b1&!v_Wg4_b2)&v_Slp4)&!v_Nkd4_b1)&!v_En4)&v_Ciact4_b1))|((((((v_Wg4_b1&!v_Wg4_b2)&v_Slp4)&v_Nkd4_b1)&!v_Nkd4_b2)&!v_En4)&v_Ciact4_b1))|(((((((v_Wg4_b1&!v_Wg4_b2)&v_Slp4)&v_Nkd4_b1)&v_Nkd4_b2)&!v_En4)&v_Ciact4_b1)&v_Ciact4_b2))|(v_Wg4_b1&v_Wg4_b2)) +v_Wg4_b2, ((((v_Wg4_b1&v_Slp4)&!v_En4)&v_Ciact4_b1)&v_Ciact4_b2) +v_Wg5_b1, ((((((((((!v_Wg5_b1&v_Slp5)&!v_Nkd5_b1)&!v_En5)&v_Ciact5_b1)|(((((!v_Wg5_b1&v_Slp5)&v_Nkd5_b1)&!v_Nkd5_b2)&!v_En5)&v_Ciact5_b1))|((((((!v_Wg5_b1&v_Slp5)&v_Nkd5_b1)&v_Nkd5_b2)&!v_En5)&v_Ciact5_b1)&v_Ciact5_b2))|(((((v_Wg5_b1&!v_Wg5_b2)&v_Slp5)&!v_Nkd5_b1)&!v_En5)&v_Ciact5_b1))|((((((v_Wg5_b1&!v_Wg5_b2)&v_Slp5)&v_Nkd5_b1)&!v_Nkd5_b2)&!v_En5)&v_Ciact5_b1))|(((((((v_Wg5_b1&!v_Wg5_b2)&v_Slp5)&v_Nkd5_b1)&v_Nkd5_b2)&!v_En5)&v_Ciact5_b1)&v_Ciact5_b2))|(v_Wg5_b1&v_Wg5_b2)) +v_Wg5_b2, ((((v_Wg5_b1&v_Slp5)&!v_En5)&v_Ciact5_b1)&v_Ciact5_b2) +v_Wg6_b1, ((((((((((!v_Wg6_b1&v_Slp6)&!v_Nkd6_b1)&!v_En6)&v_Ciact6_b1)|(((((!v_Wg6_b1&v_Slp6)&v_Nkd6_b1)&!v_Nkd6_b2)&!v_En6)&v_Ciact6_b1))|((((((!v_Wg6_b1&v_Slp6)&v_Nkd6_b1)&v_Nkd6_b2)&!v_En6)&v_Ciact6_b1)&v_Ciact6_b2))|(((((v_Wg6_b1&!v_Wg6_b2)&v_Slp6)&!v_Nkd6_b1)&!v_En6)&v_Ciact6_b1))|((((((v_Wg6_b1&!v_Wg6_b2)&v_Slp6)&v_Nkd6_b1)&!v_Nkd6_b2)&!v_En6)&v_Ciact6_b1))|(((((((v_Wg6_b1&!v_Wg6_b2)&v_Slp6)&v_Nkd6_b1)&v_Nkd6_b2)&!v_En6)&v_Ciact6_b1)&v_Ciact6_b2))|(v_Wg6_b1&v_Wg6_b2)) +v_Wg6_b2, ((((v_Wg6_b1&v_Slp6)&!v_En6)&v_Ciact6_b1)&v_Ciact6_b2) diff --git a/test/T-CELL-RECEPTOR-SIGNALING.bnet b/test/T-CELL-RECEPTOR-SIGNALING.bnet new file mode 100755 index 00000000..d6b77d2b --- /dev/null +++ b/test/T-CELL-RECEPTOR-SIGNALING.bnet @@ -0,0 +1,50 @@ +targets, factors +v1, ((!v35 & v51) | v35) +v17, !v21 +v18, (v20 & v100) +v19, (v20 & v35) +v20, v94 +v21, v22 +v22, v22 +v23, v23 +v24, v94 +v28, v66 +v30, (!v31 & v72) +v31, v90 +v32, v56 +v35, ((!v24 & (v53 & v90)) | (v24 & ((!v51 & (v53 & v90)) | v51))) +v36, ((!v38 & (v40 & (v50 & v100))) | (v38 & (v50 & v100))) +v38, v50 +v39, v96 +v40, v50 +v47, (v69 & (v87 & v100)) +v50, v100 +v51, (v23 & (v24 & (!v28 & (v53 & !v85)))) +v52, (v53 & v90) +v53, v54 +v54, v54 +v56, v78 +v66, (v35 & !v90) +v68, (!v17 & ((!v52 & v99) | v52)) +v69, (v68 & (!v74 & !v84)) +v72, (!v19 & (v47 & (v73 & (v87 & (v97 & v100))))) +v73, v50 +v74, v95 +v78, v79 +v79, (!v39 & (v80 & v88)) +v80, v30 +v83, (v50 & v100) +v84, v95 +v85, (!v32 & v51) +v87, (!v36 & (v38 & v100)) +v88, v40 +v90, (!v18 & v91) +v91, v92 +v92, v92 +v93, ((!v35 & (v51 & v90)) | (v35 & v90)) +v94, v94 +v95, v95 +v96, v96 +v97, ((!v83 & v99) | (v83 & ((!v99 & v100) | v99))) +v99, v21 +v100, (v1 & (!v18 & v93)) diff --git a/test/[var_133]__[id_083]__[SIGNALING-IN-PROSTATE-CANCER].bnet b/test/[var_133]__[id_083]__[SIGNALING-IN-PROSTATE-CANCER].bnet new file mode 100644 index 00000000..7cd6d4af --- /dev/null +++ b/test/[var_133]__[id_083]__[SIGNALING-IN-PROSTATE-CANCER].bnet @@ -0,0 +1,117 @@ +targets, factors +AKT, ((!HSPs&(PIP3&!PTCH1))|(HSPs&!PTCH1)) +AMPK, ((!AMP_ATP&(!ATM&(!ATR&(!EGFR&(!FGFR3&HIF1)))))|((!AMP_ATP&(!ATM&(ATR&(!EGFR&!FGFR3))))|((!AMP_ATP&(ATM&(!EGFR&!FGFR3)))|(AMP_ATP&(!EGFR&!FGFR3))))) +AMP_ATP, !Nutrients +APAF1, ((!AKT&(!Bak&(!BAX&(!BCL2&(!Bcl_XL&(!Caspase8&(!HSPs&p53)))))))|((!AKT&(!Bak&(!BAX&(!BCL2&(!Bcl_XL&(!Caspase8&HSPs))))))|((!AKT&(!Bak&(!BAX&(!BCL2&(!Bcl_XL&Caspase8)))))|((!AKT&(!Bak&(BAX&(!BCL2&!Bcl_XL))))|(!AKT&(Bak&(!BCL2&!Bcl_XL))))))) +AR, ((Androgen&(!EP300&(!EZH2&(!GLI&(!HSPs&(!MDM2&(!NCOA3&(!NCOR1&(!NCOR2&(!PKC&(!PTEN&(!SMAD&NKX3_1))))))))))))|((Androgen&(!EP300&(!EZH2&(!GLI&(!HSPs&(!MDM2&(!NCOA3&(!NCOR1&(!NCOR2&(!PKC&(!PTEN&SMAD)))))))))))|((Androgen&(!EP300&(!EZH2&(!GLI&(!HSPs&(!MDM2&(!NCOA3&(!NCOR1&(!NCOR2&(PKC&!PTEN))))))))))|((Androgen&(!EP300&(!EZH2&(!GLI&(!HSPs&(!MDM2&(NCOA3&(!NCOR1&(!NCOR2&!PTEN)))))))))|((Androgen&(!EP300&(!EZH2&(!GLI&(HSPs&(!MDM2&(!NCOR1&(!NCOR2&!PTEN))))))))|((Androgen&(!EP300&(!EZH2&(GLI&(!MDM2&(!NCOR1&(!NCOR2&!PTEN)))))))|((Androgen&(!EP300&(EZH2&(!MDM2&(!NCOR1&(!NCOR2&!PTEN))))))|(Androgen&(EP300&(!MDM2&(!NCOR1&(!NCOR2&!PTEN)))))))))))) +AR_ERG, (AR&fused_event) +ATM, DNA_Damage +ATR, ((!DNA_Damage&p14ARF)|DNA_Damage) +AXIN1, GSK3 +Acidosis, Acidosis +Androgen, Androgen +BAD, (!AKT&(!HIF1&(!p90RSK&(!RAF&!YWHAZ)))) +BAX, ((!BCL2&(!ETS1&(!HIF1&(!JNK&(p53&!YWHAZ)))))|(!BCL2&(!ETS1&(!HIF1&(JNK&!YWHAZ))))) +BCL2, ((!BAD&(!BAX&(!DAXX&(!HSPs&(!NF_kB&(!p53&RUNX2))))))|((!BAD&(!BAX&(!DAXX&(!HSPs&(NF_kB&!p53)))))|(!BAD&(!BAX&(!DAXX&(HSPs&!p53)))))) +BIRC5, (HSPs&!p53) +BRCA1, ((!ATM&(!ATR&(!CyclinD&(E2F1&!Caspase3))))|((!ATM&(ATR&(!CyclinD&!Caspase3)))|(ATM&(!CyclinD&!Caspase3)))) +Bak, Caspase8 +Bcl_XL, (AR&(!BAD&!p53)) +CHK1_2, (ATM&(ATR&BRCA1)) +COX4I2, HIF1 +Carcinogen, Carcinogen +Caspase3, ((!Caspase8&Caspase9)|Caspase8) +Caspase8, (!cFLAR&FADD) +Caspase9, ((!AKT&(!BIRC5&(CytoC&(APAF1&PTCH1))))|(!AKT&(BIRC5&(CytoC&APAF1)))) +CyclinB, (E2F1&!p21) +CyclinD, ((!FOXO&(!GLI&(!GSK3&(MYC_MAX&(!NF_kB&(!p15&(!p21&TCF)))))))|((!FOXO&(!GLI&(!GSK3&(MYC_MAX&(NF_kB&(!p15&!p21))))))|(!FOXO&(GLI&(!GSK3&(MYC_MAX&(!p15&!p21))))))) +CytoC, ((!AKT&(!Bak&(!BAX&(!BCL2&(!Bcl_XL&(!Caspase8&p53))))))|((!AKT&(!Bak&(!BAX&(!BCL2&(!Bcl_XL&Caspase8)))))|((!AKT&(!Bak&(BAX&(!BCL2&!Bcl_XL))))|(!AKT&(Bak&(!BCL2&!Bcl_XL)))))) +DAXX, (!ATM&(!ATR&!SPOP)) +DNA_Damage, (Carcinogen&!SPOP) +Dsh, WNT +E2F1, (AR&(!MXI1&!RB1)) +EGF, EGF +EGFR, ((!Androgen&(EGF&(!FRS2&!TGFBR)))|(Androgen&(!FRS2&!TGFBR))) +EP300, AKT +ERG, ERK +ERK, ((!MEK1_2&RAF)|MEK1_2) +ETS1, ((!ERK&(!p53&RTK))|(ERK&!p53)) +EZH2, ((AKT&(E2F1&(!ERG&AR_ERG)))|(AKT&(E2F1&ERG))) +E_cadherin, ((!beta_catenin&(!ERG&(!NF_kB&(!Slug&(!Snail&AR_ERG)))))|(beta_catenin&(!ERG&(!NF_kB&(!Slug&!Snail))))) +FADD, ((!MAP3K1_3&(!PTCH1&(!SHH&TNFalpha)))|(!MAP3K1_3&(PTCH1&!SHH))) +FGF, FGF +FGFR3, (FGF&(!FRS2&(!PKC&!TGFBR))) +FOS, ((!AR&(!ERK&ETS1))|((!AR&ERK)|AR)) +FOXA1, FOXO +FOXO, (!AKT&JNK) +FRS2, (!ERK&(EGFR&(FGFR3&(!FRS2&!TGFBR)))) +GADD45, ((!p53&SMAD)|p53) +GLI, ((!SMO&(!SPOP&WNT))|(SMO&!SPOP)) +GSH, ((!MYC_MAX&(!NF_kB&p21))|((!MYC_MAX&NF_kB)|MYC_MAX)) +GSK3, (!AKT&(!Dsh&(MEK1_2&(!mTORC2&!p90RSK)))) +HIF1, ((!FOXO&(!HSPs&(!Hypoxia&(!mTORC2&(!MYC_MAX&(!p53&(!PHDs&(!VHL&mTORC1))))))))|((!FOXO&(!HSPs&(!Hypoxia&(!mTORC2&(MYC_MAX&(!p53&(!PHDs&!VHL)))))))|((!FOXO&(!HSPs&(!Hypoxia&(mTORC2&(!p53&(!PHDs&!VHL))))))|((!FOXO&(!HSPs&(Hypoxia&(!p53&(!PHDs&!VHL)))))|(!FOXO&(HSPs&(!p53&(!PHDs&!VHL)))))))) +HSPs, ((!AKT&(!BRCA1&(!Carcinogen&(!E2F1&(!FOXA1&PKC)))))|((!AKT&(!BRCA1&(!Carcinogen&(!E2F1&FOXA1))))|(!AKT&(!BRCA1&(Carcinogen&!E2F1))))) +Hypoxia, Hypoxia +IKK, ((!AKT&(!ETS1&(mTORC2&(!p53&(!PHDs&(!PKC&TAK1))))))|((!AKT&(!ETS1&(mTORC2&(!p53&(!PHDs&PKC)))))|((!AKT&(ETS1&(mTORC2&(!p53&!PHDs))))|((AKT&(!ETS1&(!p53&(!PHDs&(!PKC&TAK1)))))|((AKT&(!ETS1&(!p53&(!PHDs&PKC))))|(AKT&(ETS1&(!p53&!PHDs)))))))) +JNK, ((!ATM&(!ERK&(!GADD45&(!MAP3K1_3&(!p38&TAK1)))))|((!ATM&(!ERK&(!GADD45&(MAP3K1_3&!p38))))|((!ATM&(!ERK&(GADD45&!p38)))|(ATM&(!ERK&!p38))))) +JUN, ((!AR&(!ETS1&JNK))|((!AR&ETS1)|AR)) +MAP3K1_3, (!FOS&(!JUN&(!JNK&(!p38&RAS)))) +MDM2, ((!AKT&(!ATM&(!ATR&(DAXX&(!p14ARF&p53)))))|(AKT&(!ATM&(!ATR&(DAXX&!p14ARF))))) +MED12, !GLI +MEK1_2, ((!MAP3K1_3&(!PDK1&RAF))|((!MAP3K1_3&PDK1)|MAP3K1_3)) +MXI1, HIF1 +MYC, ((!E2F1&(!ERG&(!ERK&(!FOS&(!JUN&(!GLI&(!HIF1&(!NF_kB&(!p38&(!SHH&(!TCF&(AR_ERG&mTORC1))))))))))))|((!E2F1&(!ERG&(!ERK&(!FOS&(!JUN&(!GLI&(!HIF1&(!NF_kB&(!p38&(!SHH&(TCF&mTORC1)))))))))))|((!E2F1&(!ERG&(!ERK&(!FOS&(!JUN&(!GLI&(!HIF1&(!NF_kB&(!p38&(SHH&mTORC1))))))))))|((!E2F1&(!ERG&(!ERK&(!FOS&(!JUN&(!GLI&(!HIF1&(!NF_kB&(p38&(!SHH&(!TCF&AR_ERG)))))))))))|((!E2F1&(!ERG&(!ERK&(!FOS&(!JUN&(!GLI&(!HIF1&(!NF_kB&(p38&(!SHH&TCF))))))))))|((!E2F1&(!ERG&(!ERK&(!FOS&(!JUN&(!GLI&(!HIF1&(!NF_kB&(p38&SHH)))))))))|((!E2F1&(!ERG&(!ERK&(!FOS&(!JUN&(!GLI&(!HIF1&(NF_kB&(!p38&mTORC1)))))))))|((!E2F1&(!ERG&(!ERK&(!FOS&(!JUN&(!GLI&(!HIF1&(NF_kB&p38))))))))|((!E2F1&(!ERG&(!ERK&(!FOS&(!JUN&(GLI&(!HIF1&(!p38&mTORC1))))))))|((!E2F1&(!ERG&(!ERK&(!FOS&(!JUN&(GLI&(!HIF1&p38)))))))|((!E2F1&(!ERG&(!ERK&(!FOS&(JUN&(!HIF1&(!p38&mTORC1)))))))|((!E2F1&(!ERG&(!ERK&(!FOS&(JUN&(!HIF1&p38))))))|((!E2F1&(!ERG&(!ERK&(FOS&(!HIF1&(!p38&mTORC1))))))|((!E2F1&(!ERG&(!ERK&(FOS&(!HIF1&p38)))))|((!E2F1&(!ERG&(ERK&(!HIF1&(!p38&mTORC1)))))|((!E2F1&(!ERG&(ERK&(!HIF1&p38))))|((!E2F1&(ERG&(!HIF1&(!p38&mTORC1))))|((!E2F1&(ERG&(!HIF1&p38)))|((E2F1&(!ERG&(!ERK&(!FOS&(!JUN&(!GLI&(!HIF1&(!NF_kB&(!SHH&(!TCF&AR_ERG))))))))))|((E2F1&(!ERG&(!ERK&(!FOS&(!JUN&(!GLI&(!HIF1&(!NF_kB&(!SHH&TCF)))))))))|((E2F1&(!ERG&(!ERK&(!FOS&(!JUN&(!GLI&(!HIF1&(!NF_kB&SHH))))))))|((E2F1&(!ERG&(!ERK&(!FOS&(!JUN&(!GLI&(!HIF1&NF_kB)))))))|((E2F1&(!ERG&(!ERK&(!FOS&(!JUN&(GLI&!HIF1))))))|((E2F1&(!ERG&(!ERK&(!FOS&(JUN&!HIF1)))))|((E2F1&(!ERG&(!ERK&(FOS&!HIF1))))|((E2F1&(!ERG&(ERK&!HIF1)))|(E2F1&(ERG&!HIF1)))))))))))))))))))))))))))) +MYC_MAX, (!MXI1&(MYC&(!SMAD&!TGFBR))) +NCOA3, (p38&!SPOP) +NCOR1, !AKT +NCOR2, (!AKT&!FOXO) +NF1, !PKC +NF_kB, ((!DNA_Damage&(!E_cadherin&(IKK&(!NCOA3&(!PIP3&Snail)))))|((!DNA_Damage&(!E_cadherin&(IKK&(!NCOA3&PIP3))))|((!DNA_Damage&(!E_cadherin&(IKK&NCOA3)))|((!DNA_Damage&(E_cadherin&(!NCOA3&(!PIP3&Snail))))|((!DNA_Damage&(E_cadherin&(!NCOA3&PIP3)))|((!DNA_Damage&(E_cadherin&NCOA3))|((DNA_Damage&(!NCOA3&(!PIP3&Snail)))|((DNA_Damage&(!NCOA3&PIP3))|(DNA_Damage&NCOA3))))))))) +NKX3_1, (AR&(!ERG&(PKC&!AR_ERG))) +Nutrients, Nutrients +PDK1, ((!HIF1&(!MYC_MAX&PIP3))|((!HIF1&MYC_MAX)|HIF1)) +PHDs, (!Hypoxia&ROS) +PI3K, ((!EGFR&(!FRS2&TGFBR))|((!EGFR&FRS2)|EGFR)) +PIP3, (!p53&PI3K) +PKC, (RTK&WNT) +PTCH1, (GLI&!SHH) +PTEN, (!NF_kB&(p53&!Snail)) +RAF, ((!EZH2&RAS)|EZH2) +RAGS, (!Hypoxia&Nutrients) +RAS, ((!EGFR&(!FRS2&RTK))|((!EGFR&FRS2)|EGFR)) +RB1, (!AMPK&(CHK1_2&(!CyclinB&(!CyclinD&!p53)))) +ROS, ((!COX4I2&(!GSH&Hypoxia))|(COX4I2&!GSH)) +RTK, ((!EGFR&FGFR3)|EGFR) +RUNX2, ((!ETS1&(!FOXO&(!p38&SMAD)))|((!ETS1&(!FOXO&p38))|(ETS1&!FOXO))) +Rheb, !TSC1_2 +SHH, !ATR +SMAD, ((!AR&(!TGFBR&TNFalpha))|(!AR&TGFBR)) +SMO, (!PTCH1&SHH) +SPOP, SPOP +Slug, ((!DAXX&(!MDM2&(!NF_kB&(!p53&TCF))))|(!DAXX&(!MDM2&(NF_kB&!p53)))) +Snail, ((!beta_catenin&(!GLI&(!GSK3&(!NF_kB&SMAD))))|((!beta_catenin&(!GLI&(!GSK3&NF_kB)))|(!beta_catenin&(GLI&!GSK3)))) +TAK1, ((!TGFBR&TNFalpha)|TGFBR) +TCF, ((!beta_catenin&(!ERG&(!TAK1&AR_ERG)))|((!beta_catenin&(ERG&!TAK1))|(beta_catenin&!TAK1))) +TERT, ((!AKT&(!eEF2&(!GLI&(!HIF1&(!ZBTB17&(!MYC_MAX&(!NF1&(NF_kB&(!p53&!SMAD)))))))))|((!AKT&(!eEF2&(!GLI&(!HIF1&(!ZBTB17&(!MYC_MAX&(NF1&(!p53&!SMAD))))))))|((!AKT&(!eEF2&(!GLI&(!HIF1&(!ZBTB17&(MYC_MAX&(!p53&!SMAD)))))))|((!AKT&(!eEF2&(!GLI&(HIF1&(!ZBTB17&(!p53&!SMAD))))))|((!AKT&(!eEF2&(GLI&(!ZBTB17&(!p53&!SMAD)))))|(AKT&(!eEF2&(!ZBTB17&(!p53&!SMAD))))))))) +TGFBR, (!MED12&TGFb) +TGFb, TGFb +TNFalpha, TNFalpha +TSC1_2, ((!AKT&(!AMPK&(!ERK&(!HIF1&(!p53&(!p90RSK&!RAF))))))|((!AKT&(!AMPK&(!ERK&(!HIF1&(p53&!p90RSK)))))|((!AKT&(!AMPK&(!ERK&(!HIF1&(p53&(p90RSK&!RAF))))))|((!AKT&(!AMPK&(!ERK&(HIF1&(!p53&!p90RSK)))))|((!AKT&(!AMPK&(!ERK&(HIF1&(!p53&(p90RSK&!RAF))))))|((!AKT&(!AMPK&(!ERK&(HIF1&p53))))|((!AKT&(!AMPK&(ERK&(!HIF1&(p53&(!p90RSK&!RAF))))))|((!AKT&(!AMPK&(ERK&(HIF1&(!p53&(!p90RSK&!RAF))))))|((!AKT&(!AMPK&(ERK&(HIF1&(p53&!p90RSK)))))|((!AKT&(!AMPK&(ERK&(HIF1&(p53&(p90RSK&!RAF))))))|((!AKT&(AMPK&(!ERK&(!HIF1&(!p53&!p90RSK)))))|((!AKT&(AMPK&(!ERK&(!HIF1&(!p53&(p90RSK&!RAF))))))|((!AKT&(AMPK&(!ERK&(!HIF1&p53))))|((!AKT&(AMPK&(!ERK&HIF1)))|((!AKT&(AMPK&(ERK&(!HIF1&(!p53&(!p90RSK&!RAF))))))|((!AKT&(AMPK&(ERK&(!HIF1&(p53&!p90RSK)))))|((!AKT&(AMPK&(ERK&(!HIF1&(p53&(p90RSK&!RAF))))))|((!AKT&(AMPK&(ERK&(HIF1&(!p53&!p90RSK)))))|((!AKT&(AMPK&(ERK&(HIF1&(!p53&(p90RSK&!RAF))))))|((!AKT&(AMPK&(ERK&(HIF1&p53))))|((AKT&(!AMPK&(!ERK&(!HIF1&(p53&(!p90RSK&!RAF))))))|((AKT&(!AMPK&(!ERK&(HIF1&(!p53&(!p90RSK&!RAF))))))|((AKT&(!AMPK&(!ERK&(HIF1&(p53&!p90RSK)))))|((AKT&(!AMPK&(!ERK&(HIF1&(p53&(p90RSK&!RAF))))))|((AKT&(!AMPK&(ERK&(HIF1&(p53&(!p90RSK&!RAF))))))|((AKT&(AMPK&(!ERK&(!HIF1&(!p53&(!p90RSK&!RAF))))))|((AKT&(AMPK&(!ERK&(!HIF1&(p53&!p90RSK)))))|((AKT&(AMPK&(!ERK&(!HIF1&(p53&(p90RSK&!RAF))))))|((AKT&(AMPK&(!ERK&(HIF1&(!p53&!p90RSK)))))|((AKT&(AMPK&(!ERK&(HIF1&(!p53&(p90RSK&!RAF))))))|((AKT&(AMPK&(!ERK&(HIF1&p53))))|((AKT&(AMPK&(ERK&(!HIF1&(p53&(!p90RSK&!RAF))))))|((AKT&(AMPK&(ERK&(HIF1&(!p53&(!p90RSK&!RAF))))))|((AKT&(AMPK&(ERK&(HIF1&(p53&!p90RSK)))))|(AKT&(AMPK&(ERK&(HIF1&(p53&(p90RSK&!RAF)))))))))))))))))))))))))))))))))))))))) +VHL, (!Hypoxia&!ROS) +WNT, ((!ERG&(!p53&AR_ERG))|(ERG&!p53)) +YWHAZ, AR +ZBTB17, (AR&!MYC_MAX) +beta_catenin, ((!AXIN1&(!EZH2&(!GSK3&(!p53&YWHAZ))))|(!AXIN1&(EZH2&(!GSK3&!p53)))) +cFLAR, ((!AKT&(AR&!JNK))|(AKT&!JNK)) +eEF2, !eEF2K +eEF2K, ((!p70S6kab&p90RSK)|p70S6kab) +fused_event, fused_event +mTORC1, (AKT&(!AMPK&!TSC1_2)) +mTORC2, ((!AKT&(!AMPK&(RAGS&Rheb)))|((AKT&(!AMPK&(!RAGS&Rheb)))|((AKT&(!AMPK&RAGS))|(AKT&(AMPK&(RAGS&Rheb)))))) +p14ARF, (E2F1&(MYC_MAX&RAS)) +p15, ZBTB17 +p21, ((!AKT&(!ERK&(!HIF1&(!MDM2&(!ZBTB17&(!MYC_MAX&(!p53&(SMAD&!TERT))))))))|((!AKT&(!ERK&(!HIF1&(!MDM2&(!ZBTB17&(!MYC_MAX&(p53&!TERT)))))))|((!AKT&(!ERK&(!HIF1&(!MDM2&(ZBTB17&(!MYC_MAX&!TERT))))))|(!AKT&(!ERK&(HIF1&(!MDM2&(!MYC_MAX&!TERT)))))))) +p38, (!ERK&(!GADD45&MAP3K1_3)) +p53, ((!Acidosis&(!BCL2&(!CHK1_2&(!HIF1&(!HSPs&(!MDM2&(!p14ARF&p38)))))))|((!Acidosis&(!BCL2&(!CHK1_2&(!HIF1&(!HSPs&(!MDM2&p14ARF))))))|((!Acidosis&(!BCL2&(!CHK1_2&(HIF1&(!HSPs&!MDM2)))))|((!Acidosis&(!BCL2&(CHK1_2&(!HSPs&!MDM2))))|(Acidosis&(!BCL2&(!HSPs&!MDM2))))))) +p70S6kab, ((!mTORC2&PDK1)|mTORC2) +p90RSK, ((!ERK&PDK1)|ERK) diff --git a/test/[var_47]__[id_075]__[INFLAMMATORY-BOWEL-DISEASE].bnet b/test/[var_47]__[id_075]__[INFLAMMATORY-BOWEL-DISEASE].bnet new file mode 100644 index 00000000..1e826920 --- /dev/null +++ b/test/[var_47]__[id_075]__[INFLAMMATORY-BOWEL-DISEASE].bnet @@ -0,0 +1,47 @@ +targets, factors +CD4_NKG2D, ((PGN&!(CD4_NKG2D&((IEC_ULPB1_6|IEC_MICA_B)|IL10)))|((MDP&!(CD4_NKG2D&((IEC_ULPB1_6|IEC_MICA_B)|IL10)))|(((CD4_NKG2D&((TNFa|IL15)&!CD4_NKG2Dupregulation))&!(CD4_NKG2D&((IEC_ULPB1_6|IEC_MICA_B)|IL10)))|(LPS&!(CD4_NKG2D&((IEC_ULPB1_6|IEC_MICA_B)|IL10)))))) +CD4_NKG2Dupregulation, (CD4_NKG2D&(TNFa|IL15)) +CD8_NKG2D, ((MDP&!(CD8_NKG2D&(IEC_MICA_B|(IEC_ULPB1_6|(IL21&IL2)))))|((PGN&!(CD8_NKG2D&(IEC_MICA_B|(IEC_ULPB1_6|(IL21&IL2)))))|(LPS&!(CD8_NKG2D&(IEC_MICA_B|(IEC_ULPB1_6|(IL21&IL2))))))) +DC, ((TLR2&!(DC&IL10))|((TLR4&!(DC&IL10))|(NOD2&!(DC&IL10)))) +DEF, (IL22|(IL17|NOD2)) +FIBROBLAST, ((IL2&!(FIBROBLAST&(IL12|IFNg)))|((MACR&(TGFb|(IL13|IL4)))&!(FIBROBLAST&(IL12|IFNg)))) +GRANZB, (NK_NKG2D|(CD8_NKG2D|(NK|(DC&(!PGN|!LPS))))) +IEC_MICA_B, (((IEC_MICA_B&(TNFa&!IEC_MICA_Bupregulation))&!TGFb)|((LPS&!TGFb)|((PGN&!TGFb)|(MDP&!TGFb)))) +IEC_MICA_Bupregulation, (IEC_MICA_B&TNFa) +IEC_ULPB1_6, (CD8_NKG2D&(PGN|(LPS|MDP))) +IFNg, ((((Th17&(PGN|(LPS|MDP)))&!(IFNg&(TGFb|IL10)))&!Th2)|(((Th1&!(IFNg&(TGFb|IL10)))&!Th2)|((((IL18&(IL12&(Th0|MACR)))&!(IFNg&(TGFb|IL10)))&!Th2)|((((IL23&((PGN|(LPS|MDP))&NK))&!(IFNg&(TGFb|IL10)))&!Th2)|((((NK_NKG2D&(IEC_ULPB1_6|IEC_MICA_B))&!(IFNg&(TGFb|IL10)))&!Th2)|(((CD8_NKG2D&(IEC_ULPB1_6|IEC_MICA_B))&!(IFNg&(TGFb|IL10)))&!Th2)))))) +IL10, (Treg|((DC&LPS)|((TLR2&(NFkB&(!MACR&!IFNg)))|((MACR&(LPS&!IL4))|(Th2&!IL23))))) +IL12, ((LPS&(IFNg&((MACR&PGN)|DC)))|(TLR2&(NFkB&(DC|MACR)))) +IL13, Th2 +IL15, ((FIBROBLAST&(PGN|(LPS|MDP)))|(MACR&(IFNg|LPS))) +IL17, (((Th17_M&(PGN|(LPS|MDP)))&!(IL17&(TGFb|IL13)))|(((CD4_NKG2D&(IEC_ULPB1_6|IEC_MICA_B))&!(IL17&(TGFb|IL13)))|(Th17&!(IL17&(TGFb|IL13))))) +IL18, (LPS&(NFkB&(DC|MACR))) +IL1b, (((MACR&(NFkB&LPS))&!(IL10&IL1b))|((DC&(NFkB&LPS))&!(IL10&IL1b))) +IL2, ((Th0_M&(PGN|(LPS|MDP)))|(Th0|DC)) +IL21, (((((Th0&IL6)&!IFNg)&!IL4)&!TGFb)|Th17) +IL22, (Th17|((NK&IL23)|(((Th0&(IL22&(IL21&!IL22upregulation)))&!TGFb)|(CD4_NKG2D|(NK&(IL18&IL12)))))) +IL22upregulation, (Th0&(IL21&IL22)) +IL23, ((MACR&IL1b)|DC) +IL4, Th2 +IL6, ((DC&(PGN|LPS))|((MACR&PGN)|((Th17&IL23)|(NFkB&(!IL10|!IL4))))) +LPS, !(GRANZB|(DEF|PERFOR)) +MACR, ((NOD2&!(MACR&IL10))|((IFNg&!(MACR&IL10))|((IL15&!(MACR&IL10))|((TLR4&!(MACR&IL10))|(TLR2&!(MACR&IL10)))))) +MDP, !(PERFOR|(DEF|GRANZB)) +NFkB, (NOD2|(TLR4|TLR2)) +NK, (((DC&IL15)&!(NK&Treg))|((IL23&!(NK&Treg))|((IL18&IL10)&!(NK&Treg)))) +NK_NKG2D, ((MDP&!(NK_NKG2D&(IEC_ULPB1_6&(TGFb&(IEC_MICA_B&(IL21&IL12))))))|((PGN&!(NK_NKG2D&(IEC_ULPB1_6&(TGFb&(IEC_MICA_B&(IL21&IL12))))))|(LPS&!(NK_NKG2D&(IEC_ULPB1_6&(TGFb&(IEC_MICA_B&(IL21&IL12)))))))) +NOD2, MDP +PERFOR, (NK_NKG2D|NK) +PGN, !(GRANZB|(DEF|PERFOR)) +TGFb, (Treg|MACR) +TLR2, PGN +TLR4, LPS +TNFa, (((MACR&(IL2|(PGN|(IFNg&LPS))))&!(IL10&(TNFa&(TLR4|TLR2))))|(((CD8_NKG2D&(IEC_ULPB1_6|IEC_MICA_B))&!(IL10&(TNFa&(TLR4|TLR2))))|(((FIBROBLAST&IFNg)&!(IL10&(TNFa&(TLR4|TLR2))))|(((NFkB&LPS)&!(IL10&(TNFa&(TLR4|TLR2))))|(((CD4_NKG2D&(IEC_ULPB1_6|IEC_MICA_B))&!(IL10&(TNFa&(TLR4|TLR2))))|(((NK&((PGN|(LPS|MDP))&(IL23|(IL15|IL2))))&!(IL10&(TNFa&(TLR4|TLR2))))|((NK_NKG2D&(IEC_ULPB1_6|IEC_MICA_B))&!(IL10&(TNFa&(TLR4|TLR2)))))))))) +Th0, (MDP|(PGN|LPS)) +Th0_M, (Th0_M|(Th0&(IL23|IL12))) +Th1, ((Th0&(IL18|(IL12|IFNg)))&!(Th1&(IL4|(TGFb|(IL10|(Treg|(Th2|(IL12&(IL23|IL17))))))))) +Th17, ((Th0&(IL23|(IL6|IL1b)))&!(Th17&(IL12|(TGFb|(Treg|(IFNg|IL4)))))) +Th17_M, ((Th0_M&((PGN|(LPS|MDP))&((IL6&IL1b)|(IL23|IL2))))|Th17_M) +Th2, ((Th0&(((Th2&IL4)&!Th2upregulation)|(((IL18&IL4)&!IL12)|IL10)))&!(Th2&(TGFb|(Treg|IFNg)))) +Th2upregulation, (Th2&IL4) +Treg, ((Th0&(TGFb|TLR2))&!