SH2_contact_projection.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "id": "869437d3-4566-4865-9bfd-8bb50b04d55e",
   "metadata": {},
   "outputs": [],
   "source": [
    "import pandas as pd"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "id": "3df82b70-c574-4e0e-8971-4b115166bf99",
   "metadata": {},
   "outputs": [],
   "source": [
    "cluster_dict = {1: [1, ['SOCS1|1', 'SOCS3|1', 'CISH|1', 'SOCS2|1']],\n",
    " 2: [2, ['SOCS6|1', 'SOCS7|1']],\n",
    " 3: [2, ['SOCS4|1', 'SOCS5|1']],\n",
    " 4: [3, ['CRKL|1', 'CRK|1']],\n",
    " 5: [3, ['BCAR3|1', 'SH2D3A|1', 'SH2D3C|1']],\n",
    " 6: [4, ['SH2B1|1', 'SH2B2|1', 'SH2B3|1']],\n",
    " 7: [5, ['SHC1|1', 'SHC2|1', 'SHC3|1', 'SHC4|1']],\n",
    " 8: [5, ['FER|1', 'FES|1']],\n",
    "9: [6, ['BLNK|1', 'SH2D6|1']],\n",
    "10:[6, ['CLNK|1', 'LCP2|1']],\n",
    " 11: [7, ['VAV1|1', 'VAV2|1', 'VAV3|1']],\n",
    "12: [8, ['GRB10|1', 'GRB14|1','GRB7|1']],\n",
    "13: [9, ['INPP5D|1', 'INPPL1|1']],\n",
    "14: [9, ['SH2D1A|1', 'SH2D1B|1']],\n",
    "15: [10, ['NCK1|1', 'NCK2|1']],\n",
    "16: [10, ['GRAP2|1', 'GRAPL|1', 'GRAP|1', 'GRB2|1']],\n",
    "17: [10, ['SH2D5|1']], \n",
    "18: [11, ['DAPP1']],\n",
    "19:[12, ['HSH2D|1', 'SH2D2A|1', 'SH2D7|1']],\n",
    "20: [12, ['SH2D4A|1', 'SH2D4B|1']],\n",
    "21: [13, ['SH3BP2|1']],\n",
    "22: [13, ['ABL1|1', 'ABL2|1']],\n",
    "23: [13, ['PTK6|1', 'SRMS|1']],\n",
    "24: [13, ['CSK|1', 'MATK|1']],\n",
    "25: [13, ['RASA1|1']],\n",
    "26: [14, ['ITK|1', 'TEC|1']],\n",
    "27: [14, ['BMX|1', 'BTK|1', 'TXK|1']],\n",
    "28: [15, ['RIN2|1', 'RIN3|1', 'RIN1|1']],\n",
    "29: [16, ['STAT1|1', 'STAT3|1', 'STAT4|1']],\n",
    "30: [16, ['STAT2|1']],\n",
    "31: [17, ['STAT6|1']],\n",
    "32: [18, ['TNS1|1', 'TNS2|1', 'TNS3|1', 'TNS4|1']],\n",
    "33: [19, ['CHN2|1', 'CHN1|1']],\n",
    "34: [20, ['JAK1|1', 'JAK2|1', 'JAK3|1','TYK2|1']],\n",
    "35: [21, ['STAT5B|1', 'STAT5A|1']],\n",
    " 36: [22, ['STAP2|1', 'STAP1|1']],\n",
    " 37: [23, ['SUPT6H|1']],\n",
    "38: [24, ['SLA2|1', 'SLA|1']],\n",
    "39: [24, ['BLK|1', 'FRK|1', 'HCK|1', 'LCK|1', 'LYN|1']],\n",
    " 40: [24, ['FGR|1', 'FYN|1', 'SRC|1', 'YES1|1']],\n",
    "41: [25, ['SHB|1', 'SHF|1']],\n",
    " 42: [25, ['SHE|1','SHD|1']],\n",
    " 43: [26, ['PTPN11|1', 'PTPN11|2']],\n",
    "44: [27, ['PTPN6|1', 'PTPN6|2']],\n",
    "45: [28, ['PLCG1|1', 'PLCG1|2']],\n",
    "46: [29, ['PLCG2|1', 'PLCG2|2']],\n",
    "47: [30, ['PIK3R1|1', 'PIK3R1|2']],\n",
    "48: [31, ['PIK3R2|1', 'PIK3R2|2']],\n",
    "49: [32, ['PIK3R3|1', 'PIK3R3|2']],\n",
    "50: [33, ['RASA1|1', 'RASA1|2']],\n",
    "51: [34, ['SYK|1', 'SYK|2']],\n",
    "52: [35, ['ZAP70|1', 'ZAP70|2']]}"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "id": "267d8259-04e0-4f11-bd6b-9c002b759516",
   "metadata": {},
   "outputs": [],
   "source": [
    "uniprot_ref = 'SH2_IPR000980_uniprot_reference.csv'\n",
    "df_ref = pd.read_csv(uniprot_ref)\n",
    "identical_arch_groups = []\n",
    "for i in cluster_dict:\n",
    "    arch_arr = []\n",
    "    for j in cluster_dict[i][1]:\n",
    "        gene = (j.split('|')[0])\n",
    "        arch = df_ref.loc[df_ref['Gene']==gene, ['Interpro Domain Architecture']].values[0][0]\n",
    "        arch_arr.append(arch)\n",
    "    cluster_dict[i][1].append(set(arch_arr))\n",
    "    if len(set(arch_arr)) == 1:\n",
    "        identical_arch_groups.append(i)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "9ea8b812-5eca-4dd1-bcdf-befe17ee9030",