(Treg&(IL22|(IL23|(TNFa|(IL21|(IL6|Th17))))))) diff --git a/test/[var_60]__[id_085]__[T-LGL-SIGNALING-2008].bnet b/test/[var_60]__[id_085]__[T-LGL-SIGNALING-2008].bnet new file mode 100644 index 00000000..5c002103 --- /dev/null +++ b/test/[var_60]__[id_085]__[T-LGL-SIGNALING-2008].bnet @@ -0,0 +1,58 @@ +targets, factors +A20, (NFkB&!Apoptosis) +Apoptosis, ((!Caspase&Apoptosis)|Caspase) +BID, ((!BclxL&(!GZMB&(Caspase&(!MCL1&!Apoptosis))))|(!BclxL&(GZMB&(!MCL1&!Apoptosis)))) +BclxL, ((!GZMB&(!NFkB&(!BID&(!DISC&(STAT3&!Apoptosis)))))|(!GZMB&(NFkB&(!BID&(!DISC&!Apoptosis))))) +CD45, CD45 +CREB, (IFNg&(ERK&!Apoptosis)) +CTLA4, (TCR&!Apoptosis) +Caspase, ((!GZMB&(!IAP&(!BID&(DISC&!Apoptosis))))|((!GZMB&(!IAP&(BID&(!DISC&(TRADD&!Apoptosis)))))|((!GZMB&(!IAP&(BID&(DISC&!Apoptosis))))|((!GZMB&(IAP&(DISC&!Apoptosis)))|((GZMB&(!IAP&(!BID&(DISC&!Apoptosis))))|((GZMB&(!IAP&(BID&!Apoptosis)))|(GZMB&(IAP&(DISC&!Apoptosis))))))))) +Ceramide, (Fas&(!S1P&!Apoptosis)) +DISC, ((FasT&(!FLIP&(!Ceramide&(Fas&!Apoptosis))))|((FasT&(!FLIP&(Ceramide&!Apoptosis)))|((FasT&(FLIP&(!Ceramide&(Fas&(IL2&!Apoptosis)))))|(FasT&(FLIP&(Ceramide&!Apoptosis)))))) +ERK, (PI3K&(MEK&!Apoptosis)) +FLIP, ((!IFNg&(NFkB&(!DISC&!Apoptosis)))|((IFNg&(!NFkB&(CREB&(!DISC&!Apoptosis))))|(IFNg&(NFkB&(!DISC&!Apoptosis))))) +FYN, ((!IL2RB&(TCR&!Apoptosis))|(IL2RB&!Apoptosis)) +Fas, (FasT&(FasL&(!sFas&!Apoptosis))) +FasL, ((!NFAT&(!NFkB&(!ERK&(STAT3&!Apoptosis))))|((!NFAT&(!NFkB&(ERK&!Apoptosis)))|((!NFAT&(NFkB&!Apoptosis))|(NFAT&!Apoptosis)))) +FasT, (NFkB&!Apoptosis) +GAP, ((!PDGFR&(RAS&(!IL2&(!Apoptosis&!IL15))))|((PDGFR&(!GAP&(RAS&(!IL2&(!Apoptosis&!IL15)))))|(PDGFR&(GAP&(!IL2&(!Apoptosis&!IL15)))))) +GPCR, (S1P&!Apoptosis) +GRB2, ((!ZAP70&(IL2RB&!Apoptosis))|(ZAP70&!Apoptosis)) +GZMB, ((!IFNg&(Tbet&!Apoptosis))|((IFNg&(!CREB&(Tbet&!Apoptosis)))|(IFNg&(CREB&!Apoptosis)))) +IAP, (NFkB&(!BID&!Apoptosis)) +IFNg, ((IFNgT&(!SMAD&(!P2&(!IL2&(!Apoptosis&(!Stimuli&IL15))))))|((IFNgT&(!SMAD&(!P2&(!IL2&(!Apoptosis&Stimuli)))))|(IFNgT&(!SMAD&(!P2&(IL2&!Apoptosis)))))) +IFNgT, ((!NFAT&(!Tbet&(STAT3&!Apoptosis)))|((!NFAT&(Tbet&!Apoptosis))|(NFAT&!Apoptosis))) +IL15, IL15 +IL2, ((!NFAT&(!NFkB&(!Tbet&(STAT3&!Apoptosis))))|((!NFAT&(NFkB&(!Tbet&!Apoptosis)))|(NFAT&(!Tbet&!Apoptosis)))) +IL2RA, (!IL2RA&(IL2RAT&(IL2&!Apoptosis))) +IL2RAT, ((!NFkB&(STAT3&(IL2&!Apoptosis)))|(NFkB&(IL2&!Apoptosis))) +IL2RB, ((IL2RBT&(!IL2&(!Apoptosis&IL15)))|(IL2RBT&(IL2&!Apoptosis))) +IL2RBT, (ERK&(Tbet&!Apoptosis)) +JAK, ((!IFNg&(!IL2RB&(!IL2RA&(RANTES&(!SOCS&(!Apoptosis&!CD45))))))|((!IFNg&(!IL2RB&(IL2RA&(!SOCS&(!Apoptosis&!CD45)))))|((!IFNg&(IL2RB&(!SOCS&(!Apoptosis&!CD45))))|(IFNg&(!SOCS&(!Apoptosis&!CD45)))))) +LCK, ((!ZAP70&(!IL2RB&(!TCR&(!Apoptosis&CD45))))|((!ZAP70&(!IL2RB&(TCR&!Apoptosis)))|((!ZAP70&(IL2RB&!Apoptosis))|(ZAP70&(!Apoptosis&CD45))))) +MCL1, (NFkB&(PI3K&(IL2RB&(STAT3&!Apoptosis)))) +MEK, (RAS&!Apoptosis) +NFAT, (PI3K&!Apoptosis) +NFkB, ((!TPL2&(!FLIP&(PI3K&!Apoptosis)))|((!TPL2&(FLIP&(!IAP&(PI3K&!Apoptosis))))|((!TPL2&(FLIP&(IAP&(!PI3K&(TRADD&!Apoptosis)))))|((!TPL2&(FLIP&(IAP&(PI3K&!Apoptosis))))|(TPL2&!Apoptosis))))) +P2, ((!IFNg&(P2&(!Apoptosis&!Stimuli2)))|(IFNg&(!Apoptosis&!Stimuli2))) +PDGF, PDGF +PDGFR, ((!S1P&(!Apoptosis&PDGF))|(S1P&!Apoptosis)) +PI3K, ((!PDGFR&(RAS&!Apoptosis))|(PDGFR&!Apoptosis)) +PLCG1, ((!PDGFR&(GRB2&!Apoptosis))|(PDGFR&!Apoptosis)) +RANTES, (NFkB&!Apoptosis) +RAS, ((!GAP&(!GRB2&(PLCG1&!Apoptosis)))|(!GAP&(GRB2&!Apoptosis))) +S1P, (!Ceramide&(SPHK1&!Apoptosis)) +SMAD, (GPCR&!Apoptosis) +SOCS, (!IL2&(JAK&(!Apoptosis&!IL15))) +SPHK1, (PDGFR&!Apoptosis) +STAT3, (JAK&!Apoptosis) +Stimuli, Stimuli +Stimuli2, Stimuli2 +TAX, TAX +TCR, (!CTLA4&(!Apoptosis&Stimuli)) +TNF, (NFkB&!Apoptosis) +TPL2, ((!TNF&(!Apoptosis&TAX))|((TNF&(!PI3K&(!Apoptosis&TAX)))|(TNF&(PI3K&!Apoptosis)))) +TRADD, (!IAP&(TNF&(!A20&!Apoptosis))) +Tbet, ((!Tbet&(JAK&!Apoptosis))|(Tbet&!Apoptosis)) +ZAP70, (LCK&(!FYN&!Apoptosis)) +sFas, (FasT&!Apoptosis) diff --git a/test/[var_61]__[id_014]__[T-LGL-SURVIVAL-NETWORK-2008].bnet b/test/[var_61]__[id_014]__[T-LGL-SURVIVAL-NETWORK-2008].bnet new file mode 100644 index 00000000..3f57a5d9 --- /dev/null +++ b/test/[var_61]__[id_014]__[T-LGL-SURVIVAL-NETWORK-2008].bnet @@ -0,0 +1,59 @@ +targets, factors +A20, (NFKB&!Apoptosis) +Apoptosis, (Caspase|Apoptosis) +BID, ((GZMB&!((BclxL|Apoptosis)|MCL1))|(Caspase&!((BclxL|Apoptosis)|MCL1))) +BclxL, ((NFKB&!(((BID|DISC)|Apoptosis)|GZMB))|(STAT3&!(((BID|DISC)|Apoptosis)|GZMB))) +CD45, CD45 +CREB, ((ERK&IFN)&!Apoptosis) +CTLA4, (TCR&!Apoptosis) +Caspase, ((((TRADD&BID)&!(IAP|Apoptosis))|((GZMB&BID)&!(IAP|Apoptosis)))|(DISC&!Apoptosis)) +Ceramide, (Fas&!(Apoptosis|S1P)) +DISC, ((FasT&(((Fas&IL2)|(Fas&!FLIP))|Ceramide))&!Apoptosis) +ERK, ((MEK&PI3K)&!Apoptosis) +FLIP, ((NFKB&!(Apoptosis|DISC))|((CREB&IFNG)&!(Apoptosis|DISC))) +FYN, ((IL2RB&!Apoptosis)|(TCR&!Apoptosis)) +Fas, ((FasT&FasL)&!(Apoptosis|sFas)) +FasL, ((((NFAT&!Apoptosis)|(NFKB&!Apoptosis))|(STAT3&!Apoptosis))|(ERK&!Apoptosis)) +FasT, (NFKB&!Apoptosis) +GAP, (((PDGFR&GAP)&!((IL2|IL15)|Apoptosis))|(RAS&!((IL2|IL15)|Apoptosis))) +GPCR, (S1P&!Apoptosis) +GRB2, ((ZAP70&!Apoptosis)|(IL2RB&!Apoptosis)) +GZMB, ((TBET&!Apoptosis)|((CREB&IFNG)&!Apoptosis)) +IAP, (NFKB&!(BID|Apoptosis)) +IFN, IFN +IFNG, ((((IL15&IFNGT)&!((SMAD|Apoptosis)|P2))|((Stimuli&IFNGT)&!((SMAD|Apoptosis)|P2)))|((IL2&IFNGT)&!((SMAD|Apoptosis)|P2))) +IFNGT, (((NFAT&!Apoptosis)|(TBET&!Apoptosis))|(STAT3&!Apoptosis)) +IL15, IL15 +IL2, (((STAT3&!(TBET|Apoptosis))|(NFAT&!(TBET|Apoptosis)))|(NFKB&!(TBET|Apoptosis))) +IL2RA, ((IL2&IL2RAT)&!(IL2RA|Apoptosis)) +IL2RAT, ((IL2&(NFKB|STAT3))&!Apoptosis) +IL2RB, ((IL2RBT&(IL2|IL15))&!Apoptosis) +IL2RBT, ((ERK&TBET)&!Apoptosis) +JAK, ((((IL2RA&!((SOCS|Apoptosis)|CD45))|(IFNG&!((SOCS|Apoptosis)|CD45)))|(IL2RB&!((SOCS|Apoptosis)|CD45)))|(RANTES&!((SOCS|Apoptosis)|CD45))) +LCK, (((IL2RB&!(ZAP70|Apoptosis))|(TCR&!(ZAP70|Apoptosis)))|(CD45&!Apoptosis)) +MCL1, ((IL2RB&((PI3K&NFKB)&STAT3))&!Apoptosis) +MEK, (RAS&!Apoptosis) +NFAT, (PI3K&!Apoptosis) +NFKB, (((TPL2&!Apoptosis)|(PI3K&!Apoptosis))|((FLIP&(TRADD&IAP))&!Apoptosis)) +P2, ((IFNG&!(Stimuli2|Apoptosis))|(P2&!(Stimuli2|Apoptosis))) +PDGF, PDGF +PDGFR, ((S1P&!Apoptosis)|(PDGF&!Apoptosis)) +PI3K, ((PDGFR&!Apoptosis)|(RAS&!Apoptosis)) +PLCG1, ((PDGFR&!Apoptosis)|(GRB2&!Apoptosis)) +RANTES, (NFKB&!Apoptosis) +RAS, ((PLCG1&!(Apoptosis|GAP))|(GRB2&!(Apoptosis|GAP))) +S1P, (SPHK1&!(Apoptosis|Ceramide)) +SMAD, (GPCR&!Apoptosis) +SOCS, (JAK&!((IL15|IL2)|Apoptosis)) +SPHK1, (PDGFR&!Apoptosis) +STAT3, (JAK&!Apoptosis) +Stimuli, Stimuli +Stimuli2, Stimuli2 +TAX, TAX +TBET, ((JAK&!Apoptosis)|(TBET&!Apoptosis)) +TCR, (Stimuli&!(CTLA4|Apoptosis)) +TNF, (NFKB&!Apoptosis) +TPL2, (((PI3K&TNF)&!Apoptosis)|(TAX&!Apoptosis)) +TRADD, (TNF&!((IAP|A20)|Apoptosis)) +ZAP70, (LCK&!(Apoptosis|FYN)) +sFas, (FasT&!Apoptosis) diff --git a/test/[var_62]__[id_145]__[MELANOGENESIS].bnet b/test/[var_62]__[id_145]__[MELANOGENESIS].bnet new file mode 100644 index 00000000..dc1ef385 --- /dev/null +++ b/test/[var_62]__[id_145]__[MELANOGENESIS].bnet @@ -0,0 +1,53 @@ +targets, factors +AC, MC1R +ASK1, (UVB&(!Akt&!Melanin)) +ASK1_m, !Akt_m +Akt, PDK1 +Akt_m, PDK1_m +COX_2, (!GSK3b&(b_catenin|(NFAT|p38))) +CREB, (PKA|(Akt_m|MSK)) +EGFR, (UVB&!Melanin) +EP4, PGE2 +ERK, (MEK&!p38) +ERK_m, (MEK_m&!p38_m) +ETR, ET_1 +ET_1, (IL_1|P53) +GSK3b, !Akt +GSK3b_m, !Akt_m +IL_1, (UVB&!Melanin) +MC1R, a_MSH +MDM2, Akt +MEK, Raf +MEK_m, Raf_m +MITFmRNA, (b_catenin_m&CREB) +MITFprotein, (ERK_m&MITFmRNA) +MKK6, ASK1 +MKK6_m, ASK1_m +MSK, (p38_m|ERK_m) +Melanin, MITFprotein +NFAT, !GSK3b +P53, (!MDM2&(ERK|p38)) +PDE, PKA +PDK1, (PI3K&!PTEN) +PDK1_m, PI3K_m +PGE2, (COX_2|IL_1) +PI3K, EGFR +PI3K_m, ((PKC|Ras_m)&!cAMP) +PKA, cAMP +PKC, ETR +PTEN, ((Melanin&(!Akt&!ERK))|(!Melanin&(!UVB&(!Akt&!ERK)))) +Raf, (Ras&!Akt) +Raf_m, (PKC|Ras_m) +Ras, SG +Ras_m, (SG_m|cAMP) +SCF, (IL_1|P53) +SG, (EGFR&!ERK) +SG_m, (c_Kit&!ERK_m) +UVB, UVB +a_MSH, P53 +b_catenin, !GSK3b +b_catenin_m, !GSK3b_m +cAMP, (!PDE&(EP4|AC)) +c_Kit, SCF +p38, MKK6 +p38_m, MKK6_m diff --git a/test/[var_66]__[id_077]__[SIGNALING-PATHWAY-FOR-BUTHANOL-PRODUCTION].bnet b/test/[var_66]__[id_077]__[SIGNALING-PATHWAY-FOR-BUTHANOL-PRODUCTION].bnet new file mode 100644 index 00000000..0d999101 --- /dev/null +++ b/test/[var_66]__[id_077]__[SIGNALING-PATHWAY-FOR-BUTHANOL-PRODUCTION].bnet @@ -0,0 +1,58 @@ +targets, factors +n3_hydroxybutyryl_CoA, ((hbd|acetoacetyl_CoA)|crt) +EtfAB, NADH +NADH, NADH +NAD_P_H, NAD_P_H +PTS, PTS +Rnf, Rnf +acetaldehyde, (ald|acetyl_CoA) +acetate, ((ack|(glucose___PTS&acetone))|(pta&acetone)) +acetoacetate, ((acetoacetyl_CoA|ctfA)|ctfB) +acetoacetyl_CoA, (((acetyl_CoA|hbd)|ctfB)|thlA) +acetone, ((adc&!sporulation)|(acetoacetate&!sporulation)) +acetyl_CoA, (((thlA|pyruvate)|(acetate&acetoacetyl_CoA))|pfo) +ack, !(spo0A_p|sporulation) +adc, spo0A_p +adhA, spo0A_p +adhB, spo0A_p +ald, (sigK|spo0A_p) +bcd, !(spo0A_p|sporulation) +bdhAB, spo0A_p +buk1, !(spo0A_p|sporulation) +butanal, ((butyryl_CoA|bdhAB)|ald) +butanol, (((((bdhAB&!sporulation)|(adhB&!sporulation))|(NAD_P_H&!sporulation))|(butanal&!sporulation))|(adhA&!sporulation)) +butyrate, (((buk1&!butyrate)|(ptb&!butyrate))|(glucose___PTS&!butyrate)) +butyryl_CoA, ((((bcd|(butyrate&acetoacetyl_CoA))|ald)|EtfAB)|crotonoyl_CoA) +cell_membrane, ((butyrate&!(acetone|ethanol))|(glucose&!((butanol|acetone)|ethanol))) +crotonoyl_CoA, ((crt|ferredoxin)|n3_hydroxybutyryl_CoA) +crt, !(sporulation|spo0A_p) +ctfA, spo0A_p +ctfB, spo0A_p +ethanol, (((adhA&!(ald|sporulation))|(acetaldehyde&!(ald|sporulation)))|(adhB&!(ald|sporulation))) +fba, fba +ferredoxin, Rnf +gap_pgk_tpi_pgm__X276_23705_eno, gap_pgk_tpi_pgm__X276_23705_eno +glucose, glucose +glucose___PTS, (((PTS&(cell_membrane&glucose))&!(sporulation&!cell_membrane))|((glucose&(cell_membrane&PTS))&!(sporulation&!cell_membrane))) +hbd, !(sporulation|spo0A_p) +pfk, pfk +pfo, pfo +pgi, pgi +phosphorylation, phosphorylation +pta, !(spo0A_p|sporulation) +ptb, !(sporulation|spo0A_p) +pyk, pfk +pyruvate, ((((fba|pgi)|glucose___PTS)|pyk)|gap_pgk_tpi_pgm__X276_23705_eno) +sigA, sigA +sigE, (sigF|spo0A_p) +sigF, ((spoIIE&!(spoIIAB&!spoIIE))|(sigH&!(spoIIAB&!spoIIE))) +sigG, sigE +sigH, sigA +sigK, sigG +spo0A, (sigK|spo0A_p) +spo0A_p, ((((spo0A&phosphorylation)&!sporulation)|((sigA&(spo0A&phosphorylation))&!sporulation))|((phosphorylation&spo0A)&!sporulation)) +spoIIAA, (spoIIE|(spo0A_p&sigH)) +spoIIAB, ((spo0A_p&sigH)&!(spoIIAA&spoIIE)) +spoIIE, spoIIE +sporulation, (((((spo0A_p&!cell_membrane)|(sigE&(sigA&!cell_membrane)))|(sigG&(sigA&!cell_membrane)))|(sigH&!cell_membrane))|(sigK&(!cell_membrane&sigA))) +thlA, spo0A_p diff --git a/test/[var_70]__[id_051]__[COLITIS-ASSOCIATED-COLON-CANCER].bnet b/test/[var_70]__[id_051]__[COLITIS-ASSOCIATED-COLON-CANCER].bnet new file mode 100644 index 00000000..d2408ead --- /dev/null +++ b/test/[var_70]__[id_051]__[COLITIS-ASSOCIATED-COLON-CANCER].bnet @@ -0,0 +1,67 @@ +targets, factors +AKT, (PI3K&!(CASP3|PP2A)) +APC, APC +ASK1, (ROS&!P21) +ATM, ROS +BAX, (((TBID&PP2A)&!AKT)|((P53&PP2A)&!AKT)) +BCATENIN, !(APC&GSK3B) +BCL2, ((STAT3&!(PP2A|P53))|(NFKB&!(PP2A|P53))) +CASP3, ((CASP8&!IAP)|(CASP9&!IAP)) +CASP8, (FADD_&!(CFLIP|P21)) +CASP9, (CYTC&!(IAP|P21)) +CCL2, NFKB +CERAMIDE, (SMASE&!SPHK1) +CFLIP, NFKB +COX2, (TNFR&S1P) +CTL, (IFNG&!TGFB) +CYTC, MOMP +DC, ((CCL2&!IL10)|(TNFA&!IL10)) +EP2, PGE2 +ERK, MEK +FADD_, (FAS|TNFR) +FAS, CTL +GP130, IL6 +GSK3B, !(AKT|EP2) +IAP, ((NFKB&!SMAC)|(STAT3&!SMAC)) +IFNG, (CTL|TH1) +IKB, !IKK +IKK, (AKT|(TNFR&S1P)) +IL10, (TREG|TH2) +IL12, (DC|MAC) +IL4, (DC|TH2) +IL6, ((MAC|DC)|NFKB) +JAK, (GP130&!SOCS) +JNK, (MEKK1|ASK1) +JUN, (((BCATENIN&JNK)&!GSK3B)|((ERK&JNK)&!GSK3B)) +MAC, ((CCL2&!IL10)|(IFNG&!IL10)) +MDM2, ((P53&AKT)&!(ATM|GSK3B)) +MEK, (RAF|ROS) +MEKK1, ((TNFR|TGFR)|CERAMIDE) +MOMP, (((TBID&!BCL2)|(BAX&!BCL2))|(CERAMIDE&!BCL2)) +NFKB, !IKB +P21, ((SMAD&!(GSK3B|CASP3))|(P53&!(GSK3B|CASP3))) +P53, (((ATM&!MDM2)|(JNK&!MDM2))|(PTEN&!MDM2)) +PGE2, COX2 +PI3K, ((EP2&!PTEN)|(RAS&!PTEN)) +PP2A, (CERAMIDE&!AKT) +PTEN, (P53&!(NFKB|JUN)) +RAF, (CERAMIDE|RAS) +RAS, (EP2|GP130) +ROS, (TNFR&!SOD) +S1P, SPHK1 +SMAC, MOMP +SMAD, (TGFR&!JUN) +SMAD7, (NFKB|SMAD) +SMASE, (FADD_|P53) +SOCS, STAT3 +SOD, (NFKB|STAT3) +SPHK1, (ERK|TNFR) +STAT3, JAK +TBID, (CASP8&!BCL2) +TGFB, TREG +TGFR, (TGFB&!SMAD7) +TH1, ((IFNG&!((TGFB|IL4)|IL10))|(IL12&!((TGFB|IL4)|IL10))) +TH2, (IL4&!(IFNG|TGFB)) +TNFA, MAC +TNFR, TNFA +TREG, ((DC&!IL6)|(IL10&!IL6)) diff --git a/test/[var_86]__[id_019]__[IL-6-SIGNALING].bnet b/test/[var_86]__[id_019]__[IL-6-SIGNALING].bnet new file mode 100644 index 00000000..9af3e689 --- /dev/null +++ b/test/[var_86]__[id_019]__[IL-6-SIGNALING].bnet @@ -0,0 +1,56 @@ +targets, factors +ca, ip3 +cam_ca, ca +camk24, cam_ca +cyt_ptpe, cyt_ptpe +dum_gab1_kin_or_jak1_gab1_mem_p, (jak1|gab1_kin) +dum_gp80_a_il6rc, (gp80s_a|gp80m_a) +dum_il6rc_p_or_grb2_vav, (grb2_sos|il6rc_p) +dum_mtorc1_or_pkcd_stat3_ta, (mtorc1|pkcd) +erk12, mek1 +gab1_kin, gab1_kin +gab1_mem, (grb2_sos|(erk12&pip3)) +gab1_mem_p, (gab1_mem&dum_gab1_kin_or_jak1_gab1_mem_p) +gp130m, gp130m +gp130s, (!(camk24|mk2)|!(mk2|camk24)) +gp80m_a, il6 +gp80s_a, (il6&!gp130s) +grb2_sos, (il6rc_p|shp2) +il6, il6 +il6rc, (gp130m&dum_gp80_a_il6rc) +il6rc_p, ((il6rc&jak1)&!(shp2_a|shp2)) +ip3, plcg +jak1, (!(((shp2_a|socs1)|socs3)|shp2)|!(((socs3|shp2)|shp2_a)|socs1)) +mek1, raf1 +mek4, mekk1 +mek6, il6rc_p +mekk1, rac1 +mk2, p38 +mtor, mtor +mtorc1, mtor +nfkb, nfkb +p38, mek6 +pdk1, pdk1 +phlpp, phlpp +pi3k, (ras|(gab1_mem_p&!shp2_a)) +pias1, pias1 +pias3, pias3 +pip3, (pi3k&!pten) +pkcd, mek4 +plcg, gab1_mem_p +pten, pten +rac1, vav +raf1, ras +ras, (grb2_sos&!ras_gap) +ras_gap, (gab1_mem_p&!shp2_a) +ros, ros +ship, ship +shp2, ((il6rc_p&jak1)&!((socs3|sirp1a)|ros)) +shp2_a, ((gab1_mem_p&shp2)&!(sirp1a|ros)) +sirp1a, sirp1a +slim, slim +socs1, stat3_ta +socs3, (((erk12|nfkb)|stat3_ta)|p38) +stat3_py, ((il6rc_p&jak1)&!((cyt_ptpe|shp2)|shp2_a)) +stat3_ta, ((dum_mtorc1_or_pkcd_stat3_ta&stat3_py)&!(slim|pias3)) +vav, (dum_il6rc_p_or_grb2_vav&!socs1) diff --git a/test/ascidian_embryo_validation.bnet b/test/ascidian_embryo_validation.bnet new file mode 100644 index 00000000..c9c2571c --- /dev/null +++ b/test/ascidian_embryo_validation.bnet @@ -0,0 +1,48 @@ +targets, factors +nErk_signaling, (nFgf8_17_18&nFgf9_16_20)|(!nEfna_d) +nFoxc, (nErk_signaling&nFoxa_a&nDlx_b&nDmrt_a&nOtx&nSox1_2_3&nSox4_11_12)|(!nErk_signaling&!nFoxc&!nNodal) +nId, (nErk_signaling&nDlk&nNeurog&nNodal)|(!nId&!nTfap2_r_b) +nLhx3_4, (nErk_signaling&nCtnnb&nFoxa_a&nFoxd&nZic_r_b) +nMesp, (nErk_signaling&nLhx3_4&nTbx6_r_b)|(!nMesp) +nMrf, (nDlk&nNodal&nTbx6_r_b&nZic_r_b)|(!nErk_signaling&!nMrf) +nMsx, (nErk_signaling&nNodal&nOtx&nSox1_2_3&nTbx2_3)|(!nFoxa_a) +nNodal, (nErk_signaling&nSox1_2_3&nZic_r_a)|(!nAdmp&!nFoxa_a&!nFoxd&!nGdf1_3_r&!nNodal&!nSox4_11_12&!nWnttun5) +nOtx, (nErk_signaling&nFoxa_a&nGata_a&nSox1_2_3&nZic_r_a)|(!nAdmp&!nFoxd&!nGdf1_3_r&!nOtx&!nWnttun5) +nPax3_7, (nErk_signaling&nNodal)|(!nFoxa_a&!nPax3_7) +nPax6, (nErk_signaling&nDlk&nFoxa_a&nFoxd&nNodal&nZic_r_b)|(!nFoxb&!nPax6&!nSox4_11_12) +nTfap2_r_b, (nGata_a)|(!nErk_signaling&!nCtnnb) +nTwist_r_a_b, (nErk_signaling&nFoxa_a&nFoxd&nHand_r&nNodal&nOtx&nZic_r_b)|(!nFoxd) +nZic_r_b, (nErk_signaling&nCtnnb&nDlx_b&nFoxa_a&nFoxd&nGata_a&nSox1_2_3&nTbx6_r_b&nTp53_a&nTp53_b&nWnt5)|(!nCtnnb&!nFoxc&!nHes_a&!nPrdm1_r_a&!nPrdm1_r_b&!nZic_r_b) +nFgf8_17_18, (nAdmp&nErk_signaling&nFoxd&nNeurog&nNodal)|(!nDlk&!nErk_signaling&!nFoxb&!nNeurog&!nSnai&!nSox4_11_12) +nFgf9_16_20, (nCtnnb&nFoxd)|(!nErk_signaling&!nNodal&!nPem1) +nFoxa_a, (nCtnnb&nFoxd)|(!nHes_a&!nPem1&!nPrdm1_r_a&!nSnai) +nBrachyury, (nFoxa_a&nDlk&nErk_signaling&nFoxd&nTp53_a&nTp53_b&nZic_r_b)|(!nBrachyury&!nSnai) +nDlk, (nFoxa_a&nErk_signaling&nFoxd&nNeurog&nNodal&nZic_r_b)|(!nFoxa_a&!nDlk&!nSox4_11_12) +nDmrt_a, (nFoxa_a&nErk_signaling&nSox4_11_12)|(!nDmrt_a&!nFoxd) +nFoxb, (nFoxa_a&nFoxd)|(!nDlk&!nErk_signaling&!nFoxb&!nPem1) +nAdmp, (nZic_r_a)|(!nAdmp&!nPem1) +nTbx2_3, (nAdmp&nBmp2_4)|(!nTbx2_3) +nBmp2_4, (!nBmp2_4) +nCtnnb, nCtnnb +nEfna_d, (nDlk&nGata_a&nPrdm1_r_a&nPrdm1_r_b&nSnai)|(!nCtnnb&!nZic_r_b) +nFoxd, (nCtnnb&nTwist_r_a_b)|(!nFoxd) +nTbx6_r_b, (nCtnnb&nMrf&nNodal&nZic_r_a&nZic_r_b)|(!nTbx6_r_b) +nNeurog, (nDlk&nFoxd&nNodal&nZic_r_b)|(!nNeurog&!nSox4_11_12) +nDlx_b, (nSox1_2_3)|(!nDlx_b&!nFoxd) +nHand_r, (nFoxa_a&nFoxd&nNodal)|(!nHand_r) +nPrdm1_r_a, (!nFoxd&!nPrdm1_r_a) +nPrdm1_r_b, (!nFoxd&!nPrdm1_r_a) +nWnt5, (nFoxd&nZic_r_a&nZic_r_b)|(!nWnt5) +nGata_a, nGata_a +nGdf1_3_r, nGdf1_3_r +nHes_a, nHes_a +nLefty, (nNodal&nZic_r_a)|(!nLefty) +nLmx1, (nMsx&nNodal&nZic_r_b)|(!nLmx1) +nSnai, (nNeurog&nNodal&nTbx6_r_b&nZic_r_a&nZic_r_b)|(!nSnai&!nSox4_11_12) +nPem1, nPem1 +nSox1_2_3, (!nPem1&!nSox1_2_3) +nSox4_11_12, nSox4_11_12 +nTp53_a, nTp53_a +nTp53_b, nTp53_b +nWnttun5, (nZic_r_a) +nZic_r_a, nZic_r_a diff --git a/test/flobak_2015.bnet b/test/flobak_2015.bnet new file mode 100644 index 00000000..5b68cc68 --- /dev/null +++ b/test/flobak_2015.bnet @@ -0,0 +1,66 @@ +targets, factors +betaTrCP, (Axin|GSK3|CK1) +DKK1gene, (TCF)&!(cMYC) +MLK3, (Rac) +Ras, (SOS|SHP2) +IRS1, !(S6K|ERK|IKKB) +PTEN, (PTENgene)&!(GSK3) +LRP, (Fz|ERK|JNK1|p38alpha)&!(DKK1) +betacatenin, (IKKA)&!(betaTrCP) +p53, (p38alpha)&!(MDM2) +PI3K, (GAB|IRS1|Ras) +GSK3, !(LRP|RSK|S6K|ERK|p38alpha|Dvl|AKT) +GRAP2, !(p38alpha) +MAP3K8, (IKKB) +RTPK, (RTPKgene|MMP)&!(p38alpha|MEK) +PDK1, (PI3K)&!(PTEN) +FOXO, !(AKT|NLK) +pras40, !(AKT) +Axin, !(LRP) +DUSP1, (p38alpha|MSK) +JNK1, (MKK7|MKK4)&!(DUSP1) +TSC2, (GSK3)&!(IKKB|AKT|RSK|ERK) +GAB, (GRB2)&!(ERK) +RSK, (ERK|PDK1) +DKK1, (DKK1gene) +DUSP6, (ERK|mTORC1) +MMP, (LEF) +MEK, (Raf|MAP3K8)&!(ERK) +SFRP1, (SFRP1gene) +TCF, (betacatenin)&!(NLK) +mTORC2, (TSC2)&!(S6K) +mTORC1, (Rheb|RSK)&!(pras40) +ERK, (MEK)&!(DUSP6) +MKK3, (ASK1|TAK1) +MKK4, (MEKK4|MLK3|TAK1|GRAP2) +SHC1, (RTPK)&!(PTEN) +CK1, !(LRP) +MDM2gene, (NFkB|p53) +NFkB, (IKKA|IKKB|MSK) +NLK, (TAK1) +MKK7, (TAK1|GRAP2) +SHP2, (GAB) +RTPKgene, (FOXO) +p38alpha, (MKK3|MKK4)&!(DUSP1) +TAK1, (TAB1) +Rheb, !(TSC2) +IKKA, (AKT) +IKKB, (TAK1)&!(p53) +MEKK4, (Rac) +Egr1, !(TCF) +PTENgene, (Egr1) +MSK, (ERK|p38alpha) +ASK1, !(AKT) +S6K, (PDK1|mTORC1) +AKT, (PDK1|mTORC2) +LEF, (betacatenin) +SFRP1gene, !(cMYC) +Fz, !(SFRP1) +Rac, (Dvl|mTORC2) +SOS, (GRB2)&!(ERK) +Raf, (Ras)&!(Rheb|AKT|ERK) +MDM2, (AKT|MDM2gene)&!(S6K) +cMYC, (TCF) +GRB2, (SHC1) +TAB1, !(p38alpha) +Dvl, (Fz) diff --git a/test/fumia_2013.bnet b/test/fumia_2013.bnet new file mode 100644 index 00000000..7689c20f --- /dev/null +++ b/test/fumia_2013.bnet @@ -0,0 +1,85 @@ +targets, factors +TNFa, TNFa +eEF2, !(eEF2K) +Gli, Gli +Ras, (RTK)&!(NF1) +Miz_1, !(Myc_Max) +Myc_Max, (Myc|Max)&!(Smad_E2F|TGFb|MXI1) +p53, (HIF1|CHK1_2)&!(Mdm2|Bcl_2) +PI3K, (hTERT|Ras) +Myc, (NF_kB|TCF|Gli|FosJun|E2F|ERK_1_2)&!(HIF1) +p90RSK, (PDK1|ERK_1_2) +PDK1, (Myc_Max|PIP3|HIF1) +Smad_Miz_1, (Miz_1|Smad) +p14ARF, (Ras|E2F|Myc_Max) +Snail, (NF_kB|Smad_Miz_1)&!(GSK_3|p53) +eEF2K, (p90RSK|p70) +AMPK, (AMP_ATP|HIF1|ATM_ATR)&!(GFs) +Hypoxia, Hypoxia +Smad, (TGFb)&!(TNFa) +hTERT, (Myc_Max|NF1|HIF1|AKT|NF_kB)&!(Smad_Miz_1|p53|eEF2) +E2F_CyclinE, (E2F|CyclinE) +Smad_E2F, (Smad) +cdc20, (CyclinB)&!(cdh1) +Max, Max +RTK, (GFs) +p70, (mTOR|PDK1) +HIF1, (mTOR|Myc_Max|Hypoxia)&!(VHL|FOXO|p53|PHDs) +Rb, !(CyclinB|CyclinE|CyclinD|CyclinA|Mdm2) +p53_Mdm2, (Mdm2|p53) +TAK1, (TNFa) +E2F, (E2F)&!(Rb|CyclinA|CyclinB) +WNT, (Gli)&!(p53) +DNA_Damage, (ROS|Mutagen) +IKK, (TAK1|PKC|mTOR|AKT)&!(p53|PHDs) +AKT, (PDK1|PIP3) +ATM_ATR, (DNA_Damage) +GFs, GFs +RHEB, !(TSC1_2) +Mdm2, (AKT|p53)&!(ATM_ATR|p14ARF) +NF1, (PKC) +RAGS, (Nutrients)&!(Hypoxia) +CyclinE, (E2F)&!(CyclinA|Rb|p27|p21) +CyclinD, (Gli|NF_kB|TCF|FosJun|Myc_Max)&!(p21|GSK_3|p15|FOXO|p27) +PHDs, !(Hypoxia|ROS) +JNK, (TGFb) +PTEN, !(p53_PTEN) +Mutagen, Mutagen +NF_kB, (IKK|PIP3|Snail)&!(E_cadherin) +p15, (Smad_Miz_1|Miz_1) +mTOR, (RHEB|RAGS|AKT)&!(AMPK) +Dsh, (WNT) +FOXO, !(AKT) +PKC, (WNT|RTK) +p21, (p53|Smad_Miz_1|HIF1)&!(AKT|Myc_Max|hTERT) +p27, (Smad_Miz_1|HIF1)&!(Myc_Max|CyclinD|AKT|CyclinB|CyclinA) +GSK_3_APC, (GSK_3|APC) +TCF, (b_catenin)&!(TAK1) +TSC1_2, (AMPK|HIF1|p53)&!(RAF|AKT|ERK_1_2|p90RSK) +ROS, !(COX412|GSH) +PIP3, (PI3K)&!(PTEN) +CyclinA, (E2F_CyclinE|CyclinA|cdh1_UbcH10)&!(p27|cdc20|p21|Rb) +FosJun, (ERK_1_2|JNK) +CyclinB, !(p53|cdc20|cdh1|p27|p21) +COX412, (HIF1) +Bcl_2, (NF_kB)&!(p53|BAX|BAD) +cdh1, (cdc20)&!(CyclinA|CyclinB) +AMP_ATP, !(Nutrients) +GSK_3, !(mTOR|p90RSK|Dsh|AKT) +E_cadherin, !(NF_kB|Snail|Slug) +UbcH10, (CyclinB|CyclinA|UbcH10|cdc20)&!(cdh1) +b_catenin, !(GSK_3_APC|p53) +MXI1, (HIF1) +Nutrients, Nutrients +VHL, !(Hypoxia|ROS) +GSH, (NF_kB|p21|Myc_Max) +CHK1_2, (ATM_ATR) +BAD, !(p90RSK|HIF1|RAF|AKT) +Slug, (NF_kB|TCF)&!(p53_Mdm2) +ERK_1_2, (RAF) +APC, !(PTEN) +RAF, (Ras|PKC) +TGFb, (HIF1) +BAX, (JNK|p53)&!(HIF1|Bcl_2) +cdh1_UbcH10, (UbcH10|cdh1) +p53_PTEN, (p53|PTEN) diff --git a/test/steinway_2015.bnet b/test/steinway_2015.bnet new file mode 100644 index 00000000..03799be1 --- /dev/null +++ b/test/steinway_2015.bnet @@ -0,0 +1,69 @@ +targets, factors +GLI, (TCF_LEF)&!(SUFU) +RAS, (TCF_LEF|SRC|SOS_GRB2)&!(GSK3b) +NfkB, (IKKa) +RKIP, !(ERK|SNAI1) +bTrCP, !(Csn) +ILK, (SMAD) +LOXL23, (HIF1a) +IGF1R, (IGF1) +SHH, (GLI|SMAD) +TGFbR, (TGFb) +SOS_GRB2, (cMet|PDGFR|IGF1R|EGFR|FGFR|TGFbR)&!(ERK) +PI3K, (RAS) +HEY1, (CSL|SMAD) +SUFU, !(FUS) +E_Cadherin, (b_Catenin_memb)&!(SNAI2|SNAI1|FOXC2|HEY1|TWIST1|ZEB1|ZEB2) +DSH, (Frizzled) +Jagged, (TCF_LEF|SMAD) +b_Catenin_nuc, !(SUFU|Dest_compl|E_Cadherin|b_Catenin_memb) +FGF, FGF +HGF, HGF +NOTCH, (Jagged|DELTA) +AXIN2, (TCF_LEF|AXIN2) +CHD1L, CHD1L +NOTCH_ic, (NOTCH) +MEK, (RAF)&!(RKIP) +ZEB2, (SNAI1|HIF1a|Goosecoid)&!(miR200) +ZEB1, (SNAI1|HIF1a|Goosecoid)&!(miR200) +SMO, !(PTCH) +Hypoxia, Hypoxia +CD44, (TCF_LEF) +Dest_compl, (GSK3b|AXIN2|b_Catenin_nuc) +ERK, (MEK) +FOXC2, (SNAI1|TWIST1|Goosecoid) +TCF_LEF, (b_Catenin_nuc) +SRC, (cMet|PDGFR|IGF1R|EGFR|FGFR) +DELTA, (RAS) +TWIST1, (TCF_LEF|SNAI1|NfkB|Goosecoid|HIF1a) +IKKa, (AKT) +PTCH, !(SHH) +EGFR, (EGF) +CDC42, (CHD1L|TGFbR) +miR200, !(SNAI1|ZEB1|ZEB2) +PAK1, (CDC42) +cMet, (HGF|CD44) +PDGFR, (PDGF) +b_Catenin_memb, (E_Cadherin)&!(b_Catenin_nuc) +Frizzled, (Wnt) +SMAD, (ERK|TGFbR|ZEB1)&!(ZEB2) +Wnt, (GLI) +CSL, (NOTCH_ic) +HIF1a, (Hypoxia) +Csn, (NfkB) +EGR1, (c_fos) +FUS, (SMO) +EGF, EGF +c_fos, (ERK) +AKT, (PI3K|ILK) +IGF1, IGF1 +Goosecoid, Goosecoid +FGFR, (FGF) +GSK3b, !(DSH|Csn|AKT|Dest_compl|ERK) +STAT, (SRC) +PDGF, PDGF +RAF, (RAS) +TGFb, (GLI|SNAI1|TWIST1|Goosecoid) +SNAI1, (GLI|LIV1|EGR1|CSL|LOXL23|Goosecoid|PAK1|SMAD)&!(GSK3b|bTrCP) +SNAI2, (b_Catenin_nuc|SNAI2|ERK|TWIST1) +LIV1, (STAT) From 7dc60365e2149dc8c490c23a1ff3c2c0abd6efb0 Mon Sep 17 00:00:00 2001 From: Samuel Pastva Date: Tue, 13 Jun 2023 16:02:23 +0200 Subject: [PATCH 05/12] Resolve pyeda issues. --- nfvsmotifs/SuccessionDiagram.py | 8 ++++---- nfvsmotifs/motif_avoidant.py | 2 +- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/nfvsmotifs/SuccessionDiagram.py b/nfvsmotifs/SuccessionDiagram.py index 07a1f6c1..9d37c0cc 100644 --- a/nfvsmotifs/SuccessionDiagram.py +++ b/nfvsmotifs/SuccessionDiagram.py @@ -338,8 +338,8 @@ def expand_attractors(self, node_id: int) -> list[dict[str, int]]: retained_set[x] = least_common_child_space[x] else: """Set nodes to values based on the majority of satisfying values of functions""" - fx = self.network.get_update_function(x) - fx = aeon_to_pyeda(fx) + aeon_fx = self.network.get_update_function(x) + fx = aeon_to_pyeda(aeon_fx) n_input = len(list(fx.support)) n_poss_sat = pow(2, n_input - 1) @@ -360,8 +360,8 @@ def expand_attractors(self, node_id: int) -> list[dict[str, int]]: #retained_set[x] = 0 """Set nodes to values based on the majority of satisfying values of functions""" - fx = self.network.get_update_function(x) - fx = aeon_to_pyeda(fx) + aeon_fx = self.network.get_update_function(x) + fx = aeon_to_pyeda(aeon_fx) n_input = len(list(fx.support)) n_poss_sat = pow(2, n_input - 1) diff --git a/nfvsmotifs/motif_avoidant.py b/nfvsmotifs/motif_avoidant.py index 82fd87bc..7289c797 100644 --- a/nfvsmotifs/motif_avoidant.py +++ b/nfvsmotifs/motif_avoidant.py @@ -112,7 +112,7 @@ def _preprocess_candidates( continue var_name = network.get_variable_name(varID) variables.append(var_name) - function_expression = network.get_update_function(var) + function_expression = network.get_update_function(varID) function_bdd = expr2bdd(aeon_to_pyeda(function_expression)) update_functions[var_name] = function_bdd From 3c723746135c32c6d647eaed7056b4ab02f4fea0 Mon Sep 17 00:00:00 2001 From: Samuel Pastva Date: Tue, 20 Jun 2023 13:03:49 +0200 Subject: [PATCH 06/12] Match whitespace of `main` branch. --- nfvsmotifs/state_utils.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/nfvsmotifs/state_utils.py b/nfvsmotifs/state_utils.py index 594fe3cf..f715d540 100644 --- a/nfvsmotifs/state_utils.py +++ b/nfvsmotifs/state_utils.py @@ -115,6 +115,7 @@ def function_is_true(f: BinaryDecisionDiagram, state: dict[str, int]) -> bool: return function_restrict(f, state).is_one() + def dnf_function_is_true(dnf: list[dict[str, int]], state: dict[str, int]) -> bool: """ Returns `True` if the given DNF function evaluates to `1` for the given @@ -128,6 +129,7 @@ def dnf_function_is_true(dnf: list[dict[str, int]], state: dict[str, int]) -> bo return True return False + def remove_state_from_dnf( dnf: list[dict[str, int]], state: dict[str, int] ) -> list[dict[str, int]]: From edfb6d1cdcb5556e48abd61343b187f302a8a0dc Mon Sep 17 00:00:00 2001 From: Samuel Pastva Date: Tue, 20 Jun 2023 13:44:07 +0200 Subject: [PATCH 07/12] Remove usued code and duplicate codepath in `SuccessionDiagram`. --- nfvsmotifs/SuccessionDiagram.py | 97 +++++++++++++-------------------- 1 file changed, 38 insertions(+), 59 deletions(-) diff --git a/nfvsmotifs/SuccessionDiagram.py b/nfvsmotifs/SuccessionDiagram.py index 9d37c0cc..4444179e 100644 --- a/nfvsmotifs/SuccessionDiagram.py +++ b/nfvsmotifs/SuccessionDiagram.py @@ -8,12 +8,10 @@ import networkx as nx # type: ignore -import random # type: ignore - from nfvsmotifs.interaction_graph_utils import feedback_vertex_set from nfvsmotifs.motif_avoidant import detect_motif_avoidant_attractors from nfvsmotifs.petri_net_translation import network_to_petrinet -from nfvsmotifs.space_utils import percolate_space, intersect +from nfvsmotifs.space_utils import percolate_space from nfvsmotifs.terminal_restriction_space import get_terminal_restriction_space from nfvsmotifs.pyeda_utils import aeon_to_pyeda from nfvsmotifs.trappist_core import compute_fixed_point_reduced_STG, trappist @@ -309,72 +307,53 @@ def expand_attractors(self, node_id: int) -> list[dict[str, int]]: # This node is a fixed-point. self.attractors[node_id] = [node_space] return [node_space] - - # Fix everything in the NFVS to zero, as long as - # it isn't already fixed by our `node_space`. - # - # We add the whole node space to the retain set because we know - # the space is a trap and this will remove the corresponding unnecessary - # Petri net transitions. - retained_set = node_space.copy() - + child_spaces = [ self.node_space(child) for child in self.G.successors(node_id) # type: ignore ] + + # Initially, the retained set only contains the fixed values from the + # current node space (this elimiantes unnecessary Petri net transitions + # for values which we already proved are constant). + # + # In the following code, we then extend the retained set based on the model's NFVS + # and the current child spaces. + retained_set = node_space.copy() - # find the child space least common with NFVS - if (len(child_spaces) > 0): + + # First, if there are any child spaces present, we extend the retained set with the + # values from the one that has the least amount of fixed variables shared with the NFVS. + if len(child_spaces) > 0: + # Find the child space that has the fewest nodes in common with the NFVS: least_common_child_space = child_spaces[0] least_common_nodes = len(set(least_common_child_space) & set(self.nfvs)) for child_space in child_spaces: common_nodes = len(set(child_space) & set(self.nfvs)) - if (common_nodes < least_common_nodes): + if common_nodes < least_common_nodes: least_common_nodes = common_nodes least_common_child_space = child_space - for x in self.nfvs: - if x not in retained_set: - if x in least_common_child_space: - retained_set[x] = least_common_child_space[x] - else: - """Set nodes to values based on the majority of satisfying values of functions""" - aeon_fx = self.network.get_update_function(x) - fx = aeon_to_pyeda(aeon_fx) - n_input = len(list(fx.support)) - n_poss_sat = pow(2, n_input - 1) - - n_sat = fx.satisfy_count() - - if n_sat > n_poss_sat: - retained_set[x] = 1 - elif n_sat < n_poss_sat: - retained_set[x] = 0 - else: - #retained_set[x] = random.randint(0, 1) - retained_set[x] = 0 - #retained_set[x] = 1 - else: - for x in self.nfvs: - if x not in retained_set: - """Set all nodes to 0""" - #retained_set[x] = 0 - - """Set nodes to values based on the majority of satisfying values of functions""" - aeon_fx = self.network.get_update_function(x) - fx = aeon_to_pyeda(aeon_fx) - n_input = len(list(fx.support)) - n_poss_sat = pow(2, n_input - 1) - - n_sat = fx.satisfy_count() - - if n_sat > n_poss_sat: - retained_set[x] = 1 - elif n_sat < n_poss_sat: - retained_set[x] = 0 - else: - #retained_set[x] = random.randint(0, 1) - retained_set[x] = 0 - #retained_set[x] = 1 + for x in least_common_child_space: + if (x not in retained_set) and (x in self.nfvs): + retained_set[x] = least_common_child_space[x] + + # Then, set the remaining NFVS variables based on the majority output value in the update + # function of the relevant variable. + for x in self.nfvs: + if x in retained_set: + continue + + aeon_fx = self.network.get_update_function(x) + pyeda_fx = aeon_to_pyeda(aeon_fx) + input_count = len(list(pyeda_fx.support)) + + half_count = pow(2, input_count - 1) + sat_count = pyeda_fx.satisfy_count() + + if sat_count > half_count: + retained_set[x] = 1 + else: + retained_set[x] = 0 @@ -385,7 +364,7 @@ def expand_attractors(self, node_id: int) -> list[dict[str, int]]: return [retained_set] # old code - #terminal_restriction_space = ~state_list_to_bdd(child_spaces) + # terminal_restriction_space = ~state_list_to_bdd(child_spaces) # new code that should be the same as before terminal_restriction_space = get_terminal_restriction_space( From b4427b306f2d9aaeadb0b8e72bae908833053dec Mon Sep 17 00:00:00 2001 From: Samuel Pastva Date: Tue, 20 Jun 2023 14:13:25 +0200 Subject: [PATCH 08/12] Clean up a part of the simulation code in `motif_avoidant`. --- nfvsmotifs/motif_avoidant.py | 40 +++++++++++++++--------------------- 1 file changed, 17 insertions(+), 23 deletions(-) diff --git a/nfvsmotifs/motif_avoidant.py b/nfvsmotifs/motif_avoidant.py index 7289c797..04395304 100644 --- a/nfvsmotifs/motif_avoidant.py +++ b/nfvsmotifs/motif_avoidant.py @@ -1,6 +1,5 @@ from __future__ import annotations -from copy import deepcopy import random from copy import deepcopy from functools import reduce @@ -116,38 +115,34 @@ def _preprocess_candidates( function_bdd = expr2bdd(aeon_to_pyeda(function_expression)) update_functions[var_name] = function_bdd - #print("Finish loading functions") + # A random generator initialized with a fixed seed. Ensures simulation + # is randomized but deterministic. + generator = random.Random(1234567890) + if is_in_an_mts == False: - #symbolic_candidates = state_list_to_bdd(candidates) - symbolic_candidates = deepcopy(candidates) + # Copy is sufficient because we won't be modifying the states within the set. + candidates_dnf = candidates.copy() filtered_candidates = [] - i = 1 - for state in candidates: - #print(f"Run outside mts - {i}") - i += 1 - #state_bdd = state_to_bdd(state) - - # Remove state from the symbolic set. If we can prove that is + for state in candidates: + # Remove the state from the candidates. If we can prove that is # is not an attractor, we will put it back. - #symbolic_candidates = symbolic_candidates & ~state_bdd - symbolic_candidates = remove_state_from_dnf(symbolic_candidates, state) + candidates_dnf = remove_state_from_dnf(candidates_dnf, state) simulation = state.copy() # A copy of the state that we can overwrite. is_valid_candidate = True for _ in range(max_iterations): # Advance all variables by one step in random order. - random.shuffle(variables) + generator.shuffle(variables) for var in variables: step = function_eval(update_functions[var], simulation) assert step is not None simulation[var] = step - #if function_is_true(symbolic_candidates, simulation): - if dnf_function_is_true(symbolic_candidates, simulation): + if dnf_function_is_true(candidates_dnf, simulation): # The state can reach some other state in the candidate # set. This does not mean it cannot be an attractor, but - # it means it is sufficient to keep considering the other - # candidate. + # it means it is sufficient to keep considering + # the remaining candidates. is_valid_candidate = False break @@ -159,10 +154,9 @@ def _preprocess_candidates( break if is_valid_candidate: - # If we cannot rule out the candidate, we can put it back - # into candidate set. - #symbolic_candidates = symbolic_candidates | state_bdd - symbolic_candidates.append(state) + # If we cannot rule out the candidate, we have to put it back + # into the candidate set. + candidates_dnf.append(state) filtered_candidates.append(state) return filtered_candidates @@ -208,7 +202,7 @@ def _filter_candidates( """ Filter candidate states using reachability procedure in Pint. """ - print("Run _filter_candidates") + avoid_states = ~terminal_restriction_space | state_list_to_bdd(candidates) filtered_candidates: list[dict[str, int]] = [] From e6fa4c602d683f4e45e403bc8ca944522437300e Mon Sep 17 00:00:00 2001 From: Samuel Pastva Date: Wed, 21 Jun 2023 13:07:49 +0200 Subject: [PATCH 09/12] Correct the `is_on_an_mts` flag usage. --- nfvsmotifs/SuccessionDiagram.py | 1 + nfvsmotifs/motif_avoidant.py | 1 + 2 files changed, 2 insertions(+) diff --git a/nfvsmotifs/SuccessionDiagram.py b/nfvsmotifs/SuccessionDiagram.py index 4444179e..a47ba9ea 100644 --- a/nfvsmotifs/SuccessionDiagram.py +++ b/nfvsmotifs/SuccessionDiagram.py @@ -419,6 +419,7 @@ def expand_attractors(self, node_id: int) -> list[dict[str, int]]: candidate_seeds, terminal_restriction_space, max_iterations=1000, + is_in_an_mts=len(child_spaces) == 0, ) if len(attractors) > 0: diff --git a/nfvsmotifs/motif_avoidant.py b/nfvsmotifs/motif_avoidant.py index 04395304..6c5ea9bc 100644 --- a/nfvsmotifs/motif_avoidant.py +++ b/nfvsmotifs/motif_avoidant.py @@ -63,6 +63,7 @@ def detect_motif_avoidant_attractors( terminal_restriction_space, max_iterations, ensure_subspace=ensure_subspace, + is_in_an_mts=is_in_an_mts ) if len(candidates) == 0: From c76e079ac63afde4960fa3a5ec1baeacf1ec806a Mon Sep 17 00:00:00 2001 From: Samuel Pastva Date: Wed, 21 Jun 2023 13:08:27 +0200 Subject: [PATCH 10/12] Remove test networks. --- test.bnet | 25 --- test/A_model.bnet | 75 -------- test/CASCADE1.bnet | 66 ------- test/CASCADE2.bnet | 141 -------------- test/CASCADE3.bnet | 177 ------------------ test/Cell-Cycle-2019.bnet | 88 --------- test/Drosophila.bnet | 59 ------ test/EMT.bnet | 75 -------- test/EMT_Mechanosensing.bnet | 136 -------------- ...ion_CIP_Migration_CellCycle_Apoptosis.bnet | 121 ------------ test/SEGMENT-POLARITY-6-CELL.bnet | 103 ---------- test/T-CELL-RECEPTOR-SIGNALING.bnet | 50 ----- ..._083]__[SIGNALING-IN-PROSTATE-CANCER].bnet | 117 ------------ ...id_075]__[INFLAMMATORY-BOWEL-DISEASE].bnet | 47 ----- ...60]__[id_085]__[T-LGL-SIGNALING-2008].bnet | 58 ------ ...d_014]__[T-LGL-SURVIVAL-NETWORK-2008].bnet | 59 ------ test/[var_62]__[id_145]__[MELANOGENESIS].bnet | 53 ------ ...LING-PATHWAY-FOR-BUTHANOL-PRODUCTION].bnet | 58 ------ ...1]__[COLITIS-ASSOCIATED-COLON-CANCER].bnet | 67 ------- .../[var_86]__[id_019]__[IL-6-SIGNALING].bnet | 56 ------ test/ascidian_embryo_validation.bnet | 48 ----- test/flobak_2015.bnet | 66 ------- test/fumia_2013.bnet | 85 --------- test/steinway_2015.bnet | 69 ------- 24 files changed, 1899 deletions(-) delete mode 100644 test.bnet delete mode 100644 test/A_model.bnet delete mode 100644 test/CASCADE1.bnet delete mode 100644 test/CASCADE2.bnet delete mode 100755 test/CASCADE3.bnet delete mode 100644 test/Cell-Cycle-2019.bnet delete mode 100644 test/Drosophila.bnet delete mode 100644 test/EMT.bnet delete mode 100644 test/EMT_Mechanosensing.bnet delete mode 100644 test/Regan2020_Adhesion_CIP_Migration_CellCycle_Apoptosis.bnet delete mode 100644 test/SEGMENT-POLARITY-6-CELL.bnet delete mode 100755 test/T-CELL-RECEPTOR-SIGNALING.bnet delete mode 100644 test/[var_133]__[id_083]__[SIGNALING-IN-PROSTATE-CANCER].bnet delete mode 100644 test/[var_47]__[id_075]__[INFLAMMATORY-BOWEL-DISEASE].bnet delete mode 100644 test/[var_60]__[id_085]__[T-LGL-SIGNALING-2008].bnet delete mode 100644 test/[var_61]__[id_014]__[T-LGL-SURVIVAL-NETWORK-2008].bnet delete mode 100644 test/[var_62]__[id_145]__[MELANOGENESIS].bnet delete mode 100644 test/[var_66]__[id_077]__[SIGNALING-PATHWAY-FOR-BUTHANOL-PRODUCTION].bnet delete mode 100644 test/[var_70]__[id_051]__[COLITIS-ASSOCIATED-COLON-CANCER].bnet delete mode 100644 test/[var_86]__[id_019]__[IL-6-SIGNALING].bnet delete mode 100644 test/ascidian_embryo_validation.bnet delete mode 100644 test/flobak_2015.bnet delete mode 100644 test/fumia_2013.bnet delete mode 100644 test/steinway_2015.bnet diff --git a/test.bnet b/test.bnet deleted file mode 100644 index 46ac2e68..00000000 --- a/test.bnet +++ /dev/null @@ -1,25 +0,0 @@ -targets, fact|s -A, (!A & !B) | C -B, (!A & !B) | C -C, A & B - -#A, !E | (A & B & C) -#B, !F | (A & B & C) -#C, !D | (A & B & C) -#D, A -#E, B -#F, C - -#A, !E | (G & B & C) -#B, !F | (A & H & C) -#C, !D | (A & B & I) -#D, A -#E, B -#F, C -#G, A -#H, B -#I, C - -#A, !A | !B -#B, !A | !B -#C, A & B diff --git a/test/A_model.bnet b/test/A_model.bnet deleted file mode 100644 index 50b4300b..00000000 --- a/test/A_model.bnet +++ /dev/null @@ -1,75 +0,0 @@ -targets, factors -a_secretase, (CREB|s_NMDAR)&(!ROCK|!Cholesterol) -Ab, ((APP&BACE1)&(Sortilin|PICALM|Cholesterol))&!Autophagy -ABCA7, SREBP2 -AKT, (s_NMDAR&PI3K)&(!PTEN|!PP2A)&!CASP3 -APOE4, APOE4 -Apoer2, Reelin&!APOE4 -Apoptosis, CASP3 -APP, ERK&(!