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "id": "780b3b9f-0671-4498-a24f-35b5c806a350",
   "metadata": {},
   "outputs": [],
   "source": [
    "contacting_domains = []\n",
    "for line in open('SH2_IPR000980_interDomain_Exp.feature'):\n",
    "    line = line.strip('\\n')\n",
    "    line = line.split('\\t')\n",
    "    if len(line) >2:\n",
    "        gene = line[1].split('|')[1]+'|'+line[1].split('|')[2]\n",
    "        gene_dom_pair = line[0]+':'+gene\n",
    "        if gene_dom_pair not in contacting_domains:\n",
    "            contacting_domains.append(gene_dom_pair)\n",
    "\n",
    "\n",
    "contacting_domains_af = []\n",
    "for line in open('SH2_IPR000980_interDomain_Alphafold.feature'):\n",
    "    line = line.strip('\\n')\n",
    "    line = line.split('\\t')\n",
    "    if len(line) > 2:\n",
    "        gene = line[1].split('|')[1]+'|'+line[1].split('|')[2]\n",
    "        gene_dom_pair = line[0]+':'+gene\n",
    "        if gene_dom_pair not in contacting_domains_af:\n",
    "            contacting_domains_af.append(gene_dom_pair)\n",
    "            "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "9681b613-6e9e-445d-bdb3-6043af289811",
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "id": "5ea95a92-e749-4969-bbbc-992d36d5d35e",
   "metadata": {},
   "outputs": [],
   "source": [
    "feafile_af = 'SH2_IPR000980_interDomain_Alphafold.feature'\n",
    "feafile_exp = 'SH2_IPR000980_interDomain_Exp.feature'\n",
    "dict_known_features_af = {}\n",
    "\n",
    "genes_with_features_af = []\n",
    "for line in open(feafile_af):\n",
    "    line = line.strip('\\n')\n",
    "    line = line.split('\\t')\n",
    "    if len(line) >2:\n",
    "        get_gene = line[1].split('|')[1]+'|'+line[1].split('|')[2]\n",
    "        if get_gene not in genes_with_features_af:\n",
    "            genes_with_features_af.append(get_gene)\n",
    "        \n",
    "genes_with_features_exp = []        \n",
    "for line in open(feafile_exp):\n",
    "    line = line.strip('\\n')\n",
    "    line = line.split('\\t')\n",
    "    if len(line)>2:\n",
    "        get_gene = line[1].split('|')[1]+'|'+line[1].split('|')[2]\n",
    "        if get_gene not in genes_with_features_exp:\n",
    "            genes_with_features_exp.append(get_gene)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "id": "a8fbfde3-8c80-4632-8efe-5b1325401625",
   "metadata": {},
   "outputs": [],
   "source": [
    "dict_known_features_af={}\n",
    "for known_pair in contacting_domains_af:    \n",
    "    feature_position_aln = []\n",
    "    for line in open(feafile_af):\n",
    "        line = line.strip('\\n')\n",
    "        line = line.split('\\t')            \n",
    "        if len(line)>2:\n",
    "            get_gene = line[1].split('|')[1]+'|'+line[1].split('|')[2]\n",
    "            gene_dom_pair = line[0]+':'+get_gene\n",
    "    \n",
    "            pair, gene = known_pair.split(':')\n",
    "          \n",
    "            if known_pair == gene_dom_pair:\n",
    "    \n",
    "                feature_position_aln.append(line[3])\n",
    "#             print(gene, pair, line[3])\n",
    "    feature_position_aln = [int(i) for i in feature_position_aln]\n",
    "    dict_known_features_af[known_pair] = feature_position_aln\n",
    "\n",
    "dict_known_features_exp={}\n",
    "for known_pair in contacting_domains:    \n",
    "    feature_position_aln = []\n",