(a_secretase&(Sortilin|LRP6))|!SORL1|!(Dab1&Apoer2)|!(Dab1&Fyn)) -ATM, ROS -Autophagy, (ULK1&LC3&p62&LAMP2&beclin1)&!(Cholesterol&ROS) -BACE1, (STAT3|Cholesterol)&!PGC1a -BAD, !AKT&PP2B -BAX, ((Bim&PUMA)&p53)&!AKT&!Bcl2 -Bcl2, !BAD&(!p53|!JNK|!Bim) -BDNF, (CREB|PGC1a)&Sortilin -beclin1, (ROCK|JNK)&(!Bcl2|!CASP3) -Bim, EGR1|FOXO -Ca_ion, e_NMDAR -CASP2, p53 -CASP3, BAX&Bim -Cdk5, Ca_ion|EGR1 -Cholesterol, !CYP46A1&(SREBP2&HMGCR)|(!LPL|!ABCA7) -CIP2A, Ab -CLU, p53|EGR1 -CREB, (ERK&Jacob&s_NMDAR)|!(Jacob&e_NMDAR) -CYP46A1, !APP&Ca_ion -Dab1, Apoer2&!Fyn -Dkk1, Ab&(CLU|PICALM) -DLK, APOE4 -e_NMDAR, (Ab&Fyn)|PTEN -EGR1, JNK -ERK, !(pTau&PP2A)&((s_NMDAR&!STEP)|MKK7) -FOXO, JNK&!AKT -Fyn, ((Apoer2&Dab1)|mGluR)&!STEP -GSK3beta, (Ca_ion|PP2A)&!(AKT|LRP6) -Jacob, (s_NMDAR&ERK)|e_NMDAR -JNK, MKK7|Vangl2 -LAMP2, PIP2|TFEB -LC3, PIP2|TFEB|!PICALM -LPL, SREBP2&!SORL1 -LRP6, !APOE4|!Dkk1 -MAPT, e_NMDAR&!CREB -MDM2, p53&(!ATM&!CASP2|!GSK3beta) -mGluR, Ab -MKK7, DLK|e_NMDAR -mTOR, (AKT|ERK|Cholesterol)&!SIRT1 -p38, !STEP -p53, (p38|ATM)&!MDM2 -p62, PIP2|TFEB|!PICALM -PGC1a, (CREB|SIRT1)&p38 -PI3K, Dab1|s_NMDAR|BDNF -PICALM, !Ca_ion&!CASP3 -PIP2, !synj1 -PP2A, (!mGluR|!GSK3beta)&!APOE4&!CIP2A -PP2B, mGluR|Ca_ion -PTEN, ROCK -PUMA, !s_NMDAR&(FOXO|p53) -Reelin, !Apoptosis -RhoA, CASP2|Vangl2 -ROCK, RhoA|!SIRT1 -ROS, (Ca_ion|Ab)&!PGC1a -s_NMDAR, (Fyn|BDNF)&!STEP&!pTau -SORL1, !ROCK|BDNF -Sortilin, ROCK -SREBP2, (!Cholesterol|!APP|!ABCA7)|AKT -STAT3, Cdk5 -STEP, (PP2B)&(!s_NMDAR|!e_NMDAR) -synj1, APOE4|(!Cdk5&PP2B) -pTau, (MAPT&(GSK3beta|Cdk5|ERK))&!PP2A&!Autophagy -TFEB, (!APOE4|!mTOR)&PP2B -ULK1, !mTOR -Vangl2, Dkk1 -SIRT1, (!APOE4|!ROS) -HMGCR, BDNF|SREBP2 diff --git a/test/CASCADE1.bnet b/test/CASCADE1.bnet deleted file mode 100644 index 25674edf..00000000 --- a/test/CASCADE1.bnet +++ /dev/null @@ -1,66 +0,0 @@ -targets, factors -AKT1S1, !AKT_f -AKT_f, !mTORC2_c&PDPK1|mTORC2_c -AXIN1, !LRP_f -BTRC, !GSK3_f&!AXIN1&CK1_f|!GSK3_f&AXIN1|GSK3_f -CHUK, AKT_f -CK1_f, !LRP_f -CTNNB1, !BTRC&CHUK -DKK_f, DKK_g -DKK_g, !MYC&TCF7_f -DUSP1, !MAPK14&MSK_f|MAPK14 -DUSP6, !ERK_f&mTORC1_c|ERK_f -DVL_f, FZD_f -EGR1, !TCF7_f -ERK_f, MEK_f&!DUSP6 -FOXO_f, !AKT_f&!NLK -FZD_f, !SFRP1 -GAB_f, GRB2&!ERK_f -GRAP2, !MAPK14 -GRB2, SHC1 -GSK3_f, !DVL_f&!MAPK14&!AKT_f&!ERK_f&!RSK_f&!S6K_f&!LRP_f -IKBKB, MAP3K7&!TP53 -IRS1, !ERK_f&!S6K_f&!IKBKB -JNK_f, !MAP2K4&MAP2K7&!DUSP1|MAP2K4&!DUSP1 -KRAS, !SOS1&PTPN11|SOS1 -LEF, CTNNB1 -LRP_f, !JNK_f&!MAPK14&!ERK_f&FZD_f&!DKK_f|!JNK_f&!MAPK14&ERK_f&!DKK_f|!JNK_f&MAPK14&!DKK_f|JNK_f&!DKK_f -MAP2K3, !MAP3K7&MAP3K5|MAP3K7 -MAP2K4, !MAP3K4&!MAP3K11&!MAP3K7&GRAP2|!MAP3K4&!MAP3K11&MAP3K7|!MAP3K4&MAP3K11|MAP3K4 -MAP2K7, !MAP3K7&GRAP2|MAP3K7 -MAP3K11, RAC_f -MAP3K4, RAC_f -MAP3K5, !AKT_f -MAP3K7, TAB_f -MAP3K8, IKBKB -MAPK14, !MAP2K4&!DUSP1&MAP2K3|MAP2K4&!DUSP1 -MDM2, !AKT_f&!S6K_f&MDM2_g|AKT_f&!S6K_f -MDM2_g, !TP53&NFKB_f|TP53 -MEK_f, !ERK_f&!RAF_f&MAP3K8|!ERK_f&RAF_f -MMP_f, LEF -MSK_f, !MAPK14&ERK_f|MAPK14 -MYC, TCF7_f -NFKB_f, !MSK_f&!IKBKB&CHUK|!MSK_f&IKBKB|MSK_f -NLK, MAP3K7 -PDPK1, !PTEN&PIK3CA -PIK3CA, !KRAS&!GAB_f&IRS1|!KRAS&GAB_f|KRAS -PTEN, PTEN_g&!GSK3_f -PTEN_g, EGR1 -PTPN11, GAB_f -RAC_f, !mTORC2_c&DVL_f|mTORC2_c -RAF_f, !AKT_f&!ERK_f&KRAS&!RHEB -RHEB, !TSC_f -RSK_f, !ERK_f&PDPK1|ERK_f -RTPK_f, !MAPK14&!RTPK_g&!MEK_f&MMP_f|!MAPK14&RTPK_g&!MEK_f -RTPK_g, FOXO_f -S6K_f, !mTORC1_c&PDPK1|mTORC1_c -SFRP1, SFRP1_g -SFRP1_g, !MYC -SHC1, RTPK_f&!PTEN -SOS1, GRB2&!ERK_f -TAB_f, !MAPK14 -TCF7_f, !NLK&CTNNB1 -TP53, MAPK14&!MDM2 -TSC_f, !AKT_f&!ERK_f&!RSK_f&!IKBKB&GSK3_f -mTORC1_c, !RHEB&RSK_f&!AKT1S1|RHEB&!AKT1S1 -mTORC2_c, !S6K_f&TSC_f diff --git a/test/CASCADE2.bnet b/test/CASCADE2.bnet deleted file mode 100644 index 67e93f4a..00000000 --- a/test/CASCADE2.bnet +++ /dev/null @@ -1,141 +0,0 @@ -targets, factors -ACVR1, BMPR2 -AKT1S1, !AKT_f -AKT_f, !mTORC2_c&!PDPK1&!PPP1CA&ILK|!mTORC2_c&PDPK1&!PPP1CA|mTORC2_c&!PPP1CA -AP1_c, !SMAD4&!SMAD3&!ATF2&!FOS&JUN|!SMAD4&!SMAD3&!ATF2&FOS|!SMAD4&!SMAD3&ATF2|!SMAD4&SMAD3|SMAD4 -ARHGAP24, ROCK1 -ATF2, !MAPK14&!JNK_f&ERK_f|!MAPK14&JNK_f|MAPK14 -AXIN1, !LRP_f&GSK3_f&!PPP1CA&!PPM1A -BAD, !AKT_f&!RSK_f -BAX, TP53 -BCL2, !BAD -BMPR2, !SMURF1&!SMURF2 -BTRC, !LRP_f&!CK1_f&!AXIN1&GSK3_f|!LRP_f&!CK1_f&AXIN1|!LRP_f&CK1_f -CASP3, !CASP8&CASP9|CASP8 -CASP8, !CFLAR -CASP9, !CYCS&PPP1CA|CYCS -CBPp300_c, !TP53&!CREBBP&EP300|!TP53&CREBBP -CCND1, !TCF7_f&!RSK_f&STAT3|!TCF7_f&RSK_f|TCF7_f -CDC42, SRC&!ARHGAP24 -CFLAR, AKT_f&!ITCH -CFL_f, !LIMK2&LIMK1|LIMK2 -CHUK, !AKT_f&!PRKCA&TRAF6|!AKT_f&PRKCA|AKT_f -CK1_f, !LRP_f -CREBBP, CHUK -CSK, PRKACA -CTNNB1, CHUK&!BTRC -CYCS, !BCL2&BAX -DAAM1, DVL_f -DKK_f, DKK_g -DKK_g, TCF7_f&!MYC -DUSP1, !SKP2&!MAPK14&!DUSP1_g&MSK_f|!SKP2&!MAPK14&DUSP1_g|!SKP2&MAPK14 -DUSP1_g, !MAPK14&ERK_f|MAPK14 -DUSP6, !mTORC1_c&ERK_f|mTORC1_c -DVL_f, !FZD_f&SMAD1&!ITCH|FZD_f&!ITCH -EGR1, !TCF7_f -EP300, AKT_f&!PRKCD&!SKI -ERK_f, MEK_f&!PPP1CA&!DUSP6 -FOS, !ERK_f&!RSK_f&SRF|!ERK_f&RSK_f|ERK_f -FOXO_f, !CK1_f&!AKT_f&!NLK -FZD_f, !SFRP1 -GAB_f, !ERK_f&GRB2 -GRAP2, !MAPK14 -GRB2, SHC1 -GSK3_f, !DVL_f&!AKT_f&!MAPK14&!ERK_f&!RSK_f&!S6K_f -IKBKB, !TP53&!PLK1&MAP3K7&!PPM1A -ILK, PAK1 -ILR_f, !LIF&AP1_c|LIF -IRAK1, ILR_f&!SOCS1 -IRS1, !ERK_f&!S6K_f&!IKBKB -ITCH, JNK_f -JAK_f, ILR_f&!SOCS1&!PTPN6 -JNK_f, !DUSP1&!MAP2K4&!MAP2K7&PAK1|!DUSP1&!MAP2K4&MAP2K7|!DUSP1&MAP2K4 -JUN, !GSK3_f&JNK_f -KRAS, !PTPN11&SOS1|PTPN11 -LEF1, CTNNB1 -LIF, RAF_f -LIMK1, !RAC_f&ROCK1|RAC_f -LIMK2, !PRKCD&ROCK1 -LRP_f, !DKK_f&!FZD_f&!MAPK14&!JNK_f&ERK_f|!DKK_f&!FZD_f&!MAPK14&JNK_f|!DKK_f&!FZD_f&MAPK14|!DKK_f&FZD_f -MAP2K3, !MAP3K5&MAP3K7|MAP3K5 -MAP2K4, !GRAP2&!MAP3K7&!MAP3K11&MAP3K4|!GRAP2&!MAP3K7&MAP3K11|!GRAP2&MAP3K7|GRAP2 -MAP2K7, !GRAP2&!MAP3K7&MAPK8IP3|!GRAP2&MAP3K7|GRAP2 -MAP3K11, RAC_f -MAP3K4, RAC_f -MAP3K5, !AKT_f -MAP3K7, TAB_f -MAP3K8, IKBKB -MAPK14, !DUSP1&!MAP2K4&MAP2K3|!DUSP1&MAP2K4 -MAPK8IP3, ROCK1 -MAPKAPK2, MAPK14 -MDM2, !AKT_f&!PPP1CA&!S6K_f&!MDM2_g&MAPKAPK2|!AKT_f&!PPP1CA&!S6K_f&MDM2_g|!AKT_f&PPP1CA&!S6K_f|AKT_f&!S6K_f -MDM2_g, !TP53&NFKB_f|TP53 -MEK_f, !RAF_f&!ERK_f&MAP3K8|RAF_f&!ERK_f -MMP_f, !LEF1&STAT3|LEF1 -MSK_f, !MAPK14&ERK_f|MAPK14 -MYC, !TCF7_f&!GSK3_f&!PLK1&STAT3|!TCF7_f&!GSK3_f&PLK1|TCF7_f&!GSK3_f -NFKB_f, !CHUK&!REL_f&!IKBKB&MSK_f|!CHUK&!REL_f&IKBKB|!CHUK&REL_f|CHUK -NLK, MAP3K7 -PAK1, !RAC_f&CDC42|RAC_f -PARD6A, !TGFBR2&TGFBR1|TGFBR2 -PDPK1, !PTEN&PIK3CA -PIAS1, MAPKAPK2 -PIK3CA, !IRS1&!KRAS&GAB_f|!IRS1&KRAS|IRS1 -PLCG1, SYK -PLK1, !PDPK1&MAPKAPK2|PDPK1 -PPM1A, PTEN -PPP1CA, SMAD7&!RTPK_f -PRKACA, !NFKB_f&FOS|NFKB_f -PRKCA, PLCG1 -PRKCD, !PDPK1&CASP3|PDPK1 -PTEN, !SRC&!CBPp300_c&!PTEN_g&!GSK3_f&ROCK1|!SRC&!CBPp300_c&PTEN_g&!GSK3_f -PTEN_g, EGR1 -PTPN11, GAB_f -PTPN6, SRC -RAC_f, !DVL_f&!mTORC2_c&!VAV1&!ARHGAP24&TIAM1|!DVL_f&!mTORC2_c&VAV1&!ARHGAP24|!DVL_f&mTORC2_c&!ARHGAP24|DVL_f&!ARHGAP24 -RAF_f, !AKT_f&!RHEB&KRAS&!ERK_f -REL_f, !CBPp300_c&!STAT1&!IKBKB&MSK_f|!CBPp300_c&!STAT1&IKBKB|CBPp300_c&!STAT1 -RHEB, !TSC_f -RHOA, !RAC_f&!SMURF1&!PARD6A&DAAM1&!RND3 -RND3, ROCK1 -ROCK1, !CASP3&RHOA|CASP3 -RSK_f, !PDPK1&ERK_f|PDPK1 -RTPK_f, !MMP_f&!MEK_f&RTPK_g&!MAPK14|MMP_f&!MEK_f&!MAPK14 -RTPK_g, FOXO_f -S6K_f, !PDPK1&mTORC1_c|PDPK1 -SFRP1, SFRP1_g -SFRP1_g, !MYC -SHC1, !SRC&!ILR_f&!RTPK_f&!PTEN&TGFBR1|!SRC&!ILR_f&RTPK_f&!PTEN|!SRC&ILR_f&!PTEN|SRC&!PTEN -SKI, !AKT_f -SKP2, !CCND1&!ERK_f&EP300|!CCND1&ERK_f|CCND1 -SMAD1, !SMAD6&!GSK3_f&!ERK_f&!SKI&ACVR1&!SMURF1&!PPM1A -SMAD2, !CBPp300_c&!ERK_f&!SKI&!ACVR1&!TGFBR1&!SMURF2&!PPM1A&ITCH|!CBPp300_c&!ERK_f&!SKI&!ACVR1&TGFBR1&!SMURF2&!PPM1A|!CBPp300_c&!ERK_f&!SKI&ACVR1&!SMURF2&!PPM1A|!CBPp300_c&ERK_f&!SKI&!SMURF2&!PPM1A|CBPp300_c&!SKI&!SMURF2&!PPM1A -SMAD3, !SMAD7&!SMAD6&!GSK3_f&!AKT_f&!MAPK14&!JNK_f&!ERK_f&!SKI&!ACVR1&TGFBR1&!PPM1A|!SMAD7&!SMAD6&!GSK3_f&!AKT_f&!MAPK14&!JNK_f&!ERK_f&!SKI&ACVR1&!PPM1A|!SMAD7&!SMAD6&!GSK3_f&!AKT_f&!MAPK14&JNK_f&!ERK_f&!SKI&!PPM1A|!SMAD7&!SMAD6&!GSK3_f&!AKT_f&MAPK14&!ERK_f&!SKI&!PPM1A -SMAD4, !SMAD7&!SMAD6&!ERK_f&!PIAS1&!SMAD2&!SKI&!SMAD3&!SMAD5&SMAD1&!SMURF1|!SMAD7&!SMAD6&!ERK_f&!PIAS1&!SMAD2&!SKI&!SMAD3&SMAD5&!SMURF1|!SMAD7&!SMAD6&!ERK_f&!PIAS1&!SMAD2&!SKI&SMAD3&!SMURF1|!SMAD7&!SMAD6&!ERK_f&!PIAS1&SMAD2&!SKI&!SMURF1|!SMAD7&!SMAD6&!ERK_f&PIAS1&!SKI&!SMURF1|!SMAD7&!SMAD6&ERK_f&!SKI&!SMURF1 -SMAD5, !SKI&ACVR1&!SMURF2 -SMAD6, SMAD6_g -SMAD6_g, !SMAD2&!SMAD4&SMAD3|!SMAD2&SMAD4|SMAD2 -SMAD7, !AXIN1&!EP300&!SMAD7_g&SMURF1&!SMURF2&!ITCH|!AXIN1&!EP300&SMAD7_g&!SMURF2&!ITCH|!AXIN1&EP300&!SMURF2&!ITCH -SMAD7_g, !SMAD2&!SMAD4&SMAD3|!SMAD2&SMAD4|SMAD2 -SMURF1, SMAD7 -SMURF2, SMAD7 -SOCS1, SOCS1_g -SOCS1_g, STAT1 -SOS1, !ERK_f&!PLCG1&GRB2|!ERK_f&PLCG1 -SRC, !CSK&RTPK_f -SRF, !RSK_f&!MAPKAPK2&CFL_f|!RSK_f&MAPKAPK2|RSK_f -STAT1, !SRC&!JAK_f&!MAPK14&!PRKCD&IKBKB&!PIAS1|!SRC&!JAK_f&!MAPK14&PRKCD&!PIAS1|!SRC&!JAK_f&MAPK14&!PIAS1|!SRC&JAK_f&!PIAS1|SRC&!PIAS1 -STAT3, !SRC&!IRAK1&!JAK_f&!mTORC1_c&!MAPK14&!JNK_f&!ERK_f&!PPP1CA&PRKCD|!SRC&!IRAK1&!JAK_f&!mTORC1_c&!MAPK14&!JNK_f&ERK_f&!PPP1CA|!SRC&!IRAK1&!JAK_f&!mTORC1_c&!MAPK14&JNK_f&!PPP1CA|!SRC&!IRAK1&!JAK_f&!mTORC1_c&MAPK14&!PPP1CA|!SRC&!IRAK1&!JAK_f&mTORC1_c&!PPP1CA|!SRC&!IRAK1&JAK_f&!PPP1CA|!SRC&IRAK1&!PPP1CA|SRC&!PPP1CA -SYK, ILR_f -TAB_f, !MAPK14&TRAF6 -TCF7_f, CTNNB1&!NLK -TGFB1, !NFKB_f&!FOS&JUN|!NFKB_f&FOS|NFKB_f -TGFBR1, TGFBR2&!SMAD7&!SMAD6&!SMURF1&!SMURF2 -TGFBR2, TGFB1&!SMURF1&!SMURF2 -TIAM1, !ROCK1 -TP53, !MDM2&!MAPK14&!PRKCD&!EP300&PIAS1|!MDM2&!MAPK14&!PRKCD&EP300|!MDM2&!MAPK14&PRKCD|!MDM2&MAPK14 -TRAF6, !IRAK1&TGFBR1|IRAK1 -TSC_f, GSK3_f&!AKT_f&!ERK_f&!RSK_f&!IKBKB -VAV1, SYK -mTORC1_c, !RHEB&RSK_f&!AKT1S1|RHEB&!AKT1S1 -mTORC2_c, !PIK3CA&!S6K_f&TSC_f|PIK3CA&!S6K_f diff --git a/test/CASCADE3.bnet b/test/CASCADE3.bnet deleted file mode 100755 index 8d0cec3e..00000000 --- a/test/CASCADE3.bnet +++ /dev/null @@ -1,177 +0,0 @@ -targets, factors -ABL1, (ATM & !RB1) -ACVR1, BMPR2 -ADAM17, ERK_f -AKT1S1, !AKT_f -AKT_f, (!ATM & ((!PDPK1 & (!PHLPP1 & (!PPP1CA & mTORC2_c))) | (PDPK1 & (!PHLPP1 & !PPP1CA)))) -AP1_c, ((!FOS & SMAD4) | FOS) -APAF1, CYCS -APC, ((!AXIN1 & (!DVL_f & (GSK3_f & !PRKACA))) | (AXIN1 & (!DVL_f & !PRKACA))) -ARHGAP24, ROCK1 -ATF2, ((!ERK_f & MAPK14) | ERK_f) -ATM, ((!ATR & BRCA1) | ATR) -ATR, ((!ABL1 & CDKN2A) | ABL1) -AURKA, PAK1 -AURKB, (!ATM & CHEK1) -AXIN1, (!AURKA & (GSK3_f & (!LRP_f & (!PPM1A & !PPP1CA)))) -BAD, (!AKT_f & (!PAK1 & (!RAF_f & !RSK_f))) -BAK1, (!BCL2 & ((!BID & (!MCL1 & TP53)) | (BID & !MCL1))) -BAX, ((!BID & (!MCL1 & TP53)) | (BID & !MCL1)) -BBC3, TP53 -BCL2, (!BAD & (!BBC3 & (!BID & (CREB1 & !TP53)))) -BID, ((!CASP8 & CSNK1A1) | CASP8) -BIRC_f, (!AURKB & (!DIABLO & (STAT3 & !TP53))) -BMPR2, (!SMURF1 & !SMURF2) -BRCA1, ((!AKT_f & (!CCND1 & CHEK2)) | (AKT_f & !CCND1)) -BTRC, ((!AXIN1 & (GSK3_f & !LRP_f)) | (AXIN1 & !LRP_f)) -BUB1, ATM -CASP3, (!BIRC_f & ((!CASP8 & (CASP9 & !XIAP)) | (CASP8 & !XIAP))) -CASP8, (!CFLAR & (DD_f & !SRC)) -CASP9, (!BIRC_f & (PPP1CA & !XIAP)) -CBPp300_c, (EP300 & !TP53) -CCNB1, !CDKN1A -CCND1, (!CDKN2A & (!CHUK & (!GSK3_f & ((!RSK_f & STAT3) | RSK_f)))) -CCNE1, ((!CDC25A & (!CDKN1A & (!CDKN1B & (E2F1 & !TGFB1)))) | (CDC25A & (!CDKN1A & (!CDKN1B & !TGFB1)))) -CDC25A, (!CHEK1 & (!CHEK2 & (!CSNK1A1 & (!GSK3_f & (MYC & !SMAD3))))) -CDC42, (!ARHGAP24 & SRC) -CDH1, (!SNAI_f & !TWIST1) -CDKN1A, (!AKT_f & ((!BRCA1 & (!MDM2 & (!MYC & (!SKP2 & TP53)))) | (BRCA1 & (!MDM2 & (!MYC & !SKP2))))) -CDKN1B, (!AKT_f & (!MYC & TGFB1)) -CDKN2A, !MYC -CFLAR, ((!AKT_f & (!ITCH & MAPK14)) | (AKT_f & !ITCH)) -CFL_f, ((!LIMK1 & LIMK2) | LIMK1) -CHEK1, (!AKT_f & ATR) -CHEK2, ((!ATR & PLK1) | ATR) -CHUK, ((!AKT_f & TRAF6) | AKT_f) -CREB1, ((!AKT_f & (!ATM & (!ATR & SMAD2))) | (AKT_f & (!ATM & !ATR))) -CREBBP, CHUK -CSK, PRKACA -CSNK1A1, !LRP_f -CSNK1_f, ((!AXIN1 & DVL_f) | AXIN1) -CTNNB1, (!APC & (!BTRC & ((!CHUK & (!CSNK1A1 & (!CSNK1_f & YAP_TAZ))) | (CHUK & (!CSNK1A1 & !CSNK1_f))))) -CYCS, ((!BAK1 & (BAX & !BCL2)) | (BAK1 & !BCL2)) -DAAM1, DVL_f -DD_f, (AURKA & (!CSNK1A1 & !MAP2K7)) -DIABLO, ((!BAK1 & (BAX & (!BCL2 & !BIRC_f))) | (BAK1 & (!BCL2 & !BIRC_f))) -DKK_f, (!MYC & TCF7_f) -DUSP1, ((!ERK_f & (MSK_f & !SKP2)) | (ERK_f & !SKP2)) -DUSP6, ((!ERK_f & mTORC1_c) | ERK_f) -DVL_f, ((!FZD_f & (!ITCH & (SMAD1 & !YAP_TAZ))) | (FZD_f & (!ITCH & !YAP_TAZ))) -E2F1, (!HES1 & !RB1) -EGR1, (NFKB_f & !TCF7_f) -EP300, (AKT_f & (!PRKCD & !SKI)) -ERK_f, (!DUSP6 & (MEK_f & !PPP1CA)) -FOS, ((!ERK_f & SRF) | ERK_f) -FOXO_f, (!AKT_f & (!CREB1 & (!CSNK1A1 & (DUSP6 & (!IKBKB & !NLK))))) -FZD_f, !SFRP1 -GAB_f, (!ERK_f & GRB2) -GLI_f, (!CSNK1A1 & (!GSK3_f & (!PRKACA & !SUFU))) -GRB2, ((!RTPK_f & SHC1) | RTPK_f) -GSK3_f, (!AKT_f & (CSNK1A1 & (!DVL_f & (!ERK_f & (!MAPK14 & (!RSK_f & !S6K_f)))))) -HES1, ((!NOTCH1 & REL_f) | NOTCH1) -IKBKB, (DD_f & (!PLK1 & (!PPM1A & !TP53))) -ILK, (PAK1 & !TWIST1) -ILR_f, ((!AP1_c & LIF) | AP1_c) -IRAK1, (ILR_f & !SOCS1) -IRS1, (!ERK_f & (!IKBKB & !S6K_f)) -ITCH, JNK_f -JAK_f, (ILR_f & (!PTPN6 & !SOCS1)) -JNK_f, (!DUSP1 & ((!MAP2K4 & MAP2K7) | MAP2K4)) -JUN, (!GSK3_f & JNK_f) -KRAS, ((!PTPN11 & SOS1) | PTPN11) -LATS_f, ((!AURKA & MOB1_f) | AURKA) -LEF1, (!CSNK1_f & CTNNB1) -LIF, RAF_f -LIMK1, ((!RAC_f & ROCK1) | RAC_f) -LIMK2, (!PRKCD & ROCK1) -LRP_f, (!DKK_f & ((!ERK_f & FZD_f) | ERK_f)) -MAP2K3, ((!MAP3K5 & MAP3K7) | MAP3K5) -MAP2K4, ((!MAP3K11 & MAP3K4) | MAP3K11) -MAP2K7, ((!MAP3K7 & MAPK8IP3) | MAP3K7) -MAP3K11, RAC_f -MAP3K4, RAC_f -MAP3K5, !AKT_f -MAP3K7, ((!TAB_f & TRAF6) | TAB_f) -MAP3K8, IKBKB -MAPK14, (!DUSP1 & ((!MAP2K3 & MAP2K4) | MAP2K3)) -MAPK8IP3, ROCK1 -MAPKAPK2, MAPK14 -MCL1, (!BBC3 & ((!ERK_f & (!GSK3_f & JNK_f)) | (ERK_f & !GSK3_f))) -MDM2, (!ABL1 & ((!AKT_f & (!ATM & (!ATR & (!CDKN2A & (!CSNK1_f & (!S6K_f & TP53)))))) | (AKT_f & (!ATM & (!ATR & (!CDKN2A & (!CSNK1_f & !S6K_f))))))) -MEK_f, (!ERK_f & RAF_f) -MMP_f, ((!LEF1 & STAT3) | LEF1) -MOB1_f, STK_f -MSK_f, ((!ERK_f & MAPK14) | ERK_f) -MYC, (!GSK3_f & ((!PLK1 & STAT3) | PLK1)) -NFKB_f, (!CHEK1 & ((!IKBKB & MSK_f) | IKBKB)) -NLK, MAP3K7 -NOTCH1, ADAM17 -PAK1, ((!CDC42 & RAC_f) | CDC42) -PARD6A, ((!TGFBR1 & TGFBR2) | TGFBR1) -PDPK1, (PIK3CA & !PTEN) -PHLPP1, !GSK3_f -PIAS1, MAPKAPK2 -PIK3CA, ((!GAB_f & KRAS) | GAB_f) -PLCG1, SYK -PLK1, ((!MAPKAPK2 & PDPK1) | MAPKAPK2) -PPM1A, PTEN -PPP1CA, (!RTPK_f & SMAD7) -PRKACA, ((!FOS & NFKB_f) | FOS) -PRKCA, ((!PARD6A & (!PHLPP1 & PLCG1)) | (PARD6A & !PHLPP1)) -PRKCD, ((!CASP3 & PDPK1) | CASP3) -PRKDC, ((!ATM & ATR) | ATM) -PTCH1, GLI_f -PTEN, (!CBPp300_c & (!GSK3_f & (ROCK1 & !SRC))) -PTPN11, GAB_f -PTPN6, (!PRKCA & SRC) -RAC_f, (!ARHGAP24 & ((!PIK3CA & TIAM1) | PIK3CA)) -RAF_f, (!AKT_f & (!ERK_f & (KRAS & !RHEB))) -RB1, (!CCND1 & (!CCNE1 & ((!CHEK1 & CHEK2) | CHEK1))) -RBPJ, !HES1 -REL_f, ((!IKBKB & (PRKCA & !STAT1)) | (IKBKB & !STAT1)) -RHEB, !TSC_f -RHOA, (DAAM1 & (!PARD6A & (!RAC_f & (!RND3 & !SMURF1)))) -RND3, ROCK1 -ROCK1, ((!CASP3 & RHOA) | CASP3) -RSK_f, ((!ERK_f & PDPK1) | ERK_f) -RTPK_f, ((!FOXO_f & (!MAPK14 & (!MEK_f & MMP_f))) | (FOXO_f & (!MAPK14 & !MEK_f))) -S6K_f, ((!PDPK1 & (!PHLPP1 & mTORC1_c)) | (PDPK1 & !PHLPP1)) -SFRP1, !MYC -SHC1, (!PTEN & ((!SRC & TGFBR1) | SRC)) -SKI, !AKT_f -SKP2, ((!EP300 & ERK_f) | EP300) -SMAD1, ((!ACVR1 & (!ERK_f & (!GSK3_f & (!PPM1A & (!SKI & (!SMAD6 & (!SMURF1 & YAP_TAZ))))))) | (ACVR1 & (!ERK_f & (!GSK3_f & (!PPM1A & (!SKI & (!SMAD6 & !SMURF1))))))) -SMAD2, ((!ACVR1 & (!PPM1A & (!SKI & (!SMURF2 & TGFBR1)))) | (ACVR1 & (!PPM1A & (!SKI & !SMURF2)))) -SMAD3, ((!ACVR1 & (!AKT_f & (!ERK_f & (!GSK3_f & (!PPM1A & (!SKI & (!SMAD6 & (!SMAD7 & TGFBR1)))))))) | (ACVR1 & (!AKT_f & (!ERK_f & (!GSK3_f & (!PPM1A & (!SKI & (!SMAD6 & !SMAD7)))))))) -SMAD4, (!SKI & ((!SMAD2 & (SMAD5 & (!SMAD6 & (!SMAD7 & !SMURF1)))) | (SMAD2 & (!SMAD6 & (!SMAD7 & !SMURF1))))) -SMAD5, (ACVR1 & (!SKI & !SMURF2)) -SMAD6, ((!SMAD2 & SMAD4) | SMAD2) -SMAD7, (!AXIN1 & (!ITCH & ((!SMAD2 & (SMAD4 & !SMURF2)) | (SMAD2 & !SMURF2)))) -SMO, (CSNK1A1 & !PTCH1) -SMURF1, SMAD7 -SMURF2, SMAD7 -SNAI_f, (!GSK3_f & ((!LATS_f & PAK1) | LATS_f)) -SOCS1, STAT1 -SOS1, (!ERK_f & PLCG1) -SRC, (!CSK & ((!PRKACA & RTPK_f) | PRKACA)) -SRF, ((!CFL_f & RSK_f) | CFL_f) -STAT1, ((!IKBKB & (!PIAS1 & SRC)) | (IKBKB & !PIAS1)) -STAT3, ((!IRAK1 & (!PPP1CA & SRC)) | (IRAK1 & !PPP1CA)) -STK_f, (!AKT_f & (PHLPP1 & !RAF_f)) -SUFU, !SMO -SYK, (!CHEK1 & ILR_f) -TAB_f, (!MAPK14 & TRAF6) -TCF7_f, (CTNNB1 & !NLK) -TGFB1, ((!FOS & NFKB_f) | FOS) -TGFBR1, (!SMAD6 & (!SMAD7 & (!SMURF1 & (!SMURF2 & TGFBR2)))) -TGFBR2, (!SMURF1 & (!SMURF2 & TGFB1)) -TIAM1, !ROCK1 -TP53, (!AURKB & (EP300 & !MDM2)) -TRAF6, ((!IRAK1 & TGFBR1) | IRAK1) -TSC_f, (!AKT_f & (!ERK_f & (GSK3_f & (!IKBKB & !RSK_f)))) -TWIST1, ((!ERK_f & JNK_f) | ERK_f) -VAV1, SYK -XIAP, ((!AKT_f & (BIRC_f & !DIABLO)) | (AKT_f & !DIABLO)) -YAP_TAZ, (!BTRC & (!CSNK1_f & !LATS_f)) -mTORC1_c, (!AKT1S1 & ((!RHEB & RSK_f) | RHEB)) -mTORC2_c, ((!PIK3CA & (!S6K_f & TSC_f)) | (PIK3CA & !S6K_f)) diff --git a/test/Cell-Cycle-2019.bnet b/test/Cell-Cycle-2019.bnet deleted file mode 100644 index 5da20366..00000000 --- a/test/Cell-Cycle-2019.bnet +++ /dev/null @@ -1,88 +0,0 @@ -targets, factors -GF, GF|GF_High -RTK, !CAD&(GF_High|GF) -Grb2, RTK&GF_High -Ras, Grb2&SOS -RAF, !Casp3&Ras -mTORC2, PIP3|!S6K -PI3K, Ras|RTK -PIP3, PI3K_H|PI3K -PDK1, PI3K&PIP3 -AKT_B, !Casp3&PIP3&(PDK1|mTORC2) -p110_H, (FoxO3&!NeddL4)|(p110_H&(FoxO3|!NeddL4)) -PI3K_H, p110_H&RTK&PI3K&Ras -AKT_H, AKT_B&p110_H&PI3K_H&Ras&PIP3&PDK1&mTORC2 -FoxO3, !(AKT_B|AKT_H|ERK)|(!(AKT_H&(Plk1|Plk1_H|AKT_B|ERK))&!(Plk1&Plk1_H&ERK)) -PLCgamma, RTK&Grb2&p110_H&PI3K_H&PIP3 -NeddL4, Ca2&IP3 -FoxO1, !Plk1&!AKT_H -p21_mRNA, (FoxO1&FoxO3)|(!Myc&(FoxO1|FoxO3)) -TSC2, !AKT_H|!(AKT_B|ERK) -PRAS40, !AKT_H&(!mTORC1|!AKT_B) -Rheb, !TSC2&DAG -mTORC1, !Casp3&((Rheb&!PRAS40)|E2F1|(CyclinB&Cdk1&GSK3)) -S6K, !Casp3&mTORC1 -eIF4E, !Casp3&mTORC1 -GSK3, !AKT_H&!(S6K&ERK) -p21, p21_mRNA&!Casp3&!CyclinE -pRB, !Casp3&!CyclinD1&!CyclinA&(p27Kip1|!CyclinE) -p27Kip1, !Casp3&!CyclinD1&!(Cdk1&CyclinB)&((!CyclinE&(FoxO3&FoxO1))|(!CyclinA&(FoxO3|FoxO1))|(!CyclinE&!CyclinA)) -Myc, (ERK&(eIF4E|!GSK3))|(E2F1&!pRB&(eIF4E|ERK|!GSK3)) -CyclinD1, !CHK1&((!p21&((!GSK3&(Myc|E2F1))|(Myc&CyclinD1)|(Myc&E2F1)|(E2F1&CyclinD1)))|(!pRB&E2F1&((Myc&CyclinD1)|(Myc&!GSK3)|(CyclinD1&!GSK3)))) -E2F1, !(CAD|CyclinA|pRB)&(E2F1|Myc) -CyclinE, E2F1&Cdc6&Pre_RC&!(pRB|p27Kip1|CHK1|Casp3) -ORC, E2F1|(Pre_RC&Cdt1&Cdc6) -Cdc6, !Casp3&!(f4N_DNA&CyclinA)&((E2F1&ORC&!Plk1)|(Pre_RC&ORC&Cdc6&Cdt1)) -Cdt1, !geminin&ORC&Cdc6&!(CyclinE&CyclinA&Cdc25A)&((Pre_RC&(E2F1|Myc))|(E2F1&(Myc|!pRB))) -Pre_RC, ORC&Cdc6&Cdt1&!(Replication&f4N_DNA) -geminin, E2F1&!Cdh1&!(pAPC&Cdc20) -CyclinA_mRNA, !CAD&((E2F1&!pRB)|FoxM1) -Emi1, (E2F1|!pRB|!p21)&!(Plk1&CyclinB&Cdk1&(U_Kinetochores|A_Kinetochores)) -FoxM1, (Myc&CyclinE)|(CyclinA&Cdc25A&Cdc25B)|(Plk1&CyclinB&Cdk1) -Cdc25A, ((FoxM1&E2F1&!pRB)|(!Cdh1&(FoxM1|(E2F1&!pRB))))&(!(GSK3|CHK1)|CyclinE|CyclinA|(CyclinB&Cdk1)) -CyclinA, CyclinA_mRNA&!pAPC&((Cdc25A&(!Cdh1|Emi1))|(CyclinA&((!Cdh1&(Emi1|!UbcH10))|(Emi1&!UbcH10)))) -Wee1, !Casp3&!(Cdk1&CyclinB)&(Replication|CHK1)&(CHK1|!(Cdk1&CyclinA&Plk1)) -UbcH10, !Cdh1|(UbcH10&(Cdc20|CyclinA|CyclinB)) -CyclinB, (FoxM1|(FoxO3&CyclinB))&!(Cdh1|(pAPC&Cdc20)) -Cdc25B, FoxM1&f4N_DNA -Plk1, !Cdh1&(FoxM1|Plk1_H)&((CyclinB&Cdk1)|(CyclinA&!Wee1&Cdc25A)) -Cdc25C, f4N_DNA&Plk1&((Cdc25B&!CHK1)|(CyclinB&Cdk1)) -Cdk1, CyclinB&Cdc25C&(!CHK1|(!Wee1&Cdk1)) -pAPC, (CyclinB&Cdk1&Plk1)|(CyclinB&Cdk1&pAPC)|(pAPC&Cdc20) -Cdc20, pAPC&!Emi1&!Cdh1&(!Mad2|(!CyclinA&!(CyclinB&Cdk1))) -Cdh1, !(CyclinB&Cdk1)&!(CyclinA&(Emi1|Cdc25A)) -Replication, !CAD&Pre_RC&((E2F1&CyclinE&Cdc25A)|(Replication&CyclinA&Cdc25A&(E2F1|!f4N_DNA))) -f4N_DNA, !CAD&((Replication&((Pre_RC&CyclinA)|f4N_DNA))|(f4N_DNA&!Ect2)) -U_Kinetochores, f4N_DNA&!Cdh1&!A_Kinetochores&((CyclinB&Cdk1)|U_Kinetochores) -Mad2, U_Kinetochores&!A_Kinetochores -A_Kinetochores, f4N_DNA&!Cdh1&!(pAPC&Cdc20)&(A_Kinetochores|(U_Kinetochores&Plk1&CyclinB&Cdk1)) -Plk1_H, Plk1&FoxM1&(Plk1_H|FoxO3|FoxO1) -Ect2, f4N_DNA&Plk1_H&Cdh1&!U_Kinetochores&!A_Kinetochores -Casp8, DR4_5|Casp3 -Casp2, Casp3|(U_Kinetochores&Mad2&!(CyclinB&Cdk1)) -MCL_1, !Casp3&!Casp2&(!GSK3|(AKT_B&(ERK|!E2F1)))&(!(Cdk1&CyclinB&U_Kinetochores)) -BCLXL, !Casp3&(BCL2|!BAD)&(!U_Kinetochores|(Plk1&(!(CyclinB&Cdk1)|(BCL2&MCL_1)))|((BCL2&MCL_1)&!(CyclinB&Cdk1))) -BCL2, !(Casp3|BAD|BIM|BIK)&(!U_Kinetochores|(MCL_1&BCLXL)|(Plk1&(BCLXL|MCL_1|!(Cdk1&CyclinB)))) -BAD, Casp3|!(AKT_H|AKT_B|ERK|S6K)|(Casp8&(!(AKT_B&ERK&S6K)&!(AKT_H&(AKT_B|ERK)))) -BIK, !(MCL_1|BCLXL|BCL2) -BIM, FoxO3&GSK3&!(ERK|MCL_1|BCLXL|BCL2) -BID, Casp8|(Casp2&!(BCL2|BCLXL|MCL_1)) -BAK, (BID&(BIM|BIK|!(BCL2&BCLXL&MCL_1)))|((BIM|BIK)&!(BCLXL|MCL_1)) -BAX, (BIM&((BID|BIK)|!(BCL2&BCLXL&MCL_1)))|((BID|BIK)&!(BCL2|BCLXL)) -Cyto_C, BAX|BAK -SMAC, BAX|BAK -IAPs, !SMAC|AKT_H -Casp9, Casp3|(!IAPs&Cyto_C) -Casp3, (Casp9&Casp8)|(Casp3&(Casp9|Casp8))|(!IAPs&(Casp9|Casp8|Casp3)) -CAD, Casp3&Casp9 -ATR, Replication -CHK1, ATR -Ca2, IP3 -DAG, PLCgamma -DR4_5, Trail -ERK, MEK&!BIK -GF_High, GF_High -IP3, PLCgamma -MEK, RAF -SOS, Grb2 -Trail, Trail diff --git a/test/Drosophila.bnet b/test/Drosophila.bnet deleted file mode 100644 index ebeaa1e6..00000000 --- a/test/Drosophila.bnet +++ /dev/null @@ -1,59 +0,0 @@ -targets, factors -# 52 nodes -# 124 interactions -# taken from -# Vega, M. R. (2014, May). Analyzing toys models of Arabidopsis & Drosphila using Z3 SMT-LIB. In Independent Component Analyses, Compressive Sampling, Wavelets, Neural Net, Biosystems, & Nanoengineering XII (Vol. 9118, p. 911813). International Society f| Optics & Photonics. - -wg1, (CIA1 & SLP1 & ! (CIR1)) | (wg1 & SLP1 & ! (CIR1)) | (wg1 & CIA1 & ! (CIR1)) -wg2, (CIA2 & SLP2 & ! (CIR2)) | (wg2 & SLP2 & ! (CIR2)) | (wg2 & CIA2 & ! (CIR2)) -wg3, (CIA3 & SLP3 & ! (CIR3)) | (wg3 & SLP3 & ! (CIR3)) | (wg3 & CIA3 & ! (CIR3)) -wg4, (CIA4 & SLP4 & ! (CIR4)) | (wg4 & SLP4 & ! (CIR4)) | (wg4 & CIA4 & ! (CIR4)) -WG1, (wg1) -WG2, (wg2) -WG3, (wg3) -WG4, (wg4) -en1, (WG2 & ! (SLP1)) -en2, (WG3 & ! (SLP2)) | (WG1 & ! (SLP2)) -en3, (WG4 & ! (SLP3)) | (WG2 & ! (SLP3)) -en4, (WG3 & ! (SLP4)) -EN1, (en1) -EN2, (en2) -EN3, (en3) -EN4, (en4) -hh1, (EN1 & ! (CIR1)) -hh2, (EN2 & ! (CIR2)) -hh3, (EN3 & ! (CIR3)) -hh4, (EN4 & ! (CIR4)) -HH1, (hh1) -HH2, (hh2) -HH3, (hh3) -HH4, (hh4) -ptc1, (CIA1 & ! (EN1) & ! (CIR1)) -ptc2, (CIA2 & ! (EN2) & ! (CIR2)) -ptc3, (CIA3 & ! (EN3) & ! (CIR3)) -ptc4, (CIA4 & ! (EN4) & ! (CIR4)) -PTC1, (PTC1 & ! (HH2)) | (ptc1) -PTC2, (PTC2 & ! (HH1) & ! (HH3)) | (ptc2) -PTC3, (PTC3 & ! (HH2) & ! (HH4)) | (ptc3) -PTC4, (PTC4 & ! (HH3)) | (ptc4) -ci1, (! (EN1)) -ci2, (! (EN2)) -ci3, (! (EN3)) -ci4, (! (EN4)) -CI1, (ci1) -CI2, (ci2) -CI3, (ci3) -CI4, (ci4) -CIA1, (CI1 & hh2) | (CI1 & HH2) | (CI1 & ! (PTC1)) -CIA2, (CI2 & hh3) | (CI2 & hh1) | (CI2 & HH3) | (CI2 & HH1) | (CI2 & ! (PTC2)) -CIA3, (CI3 & hh4) | (CI3 & hh2) | (CI3 & HH4) | (CI3 & HH2) | (CI3 & ! (PTC3)) -CIA4, (CI4 & hh3) | (CI4 & HH3) | (CI4 & ! (PTC4)) -CIR1, (CI1 & PTC1 & ! (HH2) & ! (hh2)) -CIR2, (CI2 & PTC2 & ! (HH1) & ! (HH3) & ! (hh1) & ! (hh3)) -CIR3, (CI3 & PTC3 & ! (HH2) & ! (HH4) & ! (hh2) & ! (hh4)) -CIR4, (CI4 & PTC4 & ! (HH3) & ! (hh3)) -# External -SLP1, SLP1 -SLP2, SLP2 -SLP3, SLP3 -SLP4, SLP4 diff --git a/test/EMT.bnet b/test/EMT.bnet deleted file mode 100644 index b498f496..00000000 --- a/test/EMT.bnet +++ /dev/null @@ -1,75 +0,0 @@ -# n = 69 -# max SCC = 51 -# Parity and time reversal elucidate both decision-making in empirical models and attractor scaling in critical Boolean networks - -targets, factors -EGF, EGF -FGF, FGF -HGF, HGF -Goosecoid, Goosecoid -Hypoxia, Hypoxia -IGF1, IGF1 -PDGF, PDGF -CHD1L, CHD1L - -AKT, ILK | PI3K -Dest_compl, (GSK3B & AXIN2 & Bcatenin_nuc) | (GSK3B & Dest_compl) -AXIN2, AXIN2 | TCF_LEF -Bcatenin_memb, Ecadherin & ! Bcatenin_nuc -Bcatenin_nuc, ! Dest_compl & ! Bcatenin_memb & (! SUFU | ! Ecadherin) -BTrCP, ! Csn -CD44, TCF_LEF -CDC42, TGFBR | CHD1L -cfos, ERK -cMet, HGF | CD44 -Csl, NOTCH_ic -Csn, NFKB -DELTA, RAS -DSH, Frizzled -Ecadherin, Bcatenin_memb & (! SNAI1 | ! HEY1 | ! ZEB1 | ! ZEB2 | ! FOXC2 | ! TWIST1 | ! SNAI2) -EGFR, EGF -EGR1, cfos -EMT, ! Ecadherin -ERK, MEK -FGFR, FGF -FOXC2, Goosecoid | SNAI1 | TWIST1 -Frizzled, Wnt -FUS, SMO -GLI, TCF_LEF | ! SUFU -GSK3B, ! DSH & ! AKT & (! Csn | ! ERK | ! Dest_compl) -HEY1, Csl | SMAD -HIF1A, Hypoxia -IGF1R, IGF1 -IKKA, AKT -ILK, SMAD -Jagged, TCF_LEF | SMAD -LIV1, STAT -LOXL23, HIF1A -MEK, RAF | ! RKIP -miR200, ! SNAI1 & ! ZEB1 & ! ZEB2 -NFKB, IKKA -NOTCH, DELTA | Jagged -NOTCH_ic, NOTCH -PAK1, CDC42 -Patched, ! SHH -PDGFR, PDGF -PI3K, RAS -RAF, RAS -RAS, SOS_GRB2 | SRC | ! GSK3B | TCF_LEF -RKIP, ! ERK | ! SNAI1 -SHH, SMAD | GLI -SNAI2, ERK | Bcatenin_nuc | SNAI2 | TWIST1 -SMAD, (ERK | TGFBR) & (ZEB1 | ! ZEB2) -SMO, ! Patched -SNAI1, GLI | LOXL23 | SMAD | LIV1 | PAK1 | Csl | EGR1 | Goosecoid | ! BTrCP | ! GSK3B -SOS_GRB2, (PDGFR | cMet | TGFBR | FGFR | IGF1R | EGFR) & ! ERK -SRC, PDGFR | EGFR | FGFR | cMet | IGF1R -STAT, SRC -SUFU, ! FUS -TCF_LEF, Bcatenin_nuc -TGFB, Goosecoid | SNAI1 | TWIST1 | GLI -TGFBR, TGFB -TWIST1, NFKB | HIF1A | TCF_LEF | Goosecoid | SNAI1 -Wnt, GLI -ZEB1, (HIF1A | SNAI1 | Goosecoid) & ! miR200 -ZEB2, (HIF1A | SNAI1 | Goosecoid) & ! miR200 diff --git a/test/EMT_Mechanosensing.bnet b/test/EMT_Mechanosensing.bnet deleted file mode 100644 index f2537ef6..00000000 --- a/test/EMT_Mechanosensing.bnet +++ /dev/null @@ -1,136 +0,0 @@ -targets, factors -CellDensity_High, CellDensity_High -CellDensity_Low, CellDensity_Low|CellDensity_High -Stiff_ECM, Stiff_ECM -ECM, ECM|Stiff_ECM -GF, GF|GF_High -GF_High, GF_High -RTK, (!CAD)&(GF_High|GF) -Shc, (RTK&GF_High)&(FAK|Src) -Grb2, RTK&Shc -SOS, Grb2 -Ras, ((Grb2&SOS)&Src)&((IQGAP1_LeadingE|(!Merlin))|N_bcatenin_H) -RAF, ((!Casp3)&Ras)&(!SPRY2) -MEK, RAF -ERK, (MEK&(!BIK))&(FocalAdhesions|N_bcatenin_H) -mTORC2, PIP3|(!S6K) -PI3K, (FAK|Src)&(Ras|RTK) -PIP3, PI3K_H|PI3K -PDK1, PI3K&PIP3 -AKT_B, ((!Casp3)&PIP3)&(PDK1|mTORC2) -p110_H, YAP&((FoxO3&(!Nedd4L))|(p110_H&(FoxO3|(!Nedd4L)))) -PI3K_H, ((((!PTEN_c)&p110_H)&RTK)&PI3K)&Ras -AKT_H, (((((AKT_B&p110_H)&PI3K_H)&PIP3)&PDK1)&mTORC2)&(Ras|PAK1) -FoxO3, (!((AKT_B|AKT_H)|ERK))|((!(AKT_H&(((Plk1|Plk1_H)|AKT_B)|ERK)))&(!((Plk1&Plk1_H)&ERK))) -PLCgamma, ((((RTK&Grb2)&GF_High)&p110_H)&PI3K_H)&PIP3 -IP3, PLCgamma -Ca2p, IP3 -Nedd4L, Ca2p&IP3 -FoxO1, (!Plk1)&(!AKT_H) -p21_mRNA, ((FoxO1&FoxO3)|((!Myc)&(FoxO1|FoxO3)))&(!ZEB1_H) -TSC2, (!AKT_H)|(!(AKT_B|ERK)) -PRAS40, (!AKT_H)&((!mTORC1)|(!AKT_B)) -DAG, PLCgamma -Rheb, (!TSC2)&DAG -mTORC1, (!Casp3)&((((Rheb&(!PRAS40))&(!Merlin))|E2F1)|((CyclinB&Cdk1)&GSK3)) -S6K, (!Casp3)&mTORC1 -eIF4E, mTORC1&(!Casp3) -GSK3, (!AKT_H)&(!(S6K&ERK)) -Integrin, ECM -FAK, ((!Casp3)&(!(Cdk1&CyclinB)))&Integrin -Src, (Integrin&(RTK|FAK))|(Cdk1&CyclinB) -Nectin3, CellDensity_Low|CellDensity_High -Necl5, FocalAdhesions|(!(Nectin3&CellDensity_High)) -SPRY2, ((!Necl5)&RTK)&Src -J_Ecadherin, (!Casp3)&(Nectin3&(Ecadherin_mRNA_H|Ecadherin_mRNA)) -J_bcatenin, (!Casp3)&J_Ecadherin -J_acatenin, J_bcatenin -FocalAdhesions, ((Integrin&FAK)&ECM)&(Stiff_ECM|((YAP&Rac1)&IQGAP1_LeadingE)) -Stress_Fibers, ((!CellDensity_High)&Stiff_ECM)&FocalAdhesions -YAP, (FocalAdhesions&Stress_Fibers)&(!((((ApicalBasal_Pol&J_acatenin)&AMOT)&Merlin)&Lats1_2)) -TRIO, YAP -WT1, YAP -TAZ, Stress_Fibers&(!((((ApicalBasal_Pol&J_acatenin)&AMOT)&Merlin)&Lats1_2)) -Ecadherin_mRNA_H, Ecadherin_mRNA&(!(YAP&WT1)) -ApicalBasal_Pol, (ECM&((((CellDensity_High&Nectin3)&J_Ecadherin)&J_bcatenin)&J_acatenin))&(Ecadherin_mRNA_H|(!Horizontal_Pol)) -Mst1_2, ApicalBasal_Pol -Lats1_2, Mst1_2&Merlin -AMOT, Lats1_2&Merlin -miR_29c, YAP -PTEN_c, (!miR_29c)&((S6K&(!(ERK&GSK3)))|((!ERK)&(!GSK3))) -Merlin, ((J_bcatenin&J_acatenin)&(!PAK1))&(!AKT_H) -IQGAP1_LeadingE, ((!CellDensity_High)&FocalAdhesions)&((Horizontal_Pol|Rac1)|Grb2) -Horizontal_Pol, (((((!ApicalBasal_Pol)&ECM)&IQGAP1_LeadingE)&FocalAdhesions)&TAZ)&FAK -Rac1, (!Casp3)&((((FocalAdhesions&Necl5)&Horizontal_Pol)&TRIO)&(((!(miR_200&miR_34))&(!((Merlin&Nectin3)&J_Ecadherin)))|Stiff_ECM)) -PAK1, Rac1 -IKKa, AKT_H -NfkB, IKKa|PAK1 -c_Myb, NfkB|E2F1 -N_bcatenin, (!Casp3)&(!(ApicalBasal_Pol&GSK3)) -SNAI1, (((((ZEB1_H&ZEB1)&(!miR_34))&(!GSK3))|((NfkB&(ZEB1_H|ZEB1))&(!(miR_34&GSK3))))|(((NfkB|PAK1)&ZEB1_H)&ZEB1))|(PAK1&(((!GSK3)|NfkB)|((ZEB1_H|ZEB1)&(!miR_34)))) -LEF1, ((ZEB1&(!miR_200))|ZEB1_H)|NfkB -SNAI2, Twist&((SNAI2|N_bcatenin)|(N_bcatenin_H&LEF1)) -Twist, (!Casp3)&(SNAI1&(NfkB|(!miR_34))) -miR_34, (!SNAI1)|(!(ZEB1|ZEB1_H)) -miR_200, p21|((!((Twist&ZEB1_H)&SNAI1))&(!(((Twist&SNAI1)&ZEB1)&(!(miR_200|c_Myb))))) -ZEB1_H, ZEB1&((N_bcatenin_H&LEF1)&(SNAI2|(!miR_200))) -ZEB1, SNAI2|(b_catenin_TCF4&(!miR_200)) -N_bcatenin_H, (((N_bcatenin&(!miR_34))&(!J_acatenin))&(!(miR_200&GSK3)))&(!((CyclinE|CyclinA)&GSK3)) -Ecadherin_mRNA, !((((ZEB1_H&ZEB1)&SNAI1)&SNAI2)&Twist) -b_catenin_TCF4, (N_bcatenin_H&SNAI1)&SNAI2 -p21, (p21_mRNA&(!Casp3))&(!CyclinE) -pRB, (((!Casp3)&(!CyclinD1))&(!CyclinA))&(p27Kip1|(!CyclinE)) -p27Kip1, (((!Casp3)&(!CyclinD1))&(!(Cdk1&CyclinB)))&((((!((CyclinA&Necl5)&CyclinE))&(FoxO3&FoxO1))|(((!CyclinA)|(!(Necl5|CyclinE)))&(FoxO3|FoxO1)))|((!CyclinA)&(!(Necl5&CyclinE)))) -Myc, ((ERK&YAP)|((ERK|YAP)&(eIF4E&(!GSK3))))|((E2F1&(!pRB))&((eIF4E|ERK)|(!GSK3))) -CyclinD1, (!CHK1)&(((!p21)&((((!GSK3)&YAP)&(Myc|E2F1))|(((CyclinD1&YAP)&(Myc|E2F1))|(Myc&E2F1))))|(((!pRB)&E2F1)&(((Myc&CyclinD1)|(Myc&(!GSK3)))|((YAP&CyclinD1)&(!GSK3))))) -E2F1, (!((CAD|CyclinA)|pRB))&((YAP&(E2F1|Myc))|(E2F1&Myc)) -CyclinE, ((E2F1&Cdc6)&Pre_RC)&(!(((pRB|p27Kip1)|CHK1)|Casp3)) -ORC, E2F1|((Pre_RC&Cdt1)&Cdc6) -Cdc6, ((!Casp3)&(!(f4N_DNA&CyclinA)))&(((E2F1&ORC)&(!Plk1))|(((Pre_RC&ORC)&Cdc6)&Cdt1)) -Cdt1, ((((!geminin)&ORC)&Cdc6)&(!((CyclinE&CyclinA)&Cdc25A)))&((Pre_RC&(E2F1|Myc))|(E2F1&(Myc|(!pRB)))) -Pre_RC, ((ORC&Cdc6)&Cdt1)&(!(Replication&f4N_DNA)) -geminin, (E2F1&(!Cdh1))&(!(pAPC&Cdc20)) -CyclinA_mRNA, (!CAD)&((E2F1&(!pRB))|FoxM1) -Emi1, ((E2F1|(!pRB))|(!p21))&(!(((Plk1&CyclinB)&Cdk1)&(U_Kinetochores|A_Kinetochores))) -FoxM1, (((Myc|YAP)&CyclinE)|((CyclinA&Cdc25A)&Cdc25B))|((Plk1&CyclinB)&Cdk1) -Cdc25A, (((FoxM1&E2F1)&(!pRB))|((!Cdh1)&(FoxM1|(E2F1&(!pRB)))))&((((!(GSK3|CHK1))|CyclinE)|CyclinA)|(CyclinB&Cdk1)) -Wee1, (((!Casp3)&(Replication|CHK1))&(!(Cdk1&CyclinB)))&(CHK1|(!((Cdk1&CyclinA)&Plk1))) -Cdc25B, FoxM1&f4N_DNA -Plk1, ((!Cdh1)&(FoxM1|Plk1_H))&((CyclinB&Cdk1)|((CyclinA&(!Wee1))&Cdc25A)) -CyclinA, (CyclinA_mRNA&(!pAPC))&((Cdc25A&((!Cdh1)|Emi1))|(CyclinA&(((!Cdh1)&(Emi1|(!UbcH10)))|(Emi1&(!UbcH10))))) -Cdc25C, (f4N_DNA&Plk1)&((Cdc25B&(!CHK1))|(CyclinB&Cdk1)) -CyclinB, (FoxM1|(FoxO3&CyclinB))&(!(Cdh1|(pAPC&Cdc20))) -UbcH10, (!Cdh1)|(UbcH10&((Cdc20|CyclinA)|CyclinB)) -Cdk1, (CyclinB&Cdc25C)&((!CHK1)|((!Wee1)&Cdk1)) -pAPC, (((CyclinB&Cdk1)&Plk1)|((CyclinB&Cdk1)&pAPC))|(pAPC&Cdc20) -Cdc20, ((pAPC&(!Emi1))&(!Cdh1))&((!Mad2)|((!CyclinA)&(!(CyclinB&Cdk1)))) -Cdh1, (!(CyclinB&Cdk1))&(!(CyclinA&(Emi1|Cdc25A))) -Replication, ((!CAD)&Pre_RC)&(((E2F1&CyclinE)&Cdc25A)|(((Replication&CyclinA)&Cdc25A)&(E2F1|(!f4N_DNA)))) -ATR, Replication -CHK1, ATR -f4N_DNA, (!CAD)&((Replication&((Pre_RC&CyclinA)|f4N_DNA))|(f4N_DNA&(!Cytokinesis))) -Mad2, U_Kinetochores&(!A_Kinetochores) -U_Kinetochores, ((f4N_DNA&(!Cdh1))&(!A_Kinetochores))&((CyclinB&Cdk1)|U_Kinetochores) -A_Kinetochores, ((f4N_DNA&(!Cdh1))&(!(pAPC&Cdc20)))&(A_Kinetochores|((((U_Kinetochores&Src)&Plk1)&CyclinB)&Cdk1)) -Plk1_H, (Plk1&FoxM1)&((Plk1_H|FoxO3)|FoxO1) -Ect2, (((f4N_DNA&Plk1_H)&Cdh1)&(!U_Kinetochores))&(!A_Kinetochores) -Cytokinesis, (Ect2&FAK)&Src -Trail, Trail -DR4_5, Trail -Casp8, DR4_5|Casp3 -Casp2, Casp3|((U_Kinetochores&Mad2)&(!(CyclinB&Cdk1))) -MCL_1, (((!Casp3)&(!Casp2))&((!GSK3)|(AKT_B&(ERK|(!E2F1)))))&(!((Cdk1&CyclinB)&U_Kinetochores)) -BCLXL, ((!Casp3)&(BCL2&(!BAD)))&(((!U_Kinetochores)|(Plk1&((!(CyclinB&Cdk1))|(BCL2&MCL_1))))|((BCL2&MCL_1)&(!(CyclinB&Cdk1)))) -BCL2, (!(((Casp3|BAD)|BIM)|BIK))&(((!U_Kinetochores)|(MCL_1&BCLXL))|(Plk1&((BCLXL|MCL_1)|(!(Cdk1&CyclinB))))) -BAD, (Casp3|(!(((AKT_H|AKT_B)|ERK)|S6K)))|(Casp8&((!((AKT_B&ERK)&S6K))&(!(AKT_H&(AKT_B|ERK))))) -BIK, !((MCL_1|BCLXL)|BCL2) -BIM, FoxO3&(GSK3&(!(((ERK|MCL_1)|BCLXL)|BCL2))) -BID, Casp8|(Casp2&(!((BCL2|BCLXL)|MCL_1))) -BAK, (BID&((BIM|BIK)|(!((BCL2&BCLXL)&MCL_1))))|((BIM|BIK)&(!(BCLXL|MCL_1))) -BAX, (BIM&((BID|BIK)|(!((BCL2&BCLXL)&MCL_1))))|((BID|BIK)&(!(BCL2|BCLXL))) -Cyto_C, BAX|BAK -SMAC, BAX|BAK -IAPs, (!SMAC)|AKT_H -Casp9, Casp3|((!IAPs)&Cyto_C) -Casp3, ((Casp9&Casp8)|(Casp3&(Casp9|Casp8)))|((!IAPs)&((Casp9|Casp8)|Casp3)) -CAD, Casp3&Casp9 diff --git a/test/Regan2020_Adhesion_CIP_Migration_CellCycle_Apoptosis.bnet b/test/Regan2020_Adhesion_CIP_Migration_CellCycle_Apoptosis.bnet deleted file mode 100644 index d2af63b6..00000000 --- a/test/Regan2020_Adhesion_CIP_Migration_CellCycle_Apoptosis.bnet +++ /dev/null @@ -1,121 +0,0 @@ -targets, factors -CellDensity_High, CellDensity_High -CellDensity_Low, CellDensity_Low|CellDensity_High -Stiff_ECM, Stiff_ECM -ECM, ECM|Stiff_ECM -GF_High, GF_High -GF, GF|GF_High -RTK, !CAD&(GF_High|GF) -Shc, RTK&GF_High&(FAK|Src) -Grb2, Shc&RTK -SOS, Grb2 -Ras, Grb2&SOS&Src&(IQGAP1_LeadingE|(!Merlin)) -RAF, !Casp3&Ras&(!SPRY2) -MEK, RAF -ERK, MEK&!BIK -mTORC2, PIP3|!S6K -PI3K, (FAK|Src)&(Ras|RTK) -PIP3, PI3K_H|PI3K -PDK1, PI3K&PIP3 -AKT_B, !Casp3&PIP3&(PDK1|mTORC2) -p110_H, YAP&((FoxO3&!Nedd4L)|(p110_H&(FoxO3|!Nedd4L))) -PI3K_H, (!PTEN_c)&p110_H&RTK&PI3K&Ras -AKT_H, AKT_B&p110_H&PI3K_H&PIP3&PDK1&mTORC2&(Ras|PAK1) -FoxO3, !(AKT_B|AKT_H|ERK)|(!(AKT_H&(Plk1|Plk1_H|AKT_B|ERK))&!(Plk1&Plk1_H&ERK)) -PLCgamma, RTK&Grb2&p110_H&PI3K_H&PIP3 -IP3, PLCgamma -Ca2p, IP3 -Nedd4L, Ca2p&IP3 -FoxO1, !Plk1&!AKT_H -p21_mRNA, (FoxO1&FoxO3)|(!Myc&(FoxO1|FoxO3)) -TSC2, !AKT_H|!(AKT_B|ERK) -PRAS40, !AKT_H&(!mTORC1|!AKT_B) -DAG, PLCgamma -Rheb, !TSC2&DAG -mTORC1, !Casp3&((Rheb&!PRAS40&!Merlin)|E2F1|(CyclinB&Cdk1&GSK3)) -S6K, !Casp3&mTORC1 -eIF4E, !Casp3&mTORC1 -GSK3, !AKT_H&!(S6K&ERK) -Integrin, ECM -FAK, !Casp3&!(Cdk1&CyclinB)&Integrin -Src, (Integrin&(RTK|FAK))|(Cdk1&CyclinB) -Nectin3, CellDensity_Low|CellDensity_High -Necl5, FocalAdhesions|!(Nectin3&CellDensity_High) -SPRY2, !Necl5 -J_Ecadherin, !Casp3&Nectin3 -J_bcatenin, !Casp3&J_Ecadherin -J_acatenin, J_bcatenin -FocalAdhesions, Integrin&FAK&ECM&(Stiff_ECM|(YAP&Rac1&IQGAP1_LeadingE)) -Stress_Fibers, !CellDensity_High&Stiff_ECM&FocalAdhesions -YAP, FocalAdhesions&Stress_Fibers&!(ApicalBasal_Pol&J_acatenin&AMOT&Merlin&Lats1_2) -TRIO, YAP -WT1, YAP -TAZ, Stress_Fibers&!(ApicalBasal_Pol&J_acatenin&AMOT&Merlin&Lats1_2) -Ecadherin_mRNA_H, !(YAP&WT1) -ApicalBasal_Pol, CellDensity_High&Nectin3&J_Ecadherin&J_bcatenin&J_acatenin&(Ecadherin_mRNA_H|!Horizontal_Pol) -Mst1_2, ApicalBasal_Pol -Lats1_2, Mst1_2&Merlin -AMOT, Lats1_2&Merlin -Merlin, J_bcatenin&J_acatenin&(!PAK1)&(!AKT_H) -IQGAP1_LeadingE, !CellDensity_High&FocalAdhesions&(Horizontal_Pol|Rac1|Grb2) -Horizontal_Pol, !ApicalBasal_Pol&ECM&IQGAP1_LeadingE&FocalAdhesions&TAZ&FAK -Rac1, !Casp3&Stiff_ECM&FocalAdhesions&Necl5&Horizontal_Pol&TRIO -PAK1, Rac1 -miR_29c, YAP -PTEN_c, !miR_29c&((S6K&!(ERK&GSK3))|(!ERK&!GSK3)) -p21, p21_mRNA&!Casp3&!CyclinE -pRB, !Casp3&!CyclinD1&!CyclinA&(p27Kip1|!CyclinE) -p27Kip1, !Casp3&!CyclinD1&!(Cdk1&CyclinB)&((!(CyclinA&Necl5&CyclinE)&(FoxO3&FoxO1))|((!CyclinA|!(Necl5|CyclinE))&(FoxO3|FoxO1))|(!CyclinA&!(Necl5&CyclinE))) -Myc, (ERK&YAP)|((ERK|YAP)&(eIF4E&!GSK3))|(E2F1&(!pRB)&(eIF4E|ERK|!GSK3)) -CyclinD1, !CHK1&((!p21&((!GSK3&YAP&(Myc|E2F1))|(CyclinD1&YAP&(Myc|E2F1)|(Myc&E2F1))))|(!pRB&E2F1&((Myc&CyclinD1)|(Myc&!GSK3)|(YAP&CyclinD1&!GSK3)))) -E2F1, !