    "    for line in open(feafile_exp):\n",
    "        line = line.strip('\\n')\n",
    "        line = line.split('\\t')            \n",
    "        if len(line)>2:\n",
    "            get_gene = line[1].split('|')[1]+'|'+line[1].split('|')[2]\n",
    "            gene_dom_pair = line[0]+':'+get_gene\n",
    "    \n",
    "            pair, gene = known_pair.split(':')\n",
    "          \n",
    "            if known_pair == gene_dom_pair:\n",
    "    \n",
    "                feature_position_aln.append(line[3])\n",
    "    #             print(gene, pair, line[3])\n",
    "    feature_position_aln = [int(i) for i in feature_position_aln]\n",
    "    dict_known_features_exp[known_pair] = feature_position_aln\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "id": "ce690a93-f59c-48e5-ab07-863b14aa1f06",
   "metadata": {},
   "outputs": [],
   "source": [
    "for i in cluster_dict:\n",
    "    fea_arr = []\n",
    "    for j in cluster_dict[i][1][:-1]:\n",
    "        if j in genes_with_features_exp :\n",
    "            fea_arr.append('E')\n",
    "        elif j in genes_with_features_af and j not in genes_with_features_exp:\n",
    "            fea_arr.append('A')\n",
    "        elif j not in genes_with_features_af and j not in genes_with_features_exp:\n",
    "            fea_arr.append(0)\n",
    "    (cluster_dict[i][1].append(fea_arr))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "id": "b87f2d2a-788e-460b-ba7f-23dcfa37f4a1",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[1, ['SOCS1|1', 'SOCS3|1', 'CISH|1', 'SOCS2|1', {'SH2|SOCS_box'}, ['A', 0, 'A', 'E']]] [0, 'E', 'A']\n",
      "[2, ['SOCS6|1', 'SOCS7|1', {'SH2|SOCS_box'}, [0, 'A']]] [0, 'A']\n",
      "[3, ['CRKL|1', 'CRK|1', {'SH2|SH3_domain|SH3_domain'}, ['E', 0]]] [0, 'E']\n",
      "[13, ['CSK|1', 'MATK|1', {'SH3_domain|SH2|Prot_kinase_dom'}, [0, 'A']]] [0, 'A']\n",
      "[24, ['BLK|1', 'FRK|1', 'HCK|1', 'LCK|1', 'LYN|1', {'SH3_domain|SH2|Prot_kinase_dom'}, [0, 0, 'A', 'A', 'A']]] [0, 'A']\n",
      "[28, ['PLCG1|1', 'PLCG1|2', {'PH_domain|EF_hand_dom|PLipase_C_PInositol-sp_X_dom|SH2|SH2|SH3_domain|PH_domain|PLipase_C_Pinositol-sp_Y|C2_dom'}, [0, 'A']]] [0, 'A']\n"
     ]
    }
   ],
   "source": [
    "for i in cluster_dict:\n",
    "    if i in identical_arch_groups:\n",
    "        availability_list = cluster_dict[i][1][-1]\n",
    "        if 0 in cluster_dict[i][1][-1]:\n",
    "            if list(set(availability_list)) != [0]:\n",
    "                print(cluster_dict[i], list(set(availability_list)))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "id": "b98beecb-9dbe-4879-a49d-61b7e683053b",
   "metadata": {},
   "outputs": [],
   "source": [
    "#use the feature positions of the aligned sequence and generate a feature for unaligned positions \n",
    "#For plcg1 we infer features from plgc1 to plcg2 for respective N/C sh2 domain that is available\n",
    "#infer features from syk to zap70 \n",
    "#we handle these tandems separately while interdomain inference"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 18,
   "id": "82fbfeae-84c4-4497-b6f2-65bc3ab8fd26",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "{1: [1,\n",
       "  ['SOCS1|1',\n",
       "   'SOCS3|1',\n",
       "   'CISH|1',\n",
       "   'SOCS2|1',\n",
       "   {'SH2|SOCS_box'},\n",
       "   ['A', 0, 'A', 'E']]],\n",
       " 2: [2, ['SOCS6|1', 'SOCS7|1', {'SH2|SOCS_box'}, [0, 'A']]],\n",
       " 3: [2, ['SOCS4|1', 'SOCS5|1', {'SOCS4/SOCS5_dom|SH2