(CAD|CyclinA|pRB)&((YAP&(E2F1|Myc))|(E2F1&Myc)) -CyclinE, E2F1&Cdc6&Pre_RC&!(pRB|p27Kip1|CHK1|Casp3) -ORC, E2F1|(Pre_RC&Cdt1&Cdc6) -Cdc6, !Casp3&!(f4N_DNA&CyclinA)&((E2F1&ORC&!Plk1)|(Pre_RC&ORC&Cdc6&Cdt1)) -Cdt1, !geminin&ORC&Cdc6&!(CyclinE&CyclinA&Cdc25A)&((Pre_RC&(E2F1|Myc))|(E2F1&(Myc|!pRB))) -Pre_RC, ORC&Cdc6&Cdt1&!(Replication&f4N_DNA) -geminin, E2F1&!Cdh1&!(pAPC&Cdc20) -CyclinA_mRNA, !CAD&((E2F1&!pRB)|FoxM1) -Emi1, (E2F1|!pRB|!p21)&!(Plk1&CyclinB&Cdk1&(U_Kinetochores|A_Kinetochores)) -FoxM1, ((Myc|YAP)&CyclinE)|(CyclinA&Cdc25A&Cdc25B)|(Plk1&CyclinB&Cdk1) -Cdc25A, ((FoxM1&E2F1&!pRB)|(!Cdh1&(FoxM1|(E2F1&!pRB))))&(!(GSK3|CHK1)|CyclinE|CyclinA|(CyclinB&Cdk1)) -CyclinA, CyclinA_mRNA&!pAPC&((Cdc25A&(!Cdh1|Emi1))|(CyclinA&((!Cdh1&(Emi1|!UbcH10))|(Emi1&!UbcH10)))) -Wee1, !Casp3&!(Cdk1&CyclinB)&(Replication|CHK1)&(CHK1|!(Cdk1&CyclinA&Plk1)) -UbcH10, !Cdh1|(UbcH10&(Cdc20|CyclinA|CyclinB)) -CyclinB, (FoxM1|(FoxO3&CyclinB))&!(Cdh1|(pAPC&Cdc20)) -Cdc25B, FoxM1&f4N_DNA -Plk1, !Cdh1&(FoxM1|Plk1_H)&((CyclinB&Cdk1)|(CyclinA&!Wee1&Cdc25A)) -Cdc25C, f4N_DNA&Plk1&((Cdc25B&!CHK1)|(CyclinB&Cdk1)) -Cdk1, CyclinB&Cdc25C&(!CHK1|(!Wee1&Cdk1)) -pAPC, (CyclinB&Cdk1&Plk1)|(CyclinB&Cdk1&pAPC)|(pAPC&Cdc20) -Cdc20, pAPC&!Emi1&!Cdh1&(!Mad2|(!CyclinA&!(CyclinB&Cdk1))) -Cdh1, !(CyclinB&Cdk1)&!(CyclinA&(Emi1|Cdc25A)) -Replication, !CAD&Pre_RC&((E2F1&CyclinE&Cdc25A)|(Replication&CyclinA&Cdc25A&(E2F1|!f4N_DNA))) -ATR, Replication -CHK1, ATR -f4N_DNA, !CAD&((Replication&((Pre_RC&CyclinA)|f4N_DNA))|(f4N_DNA&!Cytokinesis)) -U_Kinetochores, f4N_DNA&!Cdh1&!A_Kinetochores&((CyclinB&Cdk1)|U_Kinetochores) -Mad2, U_Kinetochores&!A_Kinetochores -A_Kinetochores, f4N_DNA&!Cdh1&!(pAPC&Cdc20)&(A_Kinetochores|(U_Kinetochores&Src&Plk1&CyclinB&Cdk1)) -Plk1_H, Plk1&FoxM1&(Plk1_H|FoxO3|FoxO1) -Ect2, f4N_DNA&Plk1_H&Cdh1&!U_Kinetochores&!A_Kinetochores -Cytokinesis, Ect2&FAK&Src -Trail, Trail -DR4_5, Trail -Casp8, DR4_5|Casp3 -Casp2, Casp3|(U_Kinetochores&Mad2&!(CyclinB&Cdk1)) -MCL_1, !Casp3&!Casp2&(!GSK3|(AKT_B&(ERK|!E2F1)))&(!(Cdk1&CyclinB&U_Kinetochores)) -BCLXL, !Casp3&(BCL2|!BAD)&(!U_Kinetochores|(Plk1&(!(CyclinB&Cdk1)|(BCL2&MCL_1)))|((BCL2&MCL_1)&!(CyclinB&Cdk1))) -BCL2, !(Casp3|BAD|BIM|BIK)&(!U_Kinetochores|(MCL_1&BCLXL)|(Plk1&(BCLXL|MCL_1|!(Cdk1&CyclinB)))) -BAD, Casp3|!(AKT_H|AKT_B|ERK|S6K)|(Casp8&(!(AKT_B&ERK&S6K)&!(AKT_H&(AKT_B|ERK)))) -BIK, !(MCL_1|BCLXL|BCL2) -BIM, FoxO3&GSK3&!(ERK|MCL_1|BCLXL|BCL2) -BID, Casp8|(Casp2&!(BCL2|BCLXL|MCL_1)) -BAK, (BID&(BIM|BIK|!(BCL2&BCLXL&MCL_1)))|((BIM|BIK)&!(BCLXL|MCL_1)) -BAX, (BIM&((BID|BIK)|!(BCL2&BCLXL&MCL_1)))|((BID|BIK)&!(BCL2|BCLXL)) -Cyto_C, BAX|BAK -SMAC, BAX|BAK -IAPs, !SMAC|AKT_H -Casp9, Casp3|(!IAPs&Cyto_C) -Casp3, (Casp9&Casp8)|(Casp3&(Casp9|Casp8))|(!IAPs&(Casp9|Casp8|Casp3)) -CAD, Casp3&Casp9 diff --git a/test/SEGMENT-POLARITY-6-CELL.bnet b/test/SEGMENT-POLARITY-6-CELL.bnet deleted file mode 100644 index 67971bed..00000000 --- a/test/SEGMENT-POLARITY-6-CELL.bnet +++ /dev/null @@ -1,103 +0,0 @@ -targets, factors -v_Ci1, !v_En1 -v_Ci2, !v_En2 -v_Ci3, !v_En3 -v_Ci4, !v_En4 -v_Ci5, !v_En5 -v_Ci6, !v_En6 -v_Ciact1_b1, ((((((((!v_Dsh1&!v_Ci1)&v_Ciact1_b1)&v_Ciact1_b2)|(((!v_Dsh1&v_Ci1)&!v_Ciact1_b1)&!v_Pka1_b1))|((((!v_Dsh1&v_Ci1)&v_Ciact1_b1)&!v_Ciact1_b2)&!v_Pka1_b1))|(((!v_Dsh1&v_Ci1)&v_Ciact1_b1)&v_Ciact1_b2))|(((v_Dsh1&!v_Ci1)&v_Ciact1_b1)&v_Ciact1_b2))|(v_Dsh1&v_Ci1)) -v_Ciact1_b2, (((v_Dsh1&v_Ci1)&v_Ciact1_b1)&!v_Pka1_b1) -v_Ciact2_b1, ((((((((!v_Dsh2&!v_Ci2)&v_Ciact2_b1)&v_Ciact2_b2)|(((!v_Dsh2&v_Ci2)&!v_Ciact2_b1)&!v_Pka2_b1))|((((!v_Dsh2&v_Ci2)&v_Ciact2_b1)&!v_Ciact2_b2)&!v_Pka2_b1))|(((!v_Dsh2&v_Ci2)&v_Ciact2_b1)&v_Ciact2_b2))|(((v_Dsh2&!v_Ci2)&v_Ciact2_b1)&v_Ciact2_b2))|(v_Dsh2&v_Ci2)) -v_Ciact2_b2, (((v_Dsh2&v_Ci2)&v_Ciact2_b1)&!v_Pka2_b1) -v_Ciact3_b1, ((((((((!v_Dsh3&!v_Ci3)&v_Ciact3_b1)&v_Ciact3_b2)|(((!v_Dsh3&v_Ci3)&!v_Ciact3_b1)&!v_Pka3_b1))|((((!v_Dsh3&v_Ci3)&v_Ciact3_b1)&!v_Ciact3_b2)&!v_Pka3_b1))|(((!v_Dsh3&v_Ci3)&v_Ciact3_b1)&v_Ciact3_b2))|(((v_Dsh3&!v_Ci3)&v_Ciact3_b1)&v_Ciact3_b2))|(v_Dsh3&v_Ci3)) -v_Ciact3_b2, (((v_Dsh3&v_Ci3)&v_Ciact3_b1)&!v_Pka3_b1) -v_Ciact4_b1, ((((((((!v_Dsh4&!v_Ci4)&v_Ciact4_b1)&v_Ciact4_b2)|(((!v_Dsh4&v_Ci4)&!v_Ciact4_b1)&!v_Pka4_b1))|((((!v_Dsh4&v_Ci4)&v_Ciact4_b1)&!v_Ciact4_b2)&!v_Pka4_b1))|(((!v_Dsh4&v_Ci4)&v_Ciact4_b1)&v_Ciact4_b2))|(((v_Dsh4&!v_Ci4)&v_Ciact4_b1)&v_Ciact4_b2))|(v_Dsh4&v_Ci4)) -v_Ciact4_b2, (((v_Dsh4&v_Ci4)&v_Ciact4_b1)&!v_Pka4_b1) -v_Ciact5_b1, ((((((((!v_Dsh5&!v_Ci5)&v_Ciact5_b1)&v_Ciact5_b2)|(((!v_Dsh5&v_Ci5)&!v_Ciact5_b1)&!v_Pka5_b1))|((((!v_Dsh5&v_Ci5)&v_Ciact5_b1)&!v_Ciact5_b2)&!v_Pka5_b1))|(((!v_Dsh5&v_Ci5)&v_Ciact5_b1)&v_Ciact5_b2))|(((v_Dsh5&!v_Ci5)&v_Ciact5_b1)&v_Ciact5_b2))|(v_Dsh5&v_Ci5)) -v_Ciact5_b2, (((v_Dsh5&v_Ci5)&v_Ciact5_b1)&!v_Pka5_b1) -v_Ciact6_b1, ((((((((!v_Dsh6&!v_Ci6)&v_Ciact6_b1)&v_Ciact6_b2)|(((!v_Dsh6&v_Ci6)&!v_Ciact6_b1)&!v_Pka6_b1))|((((!v_Dsh6&v_Ci6)&v_Ciact6_b1)&!v_Ciact6_b2)&!v_Pka6_b1))|(((!v_Dsh6&v_Ci6)&v_Ciact6_b1)&v_Ciact6_b2))|(((v_Dsh6&!v_Ci6)&v_Ciact6_b1)&v_Ciact6_b2))|(v_Dsh6&v_Ci6)) -v_Ciact6_b2, (((v_Dsh6&v_Ci6)&v_Ciact6_b1)&!v_Pka6_b1) -v_Cirep1, (((!v_Dsh1&v_Ci1)&v_Pka1_b1)&v_Pka1_b2) -v_Cirep2, (((!v_Dsh2&v_Ci2)&v_Pka2_b1)&v_Pka2_b2) -v_Cirep3, (((!v_Dsh3&v_Ci3)&v_Pka3_b1)&v_Pka3_b2) -v_Cirep4, (((!v_Dsh4&v_Ci4)&v_Pka4_b1)&v_Pka4_b2) -v_Cirep5, (((!v_Dsh5&v_Ci5)&v_Pka5_b1)&v_Pka5_b2) -v_Cirep6, (((!v_Dsh6&v_Ci6)&v_Pka6_b1)&v_Pka6_b2) -v_Dsh1, v_Fz1 -v_Dsh2, v_Fz2 -v_Dsh3, v_Fz3 -v_Dsh4, v_Fz4 -v_Dsh5, v_Fz5 -v_Dsh6, v_Fz6 -v_En1, (v_Dsh1&!v_Slp1) -v_En2, (v_Dsh2&!v_Slp2) -v_En3, (v_Dsh3&!v_Slp3) -v_En4, (v_Dsh4&!v_Slp4) -v_En5, (v_Dsh5&!v_Slp5) -v_En6, (v_Dsh6&!v_Slp6) -v_Fz1, (((!v_Wg1_b1&v_Wg2_b1)&v_Wg2_b2)|v_Wg1_b1) -v_Fz2, (((((((!v_Wg1_b1&!v_Wg2_b1)&v_Wg3_b1)&v_Wg3_b2)|(!v_Wg1_b1&v_Wg2_b1))|((((v_Wg1_b1&!v_Wg1_b2)&!v_Wg2_b1)&v_Wg3_b1)&v_Wg3_b2))|((v_Wg1_b1&!v_Wg1_b2)&v_Wg2_b1))|(v_Wg1_b1&v_Wg1_b2)) -v_Fz3, (((((((!v_Wg2_b1&!v_Wg3_b1)&v_Wg4_b1)&v_Wg4_b2)|(!v_Wg2_b1&v_Wg3_b1))|((((v_Wg2_b1&!v_Wg2_b2)&!v_Wg3_b1)&v_Wg4_b1)&v_Wg4_b2))|((v_Wg2_b1&!v_Wg2_b2)&v_Wg3_b1))|(v_Wg2_b1&v_Wg2_b2)) -v_Fz4, (((((((!v_Wg3_b1&!v_Wg4_b1)&v_Wg5_b1)&v_Wg5_b2)|(!v_Wg3_b1&v_Wg4_b1))|((((v_Wg3_b1&!v_Wg3_b2)&!v_Wg4_b1)&v_Wg5_b1)&v_Wg5_b2))|((v_Wg3_b1&!v_Wg3_b2)&v_Wg4_b1))|(v_Wg3_b1&v_Wg3_b2)) -v_Fz5, (((((((!v_Wg4_b1&!v_Wg5_b1)&v_Wg6_b1)&v_Wg6_b2)|(!v_Wg4_b1&v_Wg5_b1))|((((v_Wg4_b1&!v_Wg4_b2)&!v_Wg5_b1)&v_Wg6_b1)&v_Wg6_b2))|((v_Wg4_b1&!v_Wg4_b2)&v_Wg5_b1))|(v_Wg4_b1&v_Wg4_b2)) -v_Fz6, (((!v_Wg5_b1&v_Wg6_b1)|((v_Wg5_b1&!v_Wg5_b2)&v_Wg6_b1))|(v_Wg5_b1&v_Wg5_b2)) -v_Hh1, (v_En1&!v_Cirep1) -v_Hh2, (v_En2&!v_Cirep2) -v_Hh3, (v_En3&!v_Cirep3) -v_Hh4, (v_En4&!v_Cirep4) -v_Hh5, (v_En5&!v_Cirep5) -v_Hh6, (v_En6&!v_Cirep6) -v_Nkd1_b1, (((!v_Nkd1_b1&!v_En1)|((v_Nkd1_b1&!v_Nkd1_b2)&!v_En1))|(v_Nkd1_b1&v_Nkd1_b2)) -v_Nkd1_b2, ((v_Dsh1&v_Nkd1_b1)&!v_En1) -v_Nkd2_b1, (((!v_Nkd2_b1&!v_En2)|((v_Nkd2_b1&!v_Nkd2_b2)&!v_En2))|(v_Nkd2_b1&v_Nkd2_b2)) -v_Nkd2_b2, ((v_Dsh2&v_Nkd2_b1)&!v_En2) -v_Nkd3_b1, (((!v_Nkd3_b1&!v_En3)|((v_Nkd3_b1&!v_Nkd3_b2)&!v_En3))|(v_Nkd3_b1&v_Nkd3_b2)) -v_Nkd3_b2, ((v_Dsh3&v_Nkd3_b1)&!v_En3) -v_Nkd4_b1, (((!v_Nkd4_b1&!v_En4)|((v_Nkd4_b1&!v_Nkd4_b2)&!v_En4))|(v_Nkd4_b1&v_Nkd4_b2)) -v_Nkd4_b2, ((v_Dsh4&v_Nkd4_b1)&!v_En4) -v_Nkd5_b1, (((!v_Nkd5_b1&!v_En5)|((v_Nkd5_b1&!v_Nkd5_b2)&!v_En5))|(v_Nkd5_b1&v_Nkd5_b2)) -v_Nkd5_b2, ((v_Dsh5&v_Nkd5_b1)&!v_En5) -v_Nkd6_b1, (((!v_Nkd6_b1&!v_En6)|((v_Nkd6_b1&!v_Nkd6_b2)&!v_En6))|(v_Nkd6_b1&v_Nkd6_b2)) -v_Nkd6_b2, ((v_Dsh6&v_Nkd6_b1)&!v_En6) -v_Pka1_b1, (((!v_Pka1_b1&v_Ptc1_b1)|((v_Pka1_b1&!v_Pka1_b2)&v_Ptc1_b1))|(v_Pka1_b1&v_Pka1_b2)) -v_Pka1_b2, (v_Pka1_b1&v_Ptc1_b1) -v_Pka2_b1, (((!v_Pka2_b1&v_Ptc2_b1)|((v_Pka2_b1&!v_Pka2_b2)&v_Ptc2_b1))|(v_Pka2_b1&v_Pka2_b2)) -v_Pka2_b2, (v_Pka2_b1&v_Ptc2_b1) -v_Pka3_b1, (((!v_Pka3_b1&v_Ptc3_b1)|((v_Pka3_b1&!v_Pka3_b2)&v_Ptc3_b1))|(v_Pka3_b1&v_Pka3_b2)) -v_Pka3_b2, (v_Pka3_b1&v_Ptc3_b1) -v_Pka4_b1, (((!v_Pka4_b1&v_Ptc4_b1)|((v_Pka4_b1&!v_Pka4_b2)&v_Ptc4_b1))|(v_Pka4_b1&v_Pka4_b2)) -v_Pka4_b2, (v_Pka4_b1&v_Ptc4_b1) -v_Pka5_b1, (((!v_Pka5_b1&v_Ptc5_b1)|((v_Pka5_b1&!v_Pka5_b2)&v_Ptc5_b1))|(v_Pka5_b1&v_Pka5_b2)) -v_Pka5_b2, (v_Pka5_b1&v_Ptc5_b1) -v_Pka6_b1, (((!v_Pka6_b1&v_Ptc6_b1)|((v_Pka6_b1&!v_Pka6_b2)&v_Ptc6_b1))|(v_Pka6_b1&v_Pka6_b2)) -v_Pka6_b2, (v_Pka6_b1&v_Ptc6_b1) -v_Ptc1_b1, (((((!v_En1&!v_Ptc1_b1)&!v_Hh2)|(((!v_En1&v_Ptc1_b1)&!v_Ptc1_b2)&!v_Hh2))|((!v_En1&v_Ptc1_b1)&v_Ptc1_b2))|((v_En1&v_Ptc1_b1)&v_Ptc1_b2)) -v_Ptc1_b2, (((!v_En1&v_Ciact1_b1)&v_Ptc1_b1)&!v_Hh2) -v_Ptc2_b1, (((((((!v_Hh1&!v_En2)&!v_Ptc2_b1)&!v_Hh3)|((((!v_Hh1&!v_En2)&v_Ptc2_b1)&!v_Ptc2_b2)&!v_Hh3))|(((!v_Hh1&!v_En2)&v_Ptc2_b1)&v_Ptc2_b2))|(((!v_Hh1&v_En2)&v_Ptc2_b1)&v_Ptc2_b2))|((v_Hh1&v_Ptc2_b1)&v_Ptc2_b2)) -v_Ptc2_b2, ((((!v_Hh1&!v_En2)&v_Ciact2_b1)&v_Ptc2_b1)&!v_Hh3) -v_Ptc3_b1, (((((((!v_Hh2&!v_En3)&!v_Ptc3_b1)&!v_Hh4)|((((!v_Hh2&!v_En3)&v_Ptc3_b1)&!v_Ptc3_b2)&!v_Hh4))|(((!v_Hh2&!v_En3)&v_Ptc3_b1)&v_Ptc3_b2))|(((!v_Hh2&v_En3)&v_Ptc3_b1)&v_Ptc3_b2))|((v_Hh2&v_Ptc3_b1)&v_Ptc3_b2)) -v_Ptc3_b2, ((((!v_Hh2&!v_En3)&v_Ciact3_b1)&v_Ptc3_b1)&!v_Hh4) -v_Ptc4_b1, (((((((!v_Hh3&!v_En4)&!v_Ptc4_b1)&!v_Hh5)|((((!v_Hh3&!v_En4)&v_Ptc4_b1)&!v_Ptc4_b2)&!v_Hh5))|(((!v_Hh3&!v_En4)&v_Ptc4_b1)&v_Ptc4_b2))|(((!v_Hh3&v_En4)&v_Ptc4_b1)&v_Ptc4_b2))|((v_Hh3&v_Ptc4_b1)&v_Ptc4_b2)) -v_Ptc4_b2, ((((!v_Hh3&!v_En4)&v_Ciact4_b1)&v_Ptc4_b1)&!v_Hh5) -v_Ptc5_b1, (((((((!v_Hh4&!v_En5)&!v_Ptc5_b1)&!v_Hh6)|((((!v_Hh4&!v_En5)&v_Ptc5_b1)&!v_Ptc5_b2)&!v_Hh6))|(((!v_Hh4&!v_En5)&v_Ptc5_b1)&v_Ptc5_b2))|(((!v_Hh4&v_En5)&v_Ptc5_b1)&v_Ptc5_b2))|((v_Hh4&v_Ptc5_b1)&v_Ptc5_b2)) -v_Ptc5_b2, ((((!v_Hh4&!v_En5)&v_Ciact5_b1)&v_Ptc5_b1)&!v_Hh6) -v_Ptc6_b1, (((!v_Hh5&!v_En6)|(((!v_Hh5&v_En6)&v_Ptc6_b1)&v_Ptc6_b2))|((v_Hh5&v_Ptc6_b1)&v_Ptc6_b2)) -v_Ptc6_b2, (((!v_Hh5&!v_En6)&v_Ciact6_b1)&v_Ptc6_b1) -v_Slp1, (v_Dsh1&!v_En1) -v_Slp2, (v_Dsh2&!v_En2) -v_Slp3, (v_Dsh3&!v_En3) -v_Slp4, (v_Dsh4&!v_En4) -v_Slp5, (v_Dsh5&!v_En5) -v_Slp6, (v_Dsh6&!v_En6) -v_Wg1_b1, ((((((((((!v_Wg1_b1&v_Slp1)&!v_Nkd1_b1)&!v_En1)&v_Ciact1_b1)|(((((!v_Wg1_b1&v_Slp1)&v_Nkd1_b1)&!v_Nkd1_b2)&!v_En1)&v_Ciact1_b1))|((((((!v_Wg1_b1&v_Slp1)&v_Nkd1_b1)&v_Nkd1_b2)&!v_En1)&v_Ciact1_b1)&v_Ciact1_b2))|(((((v_Wg1_b1&!v_Wg1_b2)&v_Slp1)&!v_Nkd1_b1)&!v_En1)&v_Ciact1_b1))|((((((v_Wg1_b1&!v_Wg1_b2)&v_Slp1)&v_Nkd1_b1)&!v_Nkd1_b2)&!v_En1)&v_Ciact1_b1))|(((((((v_Wg1_b1&!v_Wg1_b2)&v_Slp1)&v_Nkd1_b1)&v_Nkd1_b2)&!v_En1)&v_Ciact1_b1)&v_Ciact1_b2))|(v_Wg1_b1&v_Wg1_b2)) -v_Wg1_b2, ((((v_Wg1_b1&v_Slp1)&!v_En1)&v_Ciact1_b1)&v_Ciact1_b2) -v_Wg2_b1, ((((((((((!v_Wg2_b1&v_Slp2)&!v_Nkd2_b1)&!v_En2)&v_Ciact2_b1)|(((((!v_Wg2_b1&v_Slp2)&v_Nkd2_b1)&!v_Nkd2_b2)&!v_En2)&v_Ciact2_b1))|((((((!v_Wg2_b1&v_Slp2)&v_Nkd2_b1)&v_Nkd2_b2)&!v_En2)&v_Ciact2_b1)&v_Ciact2_b2))|(((((v_Wg2_b1&!v_Wg2_b2)&v_Slp2)&!v_Nkd2_b1)&!v_En2)&v_Ciact2_b1))|((((((v_Wg2_b1&!v_Wg2_b2)&v_Slp2)&v_Nkd2_b1)&!v_Nkd2_b2)&!v_En2)&v_Ciact2_b1))|(((((((v_Wg2_b1&!v_Wg2_b2)&v_Slp2)&v_Nkd2_b1)&v_Nkd2_b2)&!v_En2)&v_Ciact2_b1)&v_Ciact2_b2))|(v_Wg2_b1&v_Wg2_b2)) -v_Wg2_b2, ((((v_Wg2_b1&v_Slp2)&!v_En2)&v_Ciact2_b1)&v_Ciact2_b2) -v_Wg3_b1, ((((((((((!v_Wg3_b1&v_Slp3)&!v_Nkd3_b1)&!v_En3)&v_Ciact3_b1)|(((((!v_Wg3_b1&v_Slp3)&v_Nkd3_b1)&!v_Nkd3_b2)&!v_En3)&v_Ciact3_b1))|((((((!v_Wg3_b1&v_Slp3)&v_Nkd3_b1)&v_Nkd3_b2)&!v_En3)&v_Ciact3_b1)&v_Ciact3_b2))|(((((v_Wg3_b1&!v_Wg3_b2)&v_Slp3)&!v_Nkd3_b1)&!v_En3)&v_Ciact3_b1))|((((((v_Wg3_b1&!v_Wg3_b2)&v_Slp3)&v_Nkd3_b1)&!v_Nkd3_b2)&!v_En3)&v_Ciact3_b1))|(((((((v_Wg3_b1&!v_Wg3_b2)&v_Slp3)&v_Nkd3_b1)&v_Nkd3_b2)&!v_En3)&v_Ciact3_b1)&v_Ciact3_b2))|(v_Wg3_b1&v_Wg3_b2)) -v_Wg3_b2, ((((v_Wg3_b1&v_Slp3)&!v_En3)&v_Ciact3_b1)&v_Ciact3_b2) -v_Wg4_b1, ((((((((((!v_Wg4_b1&v_Slp4)&!v_Nkd4_b1)&!v_En4)&v_Ciact4_b1)|(((((!v_Wg4_b1&v_Slp4)&v_Nkd4_b1)&!v_Nkd4_b2)&!v_En4)&v_Ciact4_b1))|((((((!v_Wg4_b1&v_Slp4)&v_Nkd4_b1)&v_Nkd4_b2)&!v_En4)&v_Ciact4_b1)&v_Ciact4_b2))|(((((v_Wg4_b1&!v_Wg4_b2)&v_Slp4)&!v_Nkd4_b1)&!v_En4)&v_Ciact4_b1))|((((((v_Wg4_b1&!v_Wg4_b2)&v_Slp4)&v_Nkd4_b1)&!v_Nkd4_b2)&!v_En4)&v_Ciact4_b1))|(((((((v_Wg4_b1&!v_Wg4_b2)&v_Slp4)&v_Nkd4_b1)&v_Nkd4_b2)&!v_En4)&v_Ciact4_b1)&v_Ciact4_b2))|(v_Wg4_b1&v_Wg4_b2)) -v_Wg4_b2, ((((v_Wg4_b1&v_Slp4)&!v_En4)&v_Ciact4_b1)&v_Ciact4_b2) -v_Wg5_b1, ((((((((((!v_Wg5_b1&v_Slp5)&!v_Nkd5_b1)&!v_En5)&v_Ciact5_b1)|(((((!v_Wg5_b1&v_Slp5)&v_Nkd5_b1)&!v_Nkd5_b2)&!v_En5)&v_Ciact5_b1))|((((((!v_Wg5_b1&v_Slp5)&v_Nkd5_b1)&v_Nkd5_b2)&!v_En5)&v_Ciact5_b1)&v_Ciact5_b2))|(((((v_Wg5_b1&!v_Wg5_b2)&v_Slp5)&!v_Nkd5_b1)&!v_En5)&v_Ciact5_b1))|((((((v_Wg5_b1&!v_Wg5_b2)&v_Slp5)&v_Nkd5_b1)&!v_Nkd5_b2)&!v_En5)&v_Ciact5_b1))|(((((((v_Wg5_b1&!v_Wg5_b2)&v_Slp5)&v_Nkd5_b1)&v_Nkd5_b2)&!v_En5)&v_Ciact5_b1)&v_Ciact5_b2))|(v_Wg5_b1&v_Wg5_b2)) -v_Wg5_b2, ((((v_Wg5_b1&v_Slp5)&!v_En5)&v_Ciact5_b1)&v_Ciact5_b2) -v_Wg6_b1, ((((((((((!v_Wg6_b1&v_Slp6)&!v_Nkd6_b1)&!v_En6)&v_Ciact6_b1)|(((((!v_Wg6_b1&v_Slp6)&v_Nkd6_b1)&!v_Nkd6_b2)&!v_En6)&v_Ciact6_b1))|((((((!v_Wg6_b1&v_Slp6)&v_Nkd6_b1)&v_Nkd6_b2)&!v_En6)&v_Ciact6_b1)&v_Ciact6_b2))|(((((v_Wg6_b1&!v_Wg6_b2)&v_Slp6)&!v_Nkd6_b1)&!v_En6)&v_Ciact6_b1))|((((((v_Wg6_b1&!v_Wg6_b2)&v_Slp6)&v_Nkd6_b1)&!v_Nkd6_b2)&!v_En6)&v_Ciact6_b1))|(((((((v_Wg6_b1&!v_Wg6_b2)&v_Slp6)&v_Nkd6_b1)&v_Nkd6_b2)&!v_En6)&v_Ciact6_b1)&v_Ciact6_b2))|(v_Wg6_b1&v_Wg6_b2)) -v_Wg6_b2, ((((v_Wg6_b1&v_Slp6)&!v_En6)&v_Ciact6_b1)&v_Ciact6_b2) diff --git a/test/T-CELL-RECEPTOR-SIGNALING.bnet b/test/T-CELL-RECEPTOR-SIGNALING.bnet deleted file mode 100755 index d6b77d2b..00000000 --- a/test/T-CELL-RECEPTOR-SIGNALING.bnet +++ /dev/null @@ -1,50 +0,0 @@ -targets, factors -v1, ((!v35 & v51) | v35) -v17, !v21 -v18, (v20 & v100) -v19, (v20 & v35) -v20, v94 -v21, v22 -v22, v22 -v23, v23 -v24, v94 -v28, v66 -v30, (!v31 & v72) -v31, v90 -v32, v56 -v35, ((!v24 & (v53 & v90)) | (v24 & ((!v51 & (v53 & v90)) | v51))) -v36, ((!v38 & (v40 & (v50 & v100))) | (v38 & (v50 & v100))) -v38, v50 -v39, v96 -v40, v50 -v47, (v69 & (v87 & v100)) -v50, v100 -v51, (v23 & (v24 & (!v28 & (v53 & !v85)))) -v52, (v53 & v90) -v53, v54 -v54, v54 -v56, v78 -v66, (v35 & !v90) -v68, (!v17 & ((!v52 & v99) | v52)) -v69, (v68 & (!v74 & !v84)) -v72, (!v19 & (v47 & (v73 & (v87 & (v97 & v100))))) -v73, v50 -v74, v95 -v78, v79 -v79, (!v39 & (v80 & v88)) -v80, v30 -v83, (v50 & v100) -v84, v95 -v85, (!v32 & v51) -v87, (!v36 & (v38 & v100)) -v88, v40 -v90, (!v18 & v91) -v91, v92 -v92, v92 -v93, ((!v35 & (v51 & v90)) | (v35 & v90)) -v94, v94 -v95, v95 -v96, v96 -v97, ((!v83 & v99) | (v83 & ((!v99 & v100) | v99))) -v99, v21 -v100, (v1 & (!v18 & v93)) diff --git a/test/[var_133]__[id_083]__[SIGNALING-IN-PROSTATE-CANCER].bnet b/test/[var_133]__[id_083]__[SIGNALING-IN-PROSTATE-CANCER].bnet deleted file mode 100644 index 7cd6d4af..00000000 --- a/test/[var_133]__[id_083]__[SIGNALING-IN-PROSTATE-CANCER].bnet +++ /dev/null @@ -1,117 +0,0 @@ -targets, factors -AKT, ((!HSPs&(PIP3&!PTCH1))|(HSPs&!PTCH1)) -AMPK, ((!AMP_ATP&(!ATM&(!ATR&(!EGFR&(!FGFR3&HIF1)))))|((!AMP_ATP&(!ATM&(ATR&(!EGFR&!FGFR3))))|((!AMP_ATP&(ATM&(!EGFR&!FGFR3)))|(AMP_ATP&(!EGFR&!FGFR3))))) -AMP_ATP, !Nutrients -APAF1, ((!AKT&(!Bak&(!BAX&(!BCL2&(!Bcl_XL&(!Caspase8&(!HSPs&p53)))))))|((!AKT&(!Bak&(!BAX&(!BCL2&(!Bcl_XL&(!Caspase8&HSPs))))))|((!AKT&(!Bak&(!BAX&(!BCL2&(!Bcl_XL&Caspase8)))))|((!AKT&(!Bak&(BAX&(!BCL2&!Bcl_XL))))|(!AKT&(Bak&(!BCL2&!Bcl_XL))))))) -AR, ((Androgen&(!EP300&(!EZH2&(!GLI&(!HSPs&(!MDM2&(!NCOA3&(!NCOR1&(!NCOR2&(!PKC&(!PTEN&(!SMAD&NKX3_1))))))))))))|((Androgen&(!EP300&(!EZH2&(!GLI&(!HSPs&(!MDM2&(!NCOA3&(!NCOR1&(!NCOR2&(!PKC&(!PTEN&SMAD)))))))))))|((Androgen&(!EP300&(!EZH2&(!GLI&(!HSPs&(!MDM2&(!NCOA3&(!NCOR1&(!NCOR2&(PKC&!PTEN))))))))))|((Androgen&(!EP300&(!EZH2&(!GLI&(!HSPs&(!MDM2&(NCOA3&(!NCOR1&(!NCOR2&!PTEN)))))))))|((Androgen&(!EP300&(!EZH2&(!GLI&(HSPs&(!MDM2&(!NCOR1&(!NCOR2&!PTEN))))))))|((Androgen&(!EP300&(!EZH2&(GLI&(!MDM2&(!NCOR1&(!NCOR2&!PTEN)))))))|((Androgen&(!EP300&(EZH2&(!MDM2&(!NCOR1&(!NCOR2&!PTEN))))))|(Androgen&(EP300&(!MDM2&(!NCOR1&(!NCOR2&!PTEN)))))))))))) -AR_ERG, (AR&fused_event) -ATM, DNA_Damage -ATR, ((!DNA_Damage&p14ARF)|DNA_Damage) -AXIN1, GSK3 -Acidosis, Acidosis -Androgen, Androgen -BAD, (!AKT&(!HIF1&(!p90RSK&(!RAF&!YWHAZ)))) -BAX, ((!BCL2&(!ETS1&(!HIF1&(!JNK&(p53&!YWHAZ)))))|(!BCL2&(!ETS1&(!HIF1&(JNK&!YWHAZ))))) -BCL2, ((!BAD&(!BAX&(!DAXX&(!HSPs&(!NF_kB&(!p53&RUNX2))))))|((!BAD&(!BAX&(!DAXX&(!HSPs&(NF_kB&!p53)))))|(!BAD&(!BAX&(!DAXX&(HSPs&!p53)))))) -BIRC5, (HSPs&!p53) -BRCA1, ((!ATM&(!ATR&(!CyclinD&(E2F1&!Caspase3))))|((!ATM&(ATR&(!CyclinD&!Caspase3)))|(ATM&(!CyclinD&!Caspase3)))) -Bak, Caspase8 -Bcl_XL, (AR&(!BAD&!p53)) -CHK1_2, (ATM&(ATR&BRCA1)) -COX4I2, HIF1 -Carcinogen, Carcinogen -Caspase3, ((!Caspase8&Caspase9)|Caspase8) -Caspase8, (!cFLAR&FADD) -Caspase9, ((!AKT&(!BIRC5&(CytoC&(APAF1&PTCH1))))|(!AKT&(BIRC5&(CytoC&APAF1)))) -CyclinB, (E2F1&!p21) -CyclinD, ((!FOXO&(!GLI&(!GSK3&(MYC_MAX&(!NF_kB&(!p15&(!p21&TCF)))))))|((!FOXO&(!GLI&(!GSK3&(MYC_MAX&(NF_kB&(!p15&!p21))))))|(!FOXO&(GLI&(!GSK3&(MYC_MAX&(!p15&!p21))))))) -CytoC, ((!AKT&(!Bak&(!BAX&(!BCL2&(!Bcl_XL&(!Caspase8&p53))))))|((!AKT&(!Bak&(!BAX&(!BCL2&(!Bcl_XL&Caspase8)))))|((!AKT&(!Bak&(BAX&(!BCL2&!Bcl_XL))))|(!AKT&(Bak&(!BCL2&!Bcl_XL)))))) -DAXX, (!ATM&(!ATR&!SPOP)) -DNA_Damage, (Carcinogen&!SPOP) -Dsh, WNT -E2F1, (AR&(!MXI1&!RB1)) -EGF, EGF -EGFR, ((!Androgen&(EGF&(!FRS2&!TGFBR)))|(Androgen&(!FRS2&!TGFBR))) -EP300, AKT -ERG, ERK -ERK, ((!MEK1_2&RAF)|MEK1_2) -ETS1, ((!ERK&(!p53&RTK))|(ERK&!p53)) -EZH2, ((AKT&(E2F1&(!ERG&AR_ERG)))|(AKT&(E2F1&ERG))) -E_cadherin, ((!beta_catenin&(!ERG&(!NF_kB&(!Slug&(!Snail&AR_ERG)))))|(beta_catenin&(!ERG&(!NF_kB&(!Slug&!Snail))))) -FADD, ((!MAP3K1_3&(!PTCH1&(!SHH&TNFalpha)))|(!MAP3K1_3&(PTCH1&!SHH))) -FGF, FGF -FGFR3, (FGF&(!FRS2&(!PKC&!TGFBR))) -FOS, ((!AR&(!ERK&ETS1))|((!AR&ERK)|AR)) -FOXA1, FOXO -FOXO, (!AKT&JNK) -FRS2, (!ERK&(EGFR&(FGFR3&(!FRS2&!TGFBR)))) -GADD45, ((!p53&SMAD)|p53) -GLI, ((!SMO&(!SPOP&WNT))|(SMO&!SPOP)) -GSH, ((!MYC_MAX&(!NF_kB&p21))|((!MYC_MAX&NF_kB)|MYC_MAX)) -GSK3, (!AKT&(!Dsh&(MEK1_2&(!mTORC2&!p90RSK)))) -HIF1, ((!FOXO&(!HSPs&(!Hypoxia&(!mTORC2&(!MYC_MAX&(!p53&(!PHDs&(!VHL&mTORC1))))))))|((!FOXO&(!HSPs&(!Hypoxia&(!mTORC2&(MYC_MAX&(!p53&(!PHDs&!VHL)))))))|((!FOXO&(!HSPs&(!Hypoxia&(mTORC2&(!p53&(!PHDs&!VHL))))))|((!FOXO&(!HSPs&(Hypoxia&(!p53&(!PHDs&!VHL)))))|(!FOXO&(HSPs&(!p53&(!PHDs&!VHL)))))))) -HSPs, ((!AKT&(!BRCA1&(!Carcinogen&(!E2F1&(!FOXA1&PKC)))))|((!AKT&(!BRCA1&(!Carcinogen&(!E2F1&FOXA1))))|(!AKT&(!BRCA1&(Carcinogen&!E2F1))))) -Hypoxia, Hypoxia -IKK, ((!AKT&(!ETS1&(mTORC2&(!p53&(!PHDs&(!PKC&TAK1))))))|((!AKT&(!ETS1&(mTORC2&(!p53&(!PHDs&PKC)))))|((!AKT&(ETS1&(mTORC2&(!p53&!PHDs))))|((AKT&(!ETS1&(!p53&(!PHDs&(!PKC&TAK1)))))|((AKT&(!ETS1&(!p53&(!PHDs&PKC))))|(AKT&(ETS1&(!p53&!PHDs)))))))) -JNK, ((!ATM&(!ERK&(!GADD45&(!MAP3K1_3&(!p38&TAK1)))))|((!ATM&(!ERK&(!GADD45&(MAP3K1_3&!p38))))|((!ATM&(!ERK&(GADD45&!p38)))|(ATM&(!ERK&!p38))))) -JUN, ((!AR&(!ETS1&JNK))|((!AR&ETS1)|AR)) -MAP3K1_3, (!FOS&(!JUN&(!JNK&(!p38&RAS)))) -MDM2, ((!AKT&(!ATM&(!ATR&(DAXX&(!p14ARF&p53)))))|(AKT&(!ATM&(!ATR&(DAXX&!p14ARF))))) -MED12, !GLI -MEK1_2, ((!MAP3K1_3&(!PDK1&RAF))|((!MAP3K1_3&PDK1)|MAP3K1_3)) -MXI1, HIF1 -MYC, ((!E2F1&(!ERG&(!ERK&(!FOS&(!JUN&(!GLI&(!HIF1&(!NF_kB&(!p38&(!SHH&(!TCF&(AR_ERG&mTORC1))))))))))))|((!E2F1&(!ERG&(!ERK&(!FOS&(!JUN&(!GLI&(!HIF1&(!NF_kB&(!p38&(!SHH&(TCF&mTORC1)))))))))))|((!E2F1&(!ERG&(!ERK&(!FOS&(!JUN&(!GLI&(!HIF1&(!NF_kB&(!p38&(SHH&mTORC1))))))))))|((!E2F1&(!ERG&(!ERK&(!FOS&(!JUN&(!GLI&(!HIF1&(!NF_kB&(p38&(!SHH&(!TCF&AR_ERG)))))))))))|((!E2F1&(!ERG&(!ERK&(!FOS&(!JUN&(!GLI&(!HIF1&(!NF_kB&(p38&(!SHH&TCF))))))))))|((!E2F1&(!ERG&(!ERK&(!FOS&(!JUN&(!GLI&(!HIF1&(!NF_kB&(p38&SHH)))))))))|((!E2F1&(!ERG&(!ERK&(!FOS&(!JUN&(!GLI&(!HIF1&(NF_kB&(!p38&mTORC1)))))))))|((!E2F1&(!ERG&(!ERK&(!FOS&(!JUN&(!GLI&(!HIF1&(NF_kB&p38))))))))|((!E2F1&(!ERG&(!ERK&(!FOS&(!JUN&(GLI&(!HIF1&(!p38&mTORC1))))))))|((!E2F1&(!ERG&(!ERK&(!FOS&(!JUN&(GLI&(!HIF1&p38)))))))|((!E2F1&(!ERG&(!ERK&(!FOS&(JUN&(!HIF1&(!p38&mTORC1)))))))|((!E2F1&(!ERG&(!ERK&(!FOS&(JUN&(!HIF1&p38))))))|((!E2F1&(!ERG&(!ERK&(FOS&(!HIF1&(!p38&mTORC1))))))|((!E2F1&(!ERG&(!ERK&(FOS&(!HIF1&p38)))))|((!E2F1&(!ERG&(ERK&(!HIF1&(!p38&mTORC1)))))|((!E2F1&(!ERG&(ERK&(!HIF1&p38))))|((!E2F1&(ERG&(!HIF1&(!p38&mTORC1))))|((!E2F1&(ERG&(!HIF1&p38)))|((E2F1&(!ERG&(!ERK&(!FOS&(!JUN&(!GLI&(!HIF1&(!NF_kB&(!SHH&(!TCF&AR_ERG))))))))))|((E2F1&(!ERG&(!ERK&(!FOS&(!JUN&(!GLI&(!HIF1&(!NF_kB&(!SHH&TCF)))))))))|((E2F1&(!ERG&(!ERK&(!FOS&(!JUN&(!GLI&(!HIF1&(!NF_kB&SHH))))))))|((E2F1&(!ERG&(!ERK&(!FOS&(!JUN&(!GLI&(!HIF1&NF_kB)))))))|((E2F1&(!ERG&(!ERK&(!FOS&(!JUN&(GLI&!HIF1))))))|((E2F1&(!ERG&(!ERK&(!FOS&(JUN&!HIF1)))))|((E2F1&(!ERG&(!ERK&(FOS&!HIF1))))|((E2F1&(!ERG&(ERK&!HIF1)))|(E2F1&(ERG&!HIF1)))))))))))))))))))))))))))) -MYC_MAX, (!MXI1&(MYC&(!SMAD&!TGFBR))) -NCOA3, (p38&!SPOP) -NCOR1, !AKT -NCOR2, (!AKT&!FOXO) -NF1, !PKC -NF_kB, ((!DNA_Damage&(!E_cadherin&(IKK&(!NCOA3&(!PIP3&Snail)))))|((!DNA_Damage&(!E_cadherin&(IKK&(!NCOA3&PIP3))))|((!DNA_Damage&(!E_cadherin&(IKK&NCOA3)))|((!DNA_Damage&(E_cadherin&(!NCOA3&(!PIP3&Snail))))|((!DNA_Damage&(E_cadherin&(!NCOA3&PIP3)))|((!DNA_Damage&(E_cadherin&NCOA3))|((DNA_Damage&(!NCOA3&(!PIP3&Snail)))|((DNA_Damage&(!NCOA3&PIP3))|(DNA_Damage&NCOA3))))))))) -NKX3_1, (AR&(!ERG&(PKC&!AR_ERG))) -Nutrients, Nutrients -PDK1, ((!HIF1&(!MYC_MAX&PIP3))|((!HIF1&MYC_MAX)|HIF1)) -PHDs, (!Hypoxia&ROS) -PI3K, ((!EGFR&(!FRS2&TGFBR))|((!EGFR&FRS2)|EGFR)) -PIP3, (!p53&PI3K) -PKC, (RTK&WNT) -PTCH1, (GLI&!SHH) -PTEN, (!NF_kB&(p53&!Snail)) -RAF, ((!EZH2&RAS)|EZH2) -RAGS, (!Hypoxia&Nutrients) -RAS, ((!EGFR&(!FRS2&RTK))|((!EGFR&FRS2)|EGFR)) -RB1, (!AMPK&(CHK1_2&(!CyclinB&(!CyclinD&!p53)))) -ROS, ((!COX4I2&(!GSH&Hypoxia))|(COX4I2&!GSH)) -RTK, ((!EGFR&FGFR3)|EGFR) -RUNX2, ((!ETS1&(!FOXO&(!p38&SMAD)))|((!ETS1&(!FOXO&p38))|(ETS1&!FOXO))) -Rheb, !TSC1_2 -SHH, !ATR -SMAD, ((!AR&(!TGFBR&TNFalpha))|(!AR&TGFBR)) -SMO, (!PTCH1&SHH) -SPOP, SPOP -Slug, ((!DAXX&(!MDM2&(!NF_kB&(!p53&TCF))))|(!DAXX&(!MDM2&(NF_kB&!p53)))) -Snail, ((!beta_catenin&(!GLI&(!GSK3&(!NF_kB&SMAD))))|((!beta_catenin&(!GLI&(!GSK3&NF_kB)))|(!beta_catenin&(GLI&!GSK3)))) -TAK1, ((!TGFBR&TNFalpha)|TGFBR) -TCF, ((!beta_catenin&(!ERG&(!TAK1&AR_ERG)))|((!beta_catenin&(ERG&!TAK1))|(beta_catenin&!TAK1))) -TERT, ((!AKT&(!eEF2&(!GLI&(!HIF1&(!ZBTB17&(!MYC_MAX&(!NF1&(NF_kB&(!p53&!SMAD)))))))))|((!AKT&(!eEF2&(!GLI&(!HIF1&(!ZBTB17&(!MYC_MAX&(NF1&(!p53&!SMAD))))))))|((!AKT&(!eEF2&(!GLI&(!HIF1&(!ZBTB17&(MYC_MAX&(!p53&!SMAD)))))))|((!AKT&(!eEF2&(!GLI&(HIF1&(!ZBTB17&(!p53&!SMAD))))))|((!AKT&(!eEF2&(GLI&(!ZBTB17&(!p53&!SMAD)))))|(AKT&(!eEF2&(!ZBTB17&(!p53&!SMAD))))))))) -TGFBR, (!MED12&TGFb) -TGFb, TGFb -TNFalpha, TNFalpha -TSC1_2, ((!AKT&(!AMPK&(!ERK&(!HIF1&(!p53&(!p90RSK&!RAF))))))|((!AKT&(!AMPK&(!ERK&(!HIF1&(p53&!p90RSK)))))|((!AKT&(!AMPK&(!ERK&(!HIF1&(p53&(p90RSK&!RAF))))))|((!AKT&(!AMPK&(!ERK&(HIF1&(!p53&!p90RSK)))))|((!AKT&(!AMPK&(!ERK&(HIF1&(!p53&(p90RSK&!RAF))))))|((!AKT&(!AMPK&(!ERK&(HIF1&p53))))|((!AKT&(!AMPK&(ERK&(!HIF1&(p53&(!p90RSK&!RAF))))))|((!AKT&(!AMPK&(ERK&(HIF1&(!p53&(!p90RSK&!RAF))))))|((!AKT&(!AMPK&(ERK&(HIF1&(p53&!p90RSK)))))|((!AKT&(!AMPK&(ERK&(HIF1&(p53&(p90RSK&!RAF))))))|((!AKT&(AMPK&(!ERK&(!HIF1&(!p53&!p90RSK)))))|((!AKT&(AMPK&(!ERK&(!HIF1&(!p53&(p90RSK&!RAF))))))|((!AKT&(AMPK&(!ERK&(!HIF1&p53))))|((!AKT&(AMPK&(!ERK&HIF1)))|((!AKT&(AMPK&(ERK&(!HIF1&(!p53&(!p90RSK&!RAF))))))|((!AKT&(AMPK&(ERK&(!HIF1&(p53&!p90RSK)))))|((!AKT&(AMPK&(ERK&(!HIF1&(p53&(p90RSK&!RAF))))))|((!AKT&(AMPK&(ERK&(HIF1&(!p53&!p90RSK)))))|((!AKT&(AMPK&(ERK&(HIF1&(!p53&(p90RSK&!RAF))))))|((!AKT&(AMPK&(ERK&(HIF1&p53))))|((AKT&(!AMPK&(!ERK&(!HIF1&(p53&(!p90RSK&!RAF))))))|((AKT&(!AMPK&(!ERK&(HIF1&(!p53&(!p90RSK&!RAF))))))|((AKT&(!AMPK&(!ERK&(HIF1&(p53&!p90RSK)))))|((AKT&(!AMPK&(!ERK&(HIF1&(p53&(p90RSK&!RAF))))))|((AKT&(!AMPK&(ERK&(HIF1&(p53&(!p90RSK&!RAF))))))|((AKT&(AMPK&(!ERK&(!HIF1&(!p53&(!p90RSK&!RAF))))))|((AKT&(AMPK&(!ERK&(!HIF1&(p53&!p90RSK)))))|((AKT&(AMPK&(!ERK&(!HIF1&(p53&(p90RSK&!RAF))))))|((AKT&(AMPK&(!ERK&(HIF1&(!p53&!p90RSK)))))|((AKT&(AMPK&(!ERK&(HIF1&(!p53&(p90RSK&!RAF))))))|((AKT&(AMPK&(!ERK&(HIF1&p53))))|((AKT&(AMPK&(ERK&(!HIF1&(p53&(!p90RSK&!RAF))))))|((AKT&(AMPK&(ERK&(HIF1&(!p53&(!p90RSK&!RAF))))))|((AKT&(AMPK&(ERK&(HIF1&(p53&!p90RSK)))))|(AKT&(AMPK&(ERK&(HIF1&(p53&(p90RSK&!RAF)))))))))))))))))))))))))))))))))))))))) -VHL, (!Hypoxia&!ROS) -WNT, ((!ERG&(!p53&AR_ERG))|(ERG&!p53)) -YWHAZ, AR -ZBTB17, (AR&!MYC_MAX) -beta_catenin, ((!AXIN1&(!EZH2&(!GSK3&(!p53&YWHAZ))))|(!AXIN1&(EZH2&(!GSK3&!p53)))) -cFLAR, ((!AKT&(AR&!JNK))|(AKT&!JNK)) -eEF2, !eEF2K -eEF2K, ((!p70S6kab&p90RSK)|p70S6kab) -fused_event, fused_event -mTORC1, (AKT&(!AMPK&!TSC1_2)) -mTORC2, ((!AKT&(!AMPK&(RAGS&Rheb)))|((AKT&(!AMPK&(!RAGS&Rheb)))|((AKT&(!AMPK&RAGS))|(AKT&(AMPK&(RAGS&Rheb)))))) -p14ARF, (E2F1&(MYC_MAX&RAS)) -p15, ZBTB17 -p21, ((!AKT&(!ERK&(!HIF1&(!MDM2&(!ZBTB17&(!MYC_MAX&(!p53&(SMAD&!TERT))))))))|((!AKT&(!ERK&(!HIF1&(!MDM2&(!ZBTB17&(!MYC_MAX&(p53&!TERT)))))))|((!AKT&(!ERK&(!HIF1&(!MDM2&(ZBTB17&(!MYC_MAX&!TERT))))))|(!AKT&(!ERK&(HIF1&(!MDM2&(!MYC_MAX&!TERT)))))))) -p38, (!ERK&(!GADD45&MAP3K1_3)) -p53, ((!Acidosis&(!BCL2&(!CHK1_2&(!HIF1&(!HSPs&(!MDM2&(!p14ARF&p38)))))))|((!Acidosis&(!BCL2&(!CHK1_2&(!HIF1&(!HSPs&(!MDM2&p14ARF))))))|((!Acidosis&(!BCL2&(!CHK1_2&(HIF1&(!HSPs&!MDM2)))))|((!Acidosis&(!BCL2&(CHK1_2&(!HSPs&!MDM2))))|(Acidosis&(!BCL2&(!HSPs&!MDM2))))))) -p70S6kab, ((!mTORC2&PDK1)|mTORC2) -p90RSK, ((!ERK&PDK1)|ERK) diff --git a/test/[var_47]__[id_075]__[INFLAMMATORY-BOWEL-DISEASE].bnet b/test/[var_47]__[id_075]__[INFLAMMATORY-BOWEL-DISEASE].bnet deleted file mode 100644 index 1e826920..00000000 --- a/test/[var_47]__[id_075]__[INFLAMMATORY-BOWEL-DISEASE].bnet +++ /dev/null @@ -1,47 +0,0 @@ -targets, factors -CD4_NKG2D, ((PGN&!(CD4_NKG2D&((IEC_ULPB1_6|IEC_MICA_B)|IL10)))|((MDP&!(CD4_NKG2D&((IEC_ULPB1_6|IEC_MICA_B)|IL10)))|(((CD4_NKG2D&((TNFa|IL15)&!CD4_NKG2Dupregulation))&!(CD4_NKG2D&((IEC_ULPB1_6|IEC_MICA_B)|IL10)))|(LPS&!(CD4_NKG2D&((IEC_ULPB1_6|IEC_MICA_B)|IL10)))))) -CD4_NKG2Dupregulation, (CD4_NKG2D&(TNFa|IL15)) -CD8_NKG2D, ((MDP&!(CD8_NKG2D&(IEC_MICA_B|(IEC_ULPB1_6|(IL21&IL2)))))|((PGN&!(CD8_NKG2D&(IEC_MICA_B|(IEC_ULPB1_6|(IL21&IL2)))))|(LPS&!(CD8_NKG2D&(IEC_MICA_B|(IEC_ULPB1_6|(IL21&IL2))))))) -DC, ((TLR2&!(DC&IL10))|((TLR4&!(DC&IL10))|(NOD2&!(DC&IL10)))) -DEF, (IL22|(IL17|NOD2)) -FIBROBLAST, ((IL2&!(FIBROBLAST&(IL12|IFNg)))|((MACR&(TGFb|(IL13|IL4)))&!(FIBROBLAST&(IL12|IFNg)))) -GRANZB, (NK_NKG2D|(CD8_NKG2D|(NK|(DC&(!PGN|!LPS))))) -IEC_MICA_B, (((IEC_MICA_B&(TNFa&!IEC_MICA_Bupregulation))&!TGFb)|((LPS&!TGFb)|((PGN&!TGFb)|(MDP&!TGFb)))) -IEC_MICA_Bupregulation, (IEC_MICA_B&TNFa) -IEC_ULPB1_6, (CD8_NKG2D&(PGN|(LPS|MDP))) -IFNg, ((((Th17&(PGN|(LPS|MDP)))&!(IFNg&(TGFb|IL10)))&!Th2)|(((Th1&!(IFNg&(TGFb|IL10)))&!Th2)|((((IL18&(IL12&(Th0|MACR)))&!(IFNg&(TGFb|IL10)))&!Th2)|((((IL23&((PGN|(LPS|MDP))&NK))&!(IFNg&(TGFb|IL10)))&!Th2)|((((NK_NKG2D&(IEC_ULPB1_6|IEC_MICA_B))&!(IFNg&(TGFb|IL10)))&!Th2)|(((CD8_NKG2D&(IEC_ULPB1_6|IEC_MICA_B))&!(IFNg&(TGFb|IL10)))&!Th2)))))) -IL10, (Treg|((DC&LPS)|((TLR2&(NFkB&(!MACR&!IFNg)))|((MACR&(LPS&!IL4))|(Th2&!IL23))))) -IL12, ((LPS&(IFNg&((MACR&PGN)|DC)))|(TLR2&(NFkB&(DC|MACR)))) -IL13, Th2 -IL15, ((FIBROBLAST&(PGN|(LPS|MDP)))|(MACR&(IFNg|LPS))) -IL17, (((Th17_M&(PGN|(LPS|MDP)))&!(IL17&(TGFb|IL13)))|(((CD4_NKG2D&(IEC_ULPB1_6|IEC_MICA_B))&!(IL17&(TGFb|IL13)))|(Th17&!(IL17&(TGFb|IL13))))) -IL18, (LPS&(NFkB&(DC|MACR))) -IL1b, (((MACR&(NFkB&LPS))&!(IL10&IL1b))|((DC&(NFkB&LPS))&!(IL10&IL1b))) -IL2, ((Th0_M&(PGN|(LPS|MDP)))|(Th0|DC)) -IL21, (((((Th0&IL6)&!IFNg)&!IL4)&!TGFb)|Th17) -IL22, (Th17|((NK&IL23)|(((Th0&(IL22&(IL21&!IL22upregulation)))&!TGFb)|(CD4_NKG2D|(NK&(IL18&IL12)))))) -IL22upregulation, (Th0&(IL21&IL22)) -IL23, ((MACR&IL1b)|DC) -IL4, Th2 -IL6, ((DC&(PGN|LPS))|((MACR&PGN)|((Th17&IL23)|(NFkB&(!IL10|!IL4))))) -LPS, !(GRANZB|(DEF|PERFOR)) -MACR, ((NOD2&!(MACR&IL10))|((IFNg&!(MACR&IL10))|((IL15&!(MACR&IL10))|((TLR4&!(MACR&IL10))|(TLR2&!(MACR&IL10)))))) -MDP, !(PERFOR|(DEF|GRANZB)) -NFkB, (NOD2|(TLR4|TLR2)) -NK, (((DC&IL15)&!(NK&Treg))|((IL23&!(NK&Treg))|((IL18&IL10)&!(NK&Treg)))) -NK_NKG2D, ((MDP&!(NK_NKG2D&(IEC_ULPB1_6&(TGFb&(IEC_MICA_B&(IL21&IL12))))))|((PGN&!(NK_NKG2D&(IEC_ULPB1_6&(TGFb&(IEC_MICA_B&(IL21&IL12))))))|(LPS&!(NK_NKG2D&(IEC_ULPB1_6&(TGFb&(IEC_MICA_B&(IL21&IL12)))))))) -NOD2, MDP -PERFOR, (NK_NKG2D|NK) -PGN, !(GRANZB|(DEF|PERFOR)) -TGFb, (Treg|MACR) -TLR2, PGN -TLR4, LPS -TNFa, (((MACR&(IL2|(PGN|(IFNg&LPS))))&!(IL10&(TNFa&(TLR4|TLR2))))|(((CD8_NKG2D&(IEC_ULPB1_6|IEC_MICA_B))&!(IL10&(TNFa&(TLR4|TLR2))))|(((FIBROBLAST&IFNg)&!(IL10&(TNFa&(TLR4|TLR2))))|(((NFkB&LPS)&!(IL10&(TNFa&(TLR4|TLR2))))|(((CD4_NKG2D&(IEC_ULPB1_6|IEC_MICA_B))&!(IL10&(TNFa&(TLR4|TLR2))))|(((NK&((PGN|(LPS|MDP))&(IL23|(IL15|IL2))))&!(IL10&(TNFa&(TLR4|TLR2))))|((NK_NKG2D&(IEC_ULPB1_6|IEC_MICA_B))&!(IL10&(TNFa&(TLR4|TLR2)))))))))) -Th0, (MDP|(PGN|LPS)) -Th0_M, (Th0_M|(Th0&(IL23|IL12))) -Th1, ((Th0&(IL18|(IL12|IFNg)))&!(Th1&(IL4|(TGFb|(IL10|(Treg|(Th2|(IL12&(IL23|IL17))))))))) -Th17, ((Th0&(IL23|(IL6|IL1b)))&!(Th17&(IL12|(TGFb|(Treg|(IFNg|IL4)))))) -Th17_M, ((Th0_M&((PGN|(LPS|MDP))&((IL6&IL1b)|(IL23|IL2))))|Th17_M) -Th2, ((Th0&(((Th2&IL4)&!Th2upregulation)|(((IL18&IL4)&!IL12)|IL10)))&!(Th2&(TGFb|(Treg|IFNg)))) -Th2upregulation, (Th2&IL4) -Treg, ((Th0&(TGFb|TLR2))&!(Treg&(IL22|(IL23|(TNFa|(IL21|(IL6|Th17))))))) diff --git a/test/[var_60]__[id_085]__[T-LGL-SIGNALING-2008].bnet b/test/[var_60]__[id_085]__[T-LGL-SIGNALING-2008].bnet deleted file mode 100644 index 5c002103..00000000 --- a/test/[var_60]__[id_085]__[T-LGL-SIGNALING-2008].bnet +++ /dev/null @@ -1,58 +0,0 @@ -targets, factors -A20, (NFkB&!Apoptosis) -Apoptosis, ((!Caspase&Apoptosis)|Caspase) -BID, ((!BclxL&(!GZMB&(Caspase&(!MCL1&!Apoptosis))))|(!BclxL&(GZMB&(!MCL1&!Apoptosis)))) -BclxL, ((!GZMB&(!NFkB&(!BID&(!DISC&(STAT3&!Apoptosis)))))|(!GZMB&(NFkB&(!BID&(!DISC&!Apoptosis))))) -CD45, CD45 -CREB, (IFNg&(ERK&!Apoptosis)) -CTLA4, (TCR&!Apoptosis) -Caspase, ((!GZMB&(!IAP&(!BID&(DISC&!Apoptosis))))|((!GZMB&(!IAP&(BID&(!DISC&(TRADD&!Apoptosis)))))|((!GZMB&(!IAP&(BID&(DISC&!Apoptosis))))|((!GZMB&(IAP&(DISC&!Apoptosis)))|((GZMB&(!IAP&(!BID&(DISC&!Apoptosis))))|((GZMB&(!IAP&(BID&!Apoptosis)))|(GZMB&(IAP&(DISC&!Apoptosis))))))))) -Ceramide, (Fas&(!S1P&!Apoptosis)) -DISC, ((FasT&(!FLIP&(!Ceramide&(Fas&!Apoptosis))))|((FasT&(!FLIP&(Ceramide&!Apoptosis)))|((FasT&(FLIP&(!Ceramide&(Fas&(IL2&!Apoptosis)))))|(FasT&(FLIP&(Ceramide&!Apoptosis)))))) -ERK, (PI3K&(MEK&!Apoptosis)) -FLIP, ((!IFNg&(NFkB&(!DISC&!Apoptosis)))|((IFNg&(!NFkB&(CREB&(!DISC&!Apoptosis))))|(IFNg&(NFkB&(!DISC&!Apoptosis))))) -FYN, ((!IL2RB&(TCR&!Apoptosis))|(IL2RB&!Apoptosis)) -Fas, (FasT&(FasL&(!sFas&!Apoptosis))) -FasL, ((!NFAT&(!NFkB&(!ERK&(STAT3&!Apoptosis))))|((!NFAT&(!NFkB&(ERK&!Apoptosis)))|((!NFAT&(NFkB&!Apoptosis))|(NFAT&!Apoptosis)))) -FasT, (NFkB&!Apoptosis) -GAP, ((!PDGFR&(RAS&(!IL2&(!Apoptosis&!IL15))))|((PDGFR&(!GAP&(RAS&(!IL2&(!Apoptosis&!IL15)))))|(PDGFR&(GAP&(!IL2&(!Apoptosis&!IL15)))))) -GPCR, (S1P&!Apoptosis) -GRB2, ((!ZAP70&(IL2RB&!Apoptosis))|(ZAP70&!Apoptosis)) -GZMB, ((!IFNg&(Tbet&!Apoptosis))|((IFNg&(!CREB&(Tbet&!Apoptosis)))|(IFNg&(CREB&!Apoptosis)))) -IAP, (NFkB&(!BID&!Apoptosis)) -IFNg, ((IFNgT&(!SMAD&(!P2&(!IL2&(!Apoptosis&(!Stimuli&IL15))))))|((IFNgT&(!SMAD&(!P2&(!IL2&(!Apoptosis&Stimuli)))))|(IFNgT&(!SMAD&(!P2&(IL2&!Apoptosis)))))) -IFNgT, ((!NFAT&(!Tbet&(STAT3&!Apoptosis)))|((!NFAT&(Tbet&!Apoptosis))|(NFAT&!Apoptosis))) -IL15, IL15 -IL2, ((!NFAT&(!NFkB&(!Tbet&(STAT3&!Apoptosis))))|((!NFAT&(NFkB&(!Tbet&!Apoptosis)))|(NFAT&(!Tbet&!Apoptosis)))) -IL2RA, (!IL2RA&(IL2RAT&(IL2&!Apoptosis))) -IL2RAT, ((!NFkB&(STAT3&(IL2&!Apoptosis)))|(NFkB&(IL2&!Apoptosis))) -IL2RB, ((IL2RBT&(!IL2&(!Apoptosis&IL15)))|(IL2RBT&(IL2&!Apoptosis))) -IL2RBT, (ERK&(Tbet&!Apoptosis)) -JAK, ((!IFNg&(!IL2RB&(!IL2RA&(RANTES&(!SOCS&(!Apoptosis&!CD45))))))|((!IFNg&(!IL2RB&(IL2RA&(!SOCS&(!Apoptosis&!CD45)))))|((!IFNg&(IL2RB&(!SOCS&(!Apoptosis&!CD45))))|(IFNg&(!SOCS&(!Apoptosis&!CD45)))))) -LCK, ((!ZAP70&(!IL2RB&(!TCR&(!Apoptosis&CD45))))|((!ZAP70&(!IL2RB&(TCR&!Apoptosis)))|((!ZAP70&(IL2RB&!Apoptosis))|(ZAP70&(!Apoptosis&CD45))))) -MCL1, (NFkB&(PI3K&(IL2RB&(STAT3&!Apoptosis)))) -MEK, (RAS&!Apoptosis) -NFAT, (PI3K&!Apoptosis) -NFkB, ((!TPL2&(!FLIP&(PI3K&!Apoptosis)))|((!TPL2&(FLIP&(!IAP&(PI3K&!Apoptosis))))|((!TPL2&(FLIP&(IAP&(!PI3K&(TRADD&!Apoptosis)))))|((!TPL2&(FLIP&(IAP&(PI3K&!Apoptosis))))|(TPL2&!Apoptosis))))) -P2, ((!IFNg&(P2&(!Apoptosis&!Stimuli2)))|(IFNg&(!Apoptosis&!Stimuli2))) -PDGF, PDGF -PDGFR, ((!S1P&(!Apoptosis&PDGF))|(S1P&!Apoptosis)) -PI3K, ((!PDGFR&(RAS&!Apoptosis))|(PDGFR&!Apoptosis)) -PLCG1, ((!PDGFR&(GRB2&!Apoptosis))|(PDGFR&!Apoptosis)) -RANTES, (NFkB&!Apoptosis) -RAS, ((!GAP&(!GRB2&(PLCG1&!Apoptosis)))|(!GAP&(GRB2&!Apoptosis))) -S1P, (!Ceramide&(SPHK1&!Apoptosis)) -SMAD, (GPCR&!Apoptosis) -SOCS, (!IL2&(JAK&(!Apoptosis&!IL15))) -SPHK1, (PDGFR&!Apoptosis) -STAT3, (JAK&!Apoptosis) -Stimuli, Stimuli -Stimuli2, Stimuli2 -TAX, TAX -TCR, (!CTLA4&(!Apoptosis&Stimuli)) -TNF, (NFkB&!Apoptosis) -TPL2, ((!TNF&(!Apoptosis&TAX))|((TNF&(!PI3K&(!Apoptosis&TAX)))|(TNF&(PI3K&!Apoptosis)))) -TRADD, (!IAP&(TNF&(!A20&!Apoptosis))) -Tbet, ((!Tbet&(JAK&!Apoptosis))|(Tbet&!Apoptosis)) -ZAP70, (LCK&(!FYN&!Apoptosis)) -sFas, (FasT&!Apoptosis) diff --git a/test/[var_61]__[id_014]__[T-LGL-SURVIVAL-NETWORK-2008].bnet b/test/[var_61]__[id_014]__[T-LGL-SURVIVAL-NETWORK-2008].bnet deleted file mode 100644 index 3f57a5d9..00000000 --- a/test/[var_61]__[id_014]__[T-LGL-SURVIVAL-NETWORK-2008].bnet +++ /dev/null @@ -1,59 +0,0 @@ -targets, factors -A20, (NFKB&!Apoptosis) -Apoptosis, (Caspase|Apoptosis) -BID, ((GZMB&!((BclxL|Apoptosis)|MCL1))|(Caspase&!((BclxL|Apoptosis)|MCL1))) -BclxL, ((NFKB&!(((BID|DISC)|Apoptosis)|GZMB))|(STAT3&!(((BID|DISC)|Apoptosis)|GZMB))) -CD45, CD45 -CREB, ((ERK&IFN)&!Apoptosis) -CTLA4, (TCR&!Apoptosis) -Caspase, ((((TRADD&BID)&!(IAP|Apoptosis))|((GZMB&BID)&!(IAP|Apoptosis)))|(DISC&!Apoptosis)) -Ceramide, (Fas&!(Apoptosis|S1P)) -DISC, ((FasT&(((Fas&IL2)|(Fas&!FLIP))|Ceramide))&!Apoptosis) -ERK, ((MEK&PI3K)&!Apoptosis) -FLIP, ((NFKB&!(Apoptosis|DISC))|((CREB&IFNG)&!(Apoptosis|DISC))) -FYN, ((IL2RB&!Apoptosis)|(TCR&!Apoptosis)) -Fas, ((FasT&FasL)&!(Apoptosis|sFas)) -FasL, ((((NFAT&!Apoptosis)|(NFKB&!Apoptosis))|(STAT3&!Apoptosis))|(ERK&!Apoptosis)) -FasT, (NFKB&!Apoptosis) -GAP, (((PDGFR&GAP)&!((IL2|IL15)|Apoptosis))|(RAS&!((IL2|IL15)|Apoptosis))) -GPCR, (S1P&!Apoptosis) -GRB2, ((ZAP70&!Apoptosis)|(IL2RB&!Apoptosis)) -GZMB, ((TBET&!Apoptosis)|((CREB&IFNG)&!Apoptosis)) -IAP, (NFKB&!(BID|Apoptosis)) -IFN, IFN -IFNG, ((((IL15&IFNGT)&!((SMAD|Apoptosis)|P2))|((Stimuli&IFNGT)&!((SMAD|Apoptosis)|P2)))|((IL2&IFNGT)&!((SMAD|Apoptosis)|P2))) -IFNGT, (((NFAT&!Apoptosis)|(TBET&!Apoptosis))|(STAT3&!Apoptosis)) -IL15, IL15 -IL2, (((STAT3&!(TBET|Apoptosis))|(NFAT&!(TBET|Apoptosis)))|(NFKB&!(TBET|Apoptosis))) -IL2RA, ((IL2&IL2RAT)&!(IL2RA|Apoptosis)) -IL2RAT, ((IL2&(NFKB|STAT3))&!Apoptosis) -IL2RB, ((IL2RBT&(IL2|IL15))&!Apoptosis) -IL2RBT, ((ERK&TBET)&!Apoptosis) -JAK, ((((IL2RA&!((SOCS|Apoptosis)|CD45))|(IFNG&!((SOCS|Apoptosis)|CD45)))|(IL2RB&!((SOCS|Apoptosis)|CD45)))|(RANTES&!((SOCS|Apoptosis)|CD45))) -LCK, (((IL2RB&!(ZAP70|Apoptosis))|(TCR&!(ZAP70|Apoptosis)))|(CD45&!Apoptosis)) -MCL1, ((IL2RB&((PI3K&NFKB)&STAT3))&!Apoptosis) -MEK, (RAS&!Apoptosis) -NFAT, (PI3K&!Apoptosis) -NFKB, (((TPL2&!Apoptosis)|(PI3K&!Apoptosis))|((FLIP&(TRADD&IAP))&!Apoptosis)) -P2, ((IFNG&!(Stimuli2|Apoptosis))|(P2&!(Stimuli2|Apoptosis))) -PDGF, PDGF -PDGFR, ((S1P&!Apoptosis)|(PDGF&!Apoptosis)) -PI3K, ((PDGFR&!Apoptosis)|(RAS&!Apoptosis)) -PLCG1, ((PDGFR&!Apoptosis)|(GRB2&!Apoptosis)) -RANTES, (NFKB&!Apoptosis) -RAS, ((PLCG1&!(Apoptosis|GAP))|(GRB2&!(Apoptosis|GAP))) -S1P, (SPHK1&!(Apoptosis|Ceramide)) -SMAD, (GPCR&!Apoptosis) -SOCS, (JAK&!((IL15|IL2)|Apoptosis)) -SPHK1, (PDGFR&!Apoptosis) -STAT3, (JAK&!Apoptosis) -Stimuli, Stimuli -Stimuli2, Stimuli2 -TAX, TAX -TBET, ((JAK&!Apoptosis)|(TBET&!Apoptosis)) -TCR, (Stimuli&!(CTLA4|Apoptosis)) -TNF, (NFKB&!Apoptosis) -TPL2, (((PI3K&TNF)&!Apoptosis)|(TAX&!Apoptosis)) -TRADD, (TNF&!((IAP|A20)|Apoptosis)) -ZAP70, (LCK&!(Apoptosis|FYN)) -sFas, (FasT&!Apoptosis) diff --git a/test/[var_62]__[id_145]__[MELANOGENESIS].bnet b/test/[var_62]__[id_145]__[MELANOGENESIS].bnet deleted file mode 100644 index dc1ef385..00000000 --- a/test/[var_62]__[id_145]__[MELANOGENESIS].bnet +++ /dev/null @@ -1,53 +0,0 @@ -targets, factors -AC, MC1R -ASK1, (UVB&(!Akt&!Melanin)) -ASK1_m, !Akt_m -Akt, PDK1 -Akt_m, PDK1_m -COX_2, (!GSK3b&(b_catenin|(NFAT|p38))) -CREB, (PKA|(Akt_m|MSK)) -EGFR, (UVB&!Melanin) -EP4, PGE2 -ERK, (MEK&!p38) -ERK_m, (MEK_m&!p38_m) -ETR, ET_1 -ET_1, (IL_1|P53) -GSK3b, !Akt -GSK3b_m, !Akt_m -IL_1, (UVB&!Melanin) -MC1R, a_MSH -MDM2, Akt -MEK, Raf -MEK_m, Raf_m -MITFmRNA, (b_catenin_m&CREB) -MITFprotein, (ERK_m&MITFmRNA) -MKK6, ASK1 -MKK6_m, ASK1_m -MSK, (p38_m|ERK_m) -Melanin, MITFprotein -NFAT, !GSK3b -P53, (!MDM2&(ERK|p38)) -PDE, PKA -PDK1, (PI3K&!PTEN) -PDK1_m, PI3K_m -PGE2, (COX_2|IL_1) -PI3K, EGFR -PI3K_m, ((PKC|Ras_m)&!cAMP) -PKA, cAMP -PKC, ETR -PTEN, ((Melanin&(!Akt&!ERK))|(!Melanin&(!UVB&(!Akt&!ERK)))) -Raf, (Ras&!Akt) -Raf_m, (PKC|Ras_m) -Ras, SG -Ras_m, (SG_m|cAMP) -SCF, (IL_1|P53) -SG, (EGFR&!ERK) -SG_m, (c_Kit&!ERK_m) -UVB, UVB -a_MSH, P53 -b_catenin, !GSK3b -b_catenin_m, !GSK3b_m -cAMP, (!PDE&(EP4|AC)) -c_Kit, SCF -p38, MKK6 -p38_m, MKK6_m diff --git a/test/[var_66]__[id_077]__[SIGNALING-PATHWAY-FOR-BUTHANOL-PRODUCTION].bnet b/test/[var_66]__[id_077]__[SIGNALING-PATHWAY-FOR-BUTHANOL-PRODUCTION].bnet deleted file mode 100644 index 0d999101..00000000 --- a/test/[var_66]__[id_077]__[SIGNALING-PATHWAY-FOR-BUTHANOL-PRODUCTION].bnet +++ /dev/null @@ -1,58 +0,0 @@ -targets, factors -n3_hydroxybutyryl_CoA, ((hbd|acetoacetyl_CoA)|crt) -EtfAB, NADH -NADH, NADH -NAD_P_H, NAD_P_H -PTS, PTS -Rnf, Rnf -acetaldehyde, (ald|acetyl_CoA) -acetate, ((ack|(glucose___PTS&acetone))|(pta&acetone)) -acetoacetate, ((acetoacetyl_CoA|ctfA)|ctfB) -acetoacetyl_CoA, (((acetyl_CoA|hbd)|ctfB)|thlA) -acetone, ((adc&!sporulation)|(acetoacetate&!sporulation)) -acetyl_CoA, (((thlA|pyruvate)|(acetate&acetoacetyl_CoA))|pfo) -ack, !(spo0A_p|sporulation) -adc, spo0A_p -adhA, spo0A_p -adhB, spo0A_p -ald, (sigK|spo0A_p) -bcd, !(spo0A_p|sporulation) -bdhAB, spo0A_p -buk1, !(spo0A_p|sporulation) -butanal, ((butyryl_CoA|bdhAB)|ald) -butanol, (((((bdhAB&!sporulation)|(adhB&!sporulation))|(NAD_P_H&!sporulation))|(butanal&!sporulation))|(adhA&!sporulation)) -butyrate, (((buk1&!butyrate)|(ptb&!butyrate))|(glucose___PTS&!butyrate)) -butyryl_CoA, ((((bcd|(butyrate&acetoacetyl_CoA))|ald)|EtfAB)|crotonoyl_CoA) -cell_membrane, ((butyrate&!(acetone|ethanol))|(glucose&!((butanol|acetone)|ethanol))) -crotonoyl_CoA, ((crt|ferredoxin)|n3_hydroxybutyryl_CoA) -crt, !(sporulation|spo0A_p) -ctfA, spo0A_p -ctfB, spo0A_p -ethanol, (((adhA&!(ald|sporulation))|(acetaldehyde&!(ald|sporulation)))|(adhB&!(ald|sporulation))) -fba, fba -ferredoxin, Rnf -gap_pgk_tpi_pgm__X276_23705_eno, gap_pgk_tpi_pgm__X276_23705_eno -glucose, glucose -glucose___PTS, (((PTS&(cell_membrane&glucose))&!(sporulation&!cell_membrane))|((glucose&(cell_membrane&PTS))&!(sporulation&!cell_membrane))) -hbd, !(sporulation|spo0A_p) -pfk, pfk -pfo, pfo -pgi, pgi -phosphorylation, phosphorylation -pta, !(spo0A_p|sporulation) -ptb, !(sporulation|spo0A_p) -pyk, pfk -pyruvate, ((((fba|pgi)|glucose___PTS)|pyk)|gap_pgk_tpi_pgm__X276_23705_eno) -sigA, sigA -sigE, (sigF|spo0A_p) -sigF, ((spoIIE&!(spoIIAB&!spoIIE))|(sigH&!(spoIIAB&!spoIIE))) -sigG, sigE -sigH, sigA -sigK, sigG -spo0A, (sigK|spo0A_p) -spo0A_p, ((((spo0A&phosphorylation)&!sporulation)|((sigA&(spo0A&phosphorylation))&!sporulation))|((phosphorylation&spo0A)&!sporulation)) -spoIIAA, (spoIIE|(spo0A_p&sigH)) -spoIIAB, ((spo0A_p&sigH)&!(spoIIAA&spoIIE)) -spoIIE, spoIIE -sporulation, (((((spo0A_p&!cell_membrane)|(sigE&(sigA&!cell_membrane)))|(sigG&(sigA&!cell_membrane)))|(sigH&!cell_membrane))|(sigK&(!cell_membrane&sigA))) -thlA, spo0A_p diff --git a/test/[var_70]__[id_051]__[COLITIS-ASSOCIATED-COLON-CANCER].bnet b/test/[var_70]__[id_051]__[COLITIS-ASSOCIATED-COLON-CANCER].bnet deleted file mode 100644 index d2408ead..00000000 --- a/test/[var_70]__[id_051]__[COLITIS-ASSOCIATED-COLON-CANCER].bnet +++ /dev/null @@ -1,67 +0,0 @@ -targets, factors -AKT, (PI3K&!(CASP3|PP2A)) -APC, APC -ASK1, (ROS&!P21) -ATM, ROS -BAX, (((TBID&PP2A)&!AKT)|((P53&PP2A)&!AKT)) -BCATENIN, !(APC&GSK3B) -BCL2, ((STAT3&!(PP2A|P53))|(NFKB&!(PP2A|P53))) -CASP3, ((CASP8&!IAP)|(CASP9&!IAP)) -CASP8, (FADD_&!(CFLIP|P21)) -CASP9, (CYTC&!(IAP|P21)) -CCL2, NFKB -CERAMIDE, (SMASE&!SPHK1) -CFLIP, NFKB -COX2, (TNFR&S1P) -CTL, (IFNG&!TGFB) -CYTC, MOMP -DC, ((CCL2&!IL10)|(TNFA&!IL10)) -EP2, PGE2 -ERK, MEK -FADD_, (FAS|TNFR) -FAS, CTL -GP130, IL6 -GSK3B, !(AKT|EP2) -IAP, ((NFKB&!SMAC)|(STAT3&!SMAC)) -IFNG, (CTL|TH1) -IKB, !IKK -IKK, (AKT|(TNFR&S1P)) -IL10, (TREG|TH2) -IL12, (DC|MAC) -IL4, (DC|TH2) -IL6, ((MAC|DC)|NFKB) -JAK, (GP130&!SOCS) -JNK, (MEKK1|ASK1) -JUN, (((BCATENIN&JNK)&!GSK3B)|((ERK&JNK)&!GSK3B)) -MAC, ((CCL2&!IL10)|(IFNG&!IL10)) -MDM2, ((P53&AKT)&!(ATM|GSK3B)) -MEK, (RAF|ROS) -MEKK1, ((TNFR|TGFR)|CERAMIDE) -MOMP, (((TBID&!BCL2)|(BAX&!BCL2))|(CERAMIDE&!BCL2)) -NFKB, !IKB -P21, ((SMAD&!(GSK3B|CASP3))|(P53&!(GSK3B|CASP3))) -P53, (((ATM&!MDM2)|(JNK&!MDM2))|(PTEN&!MDM2)) -PGE2, COX2 -PI3K, ((EP2&!PTEN)|(RAS&!PTEN)) -PP2A, (CERAMIDE&!AKT) -PTEN, (P53&!(NFKB|JUN)) -RAF, (CERAMIDE|RAS) -RAS, (EP2|GP130) -ROS, (TNFR&!SOD) -S1P, SPHK1 -SMAC, MOMP -SMAD, (TGFR&!JUN) -SMAD7, (NFKB|SMAD) -SMASE, (FADD_|P53) -SOCS, STAT3 -SOD, (NFKB|STAT3) -SPHK1, (ERK|TNFR) -STAT3, JAK -TBID, (CASP8&!BCL2) -TGFB, TREG -TGFR, (TGFB&!SMAD7) -TH1, ((IFNG&!((TGFB|IL4)|IL10))|(IL12&!((TGFB|IL4)|IL10))) -TH2, (IL4&!(IFNG|TGFB)) -TNFA, MAC -TNFR, TNFA -TREG, ((DC&!IL6)|(IL10&!IL6)) diff --git a/test/[var_86]__[id_019]__[IL-6-SIGNALING].bnet b/test/[var_86]__[id_019]__[IL-6-SIGNALING].bnet deleted file mode 100644 index 9af3e689..00000000 --- a/test/[var_86]__[id_019]__[IL-6-SIGNALING].bnet +++ /dev/null @@ -1,56 +0,0 @@ -targets, factors -ca, ip3 -cam_ca, ca -camk24, cam_ca -cyt_ptpe, cyt_ptpe -dum_gab1_kin_or_jak1_gab1_mem_p, (jak1|gab1_kin) -dum_gp80_a_il6rc, (gp80s_a|gp80m_a) -dum_il6rc_p_or_grb2_vav, (grb2_sos|il6rc_p) -dum_mtorc1_or_pkcd_stat3_ta, (mtorc1|pkcd) -erk12, mek1 -gab1_kin, gab1_kin -gab1_mem, (grb2_sos|(erk12&pip3)) -gab1_mem_p, (gab1_mem&dum_gab1_kin_or_jak1_gab1_mem_p) -gp130m, gp130m -gp130s, (!(camk24|mk2)|!(mk2|camk24)) -gp80m_a, il6 -gp80s_a, (il6&!gp130s) -grb2_sos, (il6rc_p|shp2) -il6, il6 -il6rc, (gp130m&dum_gp80_a_il6rc) -il6rc_p, ((il6rc&jak1)&!(shp2_a|shp2)) -ip3, plcg -jak1, (!(((shp2_a|socs1)|socs3)|shp2)|!(((socs3|shp2)|shp2_a)|socs1)) -mek1, raf1 -mek4, mekk1 -mek6, il6rc_p -mekk1, rac1 -mk2, p38 -mtor, mtor -mtorc1, mtor -nfkb, nfkb -p38, mek6 -pdk1, pdk1 -phlpp, phlpp -pi3k, (ras|(gab1_mem_p&!shp2_a)) -pias1, pias1 -pias3, pias3 -pip3, (pi3k&!pten) -pkcd, mek4 -plcg, gab1_mem_p -pten, pten -rac1, vav -raf1, ras -ras, (grb2_sos&!ras_gap) -ras_gap, (gab1_mem_p&!shp2_a) -ros, ros -ship, ship -shp2, ((il6rc_p&jak1)&!((socs3|sirp1a)|ros)) -shp2_a, ((gab1_mem_p&shp2)&!(sirp1a|ros)) -sirp1a, sirp1a -slim, slim -socs1, stat3_ta -socs3, (((erk12|nfkb)|stat3_ta)|p38) -stat3_py, ((il6rc_p&jak1)&!((cyt_ptpe|shp2)|shp2_a)) -stat3_ta, ((dum_mtorc1_or_pkcd_stat3_ta&stat3_py)&!(slim|pias3)) -vav, (dum_il6rc_p_or_grb2_vav&!socs1) diff --git a/test/ascidian_embryo_validation.bnet b/test/ascidian_embryo_validation.bnet deleted file mode 100644 index c9c2571c..00000000 --- a/test/ascidian_embryo_validation.bnet +++ /dev/null @@ -1,48 +0,0 @@ -targets, factors -nErk_signaling, (nFgf8_17_18&nFgf9_16_20)|(!nEfna_d) -nFoxc, (nErk_signaling&nFoxa_a&nDlx_b&nDmrt_a&nOtx&nSox1_2_3&nSox4_11_12)|(!nErk_signaling&!nFoxc&!nNodal) -nId, (nErk_signaling&nDlk&nNeurog&nNodal)|(!nId&!nTfap2_r_b) -nLhx3_4, (nErk_signaling&nCtnnb&nFoxa_a&nFoxd&nZic_r_b) -nMesp, (nErk_signaling&nLhx3_4&nTbx6_r_b)|(!nMesp) -nMrf, (nDlk&nNodal&nTbx6_r_b&nZic_r_b)|(!nErk_signaling&!nMrf) -nMsx, (nErk_signaling&nNodal&nOtx&nSox1_2_3&nTbx2_3)|(!nFoxa_a) -nNodal, (nErk_signaling&nSox1_2_3&nZic_r_a)|(!nAdmp&!nFoxa_a&!nFoxd&!nGdf1_3_r&!nNodal&!nSox4_11_12&!nWnttun5) -nOtx, (nErk_signaling&nFoxa_a&nGata_a&nSox1_2_3&nZic_r_a)|(!nAdmp&!nFoxd&!nGdf1_3_r&!nOtx&!nWnttun5) -nPax3_7, (nErk_signaling&nNodal)|(!nFoxa_a&!nPax3_7) -nPax6, (nErk_signaling&nDlk&nFoxa_a&nFoxd&nNodal&nZic_r_b)|(!nFoxb&!nPax6&!nSox4_11_12) -nTfap2_r_b, (nGata_a)|(!nErk_signaling&!nCtnnb) -nTwist_r_a_b, (nErk_signaling&nFoxa_a&nFoxd&nHand_r&nNodal&nOtx&nZic_r_b)|(!nFoxd) -nZic_r_b, (nErk_signaling&nCtnnb&nDlx_b&nFoxa_a&nFoxd&nGata_a&nSox1_2_3&nTbx6_r_b&nTp53_a&nTp53_b&nWnt5)|(!nCtnnb&!nFoxc&!nHes_a&!nPrdm1_r_a&!nPrdm1_r_b&!nZic_r_b) -nFgf8_17_18, (nAdmp&nErk_signaling&nFoxd&nNeurog&nNodal)|(!nDlk&!nErk_signaling&!nFoxb&!nNeurog&!nSnai&!nSox4_11_12) -nFgf9_16_20, (nCtnnb&nFoxd)|(!nErk_signaling&!nNodal&!nPem1) -nFoxa_a, (nCtnnb&nFoxd)|(!nHes_a&!nPem1&!nPrdm1_r_a&!nSnai) -nBrachyury, (nFoxa_a&nDlk&nErk_signaling&nFoxd&nTp53_a&nTp53_b&nZic_r_b)|(!nBrachyury&!nSnai) -nDlk, (nFoxa_a&nErk_signaling&nFoxd&nNeurog&nNodal&nZic_r_b)|(!nFoxa_a&!nDlk&!nSox4_11_12) -nDmrt_a, (nFoxa_a&nErk_signaling&nSox4_11_12)|(!nDmrt_a&!nFoxd) -nFoxb, (nFoxa_a&nFoxd)|(!nDlk&!nErk_signaling&!nFoxb&!nPem1) -nAdmp, (nZic_r_a)|(!nAdmp&!nPem1) -nTbx2_3, (nAdmp&nBmp2_4)|(!nTbx2_3) -nBmp2_4, (!nBmp2_4) -nCtnnb, nCtnnb -nEfna_d, (nDlk&nGata_a&nPrdm1_r_a&nPrdm1_r_b&nSnai)|(!nCtnnb&!nZic_r_b) -nFoxd, (nCtnnb&nTwist_r_a_b)|(!nFoxd) -nTbx6_r_b, (nCtnnb&nMrf&nNodal&nZic_r_a&nZic_r_b)|(!nTbx6_r_b) -nNeurog, (nDlk&nFoxd&nNodal&nZic_r_b)|(!nNeurog&!nSox4_11_12) -nDlx_b, (nSox1_2_3)|(!nDlx_b&!nFoxd) -nHand_r, (nFoxa_a&nFoxd&nNodal)|(!nHand_r) -nPrdm1_r_a, (!nFoxd&!nPrdm1_r_a) -nPrdm1_r_b, (!nFoxd&!nPrdm1_r_a) -nWnt5, (nFoxd&nZic_r_a&nZic_r_b)|(!nWnt5) -nGata_a, nGata_a -nGdf1_3_r, nGdf1_3_r -nHes_a, nHes_a -nLefty, (nNodal&nZic_r_a)|(!nLefty) -nLmx1, (nMsx&nNodal&nZic_r_b)|(!nLmx1) -nSnai, (nNeurog&nNodal&nTbx6_r_b&nZic_r_a&nZic_r_b)|(!nSnai&!nSox4_11_12) -nPem1, nPem1 -nSox1_2_3, (!nPem1&!nSox1_2_3) -nSox4_11_12, nSox4_11_12 -nTp53_a, nTp53_a -nTp53_b, nTp53_b -nWnttun5, (nZic_r_a) -nZic_r_a, nZic_r_a diff --git a/test/flobak_2015.bnet b/test/flobak_2015.bnet deleted file mode 100644 index 5b68cc68..00000000 --- a/test/flobak_2015.bnet +++ /dev/null @@ -1,66 +0,0 @@ -targets, factors -betaTrCP, (Axin|GSK3|CK1) -DKK1gene, (TCF)&!(cMYC) -MLK3, (Rac) -Ras, (SOS|SHP2) -IRS1, !(S6K|ERK|IKKB) -PTEN, (PTENgene)&!(GSK3) -LRP, (Fz|ERK|JNK1|p38alpha)&!(DKK1) -betacatenin, (IKKA)&!(betaTrCP) -p53, (p38alpha)&!(MDM2) -PI3K, (GAB|IRS1|Ras) -GSK3, !(LRP|RSK|S6K|ERK|p38alpha|Dvl|AKT) -GRAP2, !(p38alpha) -MAP3K8, (IKKB) -RTPK, (RTPKgene|MMP)&!(p38alpha|MEK) -PDK1, (PI3K)&!(PTEN) -FOXO, !(AKT|NLK) -pras40, !(AKT) -Axin, !(LRP) -DUSP1, (p38alpha|MSK) -JNK1, (MKK7|MKK4)&!(DUSP1) -TSC2, (GSK3)&!(IKKB|AKT|RSK|ERK) -GAB, (GRB2)&!(ERK) -RSK, (ERK|PDK1) -DKK1, (DKK1gene) -DUSP6, (ERK|mTORC1) -MMP, (LEF) -MEK, (Raf|MAP3K8)&!(ERK) -SFRP1, (SFRP1gene) -TCF, (betacatenin)&!(NLK) -mTORC2, (TSC2)&!(S6K) -mTORC1, (Rheb|RSK)&!(pras40) -ERK, (MEK)&!(DUSP6) -MKK3, (ASK1|TAK1) -MKK4, (MEKK4|MLK3|TAK1|GRAP2) -SHC1, (RTPK)&!(PTEN) -CK1, !(LRP) -MDM2gene, (NFkB|p53) -NFkB, (IKKA|IKKB|MSK) -NLK, (TAK1) -MKK7, (TAK1|GRAP2) -SHP2, (GAB) -RTPKgene, (FOXO) -p38alpha, (MKK3|MKK4)&!(DUSP1) -TAK1, (TAB1) -Rheb, !(TSC2) -IKKA, (AKT) -IKKB, (TAK1)&!(p53) -MEKK4, (Rac) -Egr1, !(TCF) -PTENgene, (Egr1) -MSK, (ERK|p38alpha) -ASK1, !(AKT) -S6K, (PDK1|mTORC1) -AKT, (PDK1|mTORC2) -LEF, (betacatenin) -SFRP1gene, !(cMYC) -Fz, !(SFRP1) -Rac, (Dvl|mTORC2) -SOS, (GRB2)&!(ERK) -Raf, (Ras)&!(Rheb|AKT|ERK) -MDM2, (AKT|MDM2gene)&!(S6K) -cMYC, (TCF) -GRB2, (SHC1) -TAB1, !(p38alpha) -Dvl, (Fz) diff --git a/test/fumia_2013.bnet b/test/fumia_2013.bnet deleted file mode 100644 index 7689c20f..00000000 --- a/test/fumia_2013.bnet +++ /dev/null @@ -1,85 +0,0 @@ -targets, factors -TNFa, TNFa -eEF2, !(eEF2K) -Gli, Gli -Ras, (RTK)&!(NF1) -Miz_1, !(Myc_Max) -Myc_Max, (Myc|Max)&!(Smad_E2F|TGFb|MXI1) -p53, (HIF1|CHK1_2)&!(Mdm2|Bcl_2) -PI3K, (hTERT|Ras) -Myc, (NF_kB|TCF|Gli|FosJun|E2F|ERK_1_2)&!(HIF1) -p90RSK, (PDK1|ERK_1_2) -PDK1, (Myc_Max|PIP3|HIF1) -Smad_Miz_1, (Miz_1|Smad) -p14ARF, (Ras|E2F|Myc_Max) -Snail, (NF_kB|Smad_Miz_1)&!(GSK_3|p53) -eEF2K, (p90RSK|p70) -AMPK, (AMP_ATP|HIF1|ATM_ATR)&!(GFs) -Hypoxia, Hypoxia -Smad, (TGFb)&!(TNFa) -hTERT, (Myc_Max|NF1|HIF1|AKT|NF_kB)&!(Smad_Miz_1|p53|eEF2) -E2F_CyclinE, (E2F|CyclinE) -Smad_E2F, (Smad) -cdc20, (CyclinB)&!(cdh1) -Max, Max -RTK, (GFs) -p70, (mTOR|PDK1) -HIF1, (mTOR|Myc_Max|Hypoxia)&!(VHL|FOXO|p53|PHDs) -Rb, !(CyclinB|CyclinE|CyclinD|CyclinA|Mdm2) -p53_Mdm2, (Mdm2|p53) -TAK1, (TNFa) -E2F, (E2F)&!(Rb|CyclinA|CyclinB) -WNT, (Gli)&!(p53) -DNA_Damage, (ROS|Mutagen) -IKK, (TAK1|PKC|mTOR|AKT)&!(p53|PHDs) -AKT, (PDK1|PIP3) -ATM_ATR, (DNA_Damage) -GFs, GFs -RHEB, !(TSC1_2) -Mdm2, (AKT|p53)&!(ATM_ATR|p14ARF) -NF1, (PKC) -RAGS, (Nutrients)&!(Hypoxia) -CyclinE, (E2F)&!(CyclinA|Rb|p27|p21) -CyclinD, (Gli|NF_kB|TCF|FosJun|Myc_Max)&!(p21|GSK_3|p15|FOXO|p27) -PHDs, !(Hypoxia|ROS) -JNK, (TGFb) -PTEN, !(p53_PTEN) -Mutagen, Mutagen -NF_kB, (IKK|PIP3|Snail)&!(E_cadherin) -p15, (Smad_Miz_1|Miz_1) -mTOR, (RHEB|RAGS|AKT)&!(AMPK) -Dsh, (WNT) -FOXO, !(AKT) -PKC, (WNT|RTK) -p21, (p53|Smad_Miz_1|HIF1)&!(AKT|Myc_Max|hTERT) -p27, (Smad_Miz_1|HIF1)&!(Myc_Max|CyclinD|AKT|CyclinB|CyclinA) -GSK_3_APC, (GSK_3|APC) -TCF, (b_catenin)&!(TAK1) -TSC1_2, (AMPK|HIF1|p53)&!(RAF|AKT|ERK_1_2|p90RSK) -ROS, !(COX412|GSH) -PIP3, (PI3K)&!(PTEN) -CyclinA, (E2F_CyclinE|CyclinA|cdh1_UbcH10)&!(p27|cdc20|p21|Rb) -FosJun, (ERK_1_2|JNK) -CyclinB, !(p53|cdc20|cdh1|p27|p21) -COX412, (HIF1) -Bcl_2, (NF_kB)&!(p53|BAX|BAD) -cdh1, (cdc20)&!(CyclinA|CyclinB) -AMP_ATP, !(Nutrients) -GSK_3, !(mTOR|p90RSK|Dsh|AKT) -E_cadherin, !(NF_kB|Snail|Slug) -UbcH10, (CyclinB|CyclinA|UbcH10|cdc20)&!(cdh1) -b_catenin, !(GSK_3_APC|p53) -MXI1, (HIF1) -Nutrients, Nutrients -VHL, !(Hypoxia|ROS) -GSH, (NF_kB|p21|Myc_Max) -CHK1_2, (ATM_ATR) -BAD, !(p90RSK|HIF1|RAF|AKT) -Slug, (NF_kB|TCF)&!(p53_Mdm2) -ERK_1_2, (RAF) -APC, !(PTEN) -RAF, (Ras|PKC) -TGFb, (HIF1) -BAX, (JNK|p53)&!(HIF1|Bcl_2) -cdh1_UbcH10, (UbcH10|cdh1) -p53_PTEN, (p53|PTEN) diff --git a/test/steinway_2015.bnet b/test/steinway_2015.bnet deleted file mode 100644 index 03799be1..00000000 --- a/test/steinway_2015.bnet +++ /dev/null @@ -1,69 +0,0 @@ -targets, factors -GLI, (TCF_LEF)&!(SUFU) -RAS, (TCF_LEF|SRC|SOS_GRB2)&!(GSK3b) -NfkB, (IKKa) -RKIP, !(ERK|SNAI1) -bTrCP, !(Csn) -ILK, (SMAD) -LOXL23, (HIF1a) -IGF1R, (IGF1) -SHH, (GLI|SMAD) -TGFbR, (TGFb) -SOS_GRB2, (cMet|PDGFR|IGF1R|EGFR|FGFR|TGFbR)&!(ERK) -PI3K, (RAS) -HEY1, (CSL|SMAD) -SUFU, !(FUS) -E_Cadherin, (b_Catenin_memb)&!(SNAI2|SNAI1|FOXC2|HEY1|TWIST1|ZEB1|ZEB2) -DSH, (Frizzled) -Jagged, (TCF_LEF|SMAD) -b_Catenin_nuc, !(SUFU|Dest_compl|E_Cadherin|b_Catenin_memb) -FGF, FGF -HGF, HGF -NOTCH, (Jagged|DELTA) -AXIN2, (TCF_LEF|AXIN2) -CHD1L, CHD1L -NOTCH_ic, (NOTCH) -MEK, (RAF)&!(RKIP) -ZEB2, (SNAI1|HIF1a|Goosecoid)&!(miR200) -ZEB1, (SNAI1|HIF1a|Goosecoid)&!(miR200) -SMO, !(PTCH) -Hypoxia, Hypoxia -CD44, (TCF_LEF) -Dest_compl, (GSK3b|AXIN2|b_Catenin_nuc) -ERK, (MEK) -FOXC2, (SNAI1|TWIST1|Goosecoid) -TCF_LEF, (b_Catenin_nuc) -SRC, (cMet|PDGFR|IGF1R|EGFR|FGFR) -DELTA, (RAS) -TWIST1, (TCF_LEF|SNAI1|NfkB|Goosecoid|HIF1a) -IKKa, (AKT) -PTCH, !(SHH) -EGFR, (EGF) -CDC42, (CHD1L|TGFbR) -miR200, !(SNAI1|ZEB1|ZEB2) -PAK1, (CDC42) -cMet, (HGF|CD44) -PDGFR, (PDGF) -b_Catenin_memb, (E_Cadherin)&!(b_Catenin_nuc) -Frizzled, (Wnt) -SMAD, (ERK|TGFbR|ZEB1)&!(ZEB2) -Wnt, (GLI) -CSL, (NOTCH_ic) -HIF1a, (Hypoxia) -Csn, (NfkB) -EGR1, (c_fos) -FUS, (SMO) -EGF, EGF -c_fos, (ERK) -AKT, (PI3K|ILK) -IGF1, IGF1 -Goosecoid, Goosecoid -FGFR, (FGF) -GSK3b, !(DSH|Csn|AKT|Dest_compl|ERK) -STAT, (SRC) -PDGF, PDGF -RAF, (RAS) -TGFb, (GLI|SNAI1|TWIST1|Goosecoid) -SNAI1, (GLI|LIV1|EGR1|CSL|LOXL23|Goosecoid|PAK1|SMAD)&!(GSK3b|bTrCP) -SNAI2, (b_Catenin_nuc|SNAI2|ERK|TWIST1) -LIV1, (STAT) From 686c1ed14f4380555f3948bdc6558fc14afbbf02 Mon Sep 17 00:00:00 2001 From: Samuel Pastva Date: Wed, 21 Jun 2023 13:11:03 +0200 Subject: [PATCH 11/12] Remove unnecessary copies from the simulation algorithm. --- nfvsmotifs/motif_avoidant.py | 19 ++++++------------- 1 file changed, 6 insertions(+), 13 deletions(-) diff --git a/nfvsmotifs/motif_avoidant.py b/nfvsmotifs/motif_avoidant.py index 6c5ea9bc..dc996939 100644 --- a/nfvsmotifs/motif_avoidant.py +++ b/nfvsmotifs/motif_avoidant.py @@ -164,16 +164,12 @@ def _preprocess_candidates( else: filtered_candidates = [] for i in range(max_iterations): - #print(f"Run inside mts - {i + 1}") - random.shuffle(variables) - #symbolic_candidates = state_list_to_bdd(candidates) - symbolic_candidates = deepcopy(candidates) + generator.shuffle(variables) + candidates_dnf = candidates.copy() filtered_candidates = [] for state in candidates: - #state_bdd = state_to_bdd(state) - #symbolic_candidates = symbolic_candidates & ~state_bdd - symbolic_candidates = remove_state_from_dnf(symbolic_candidates, state) + candidates_dnf = remove_state_from_dnf(candidates_dnf, state) simulation = state.copy() for var in variables: @@ -181,17 +177,14 @@ def _preprocess_candidates( assert step is not None simulation[var] = step - #if not function_is_true(symbolic_candidates, simulation): - if not dnf_function_is_true(symbolic_candidates, simulation): - #symbolic_candidates = symbolic_candidates | state_bdd - #symbolic_candidates = symbolic_candidates | state_to_bdd(simulation) - symbolic_candidates.append(simulation) + if not dnf_function_is_true(candidates_dnf, simulation): + candidates_dnf.append(simulation) filtered_candidates.append(simulation) if len(filtered_candidates) <= 1: break - candidates = deepcopy(filtered_candidates) + candidates = filtered_candidates return filtered_candidates From 4cfa3ca96caa9eaf9b630745a8dcc3b0fd5c0b1d Mon Sep 17 00:00:00 2001 From: Samuel Pastva Date: Wed, 21 Jun 2023 13:54:57 +0200 Subject: [PATCH 12/12] Add comment about the two simulation algorithms. --- nfvsmotifs/motif_avoidant.py | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/nfvsmotifs/motif_avoidant.py b/nfvsmotifs/motif_avoidant.py index dc996939..90dd1d8d 100644 --- a/nfvsmotifs/motif_avoidant.py +++ b/nfvsmotifs/motif_avoidant.py @@ -120,6 +120,11 @@ def _preprocess_candidates( # is randomized but deterministic. generator = random.Random(1234567890) + # Use stochastic simulation to prune the set of candidate states. + # We use different simulation approach depending on whether this space + # is a minimal trap or not. In previous work, this was shown to work + # well, but in the future we need to better document the resoning + # behind these two algorithms. if is_in_an_mts == False: # Copy is sufficient because we won't be modifying the states within the set. candidates_dnf = candidates.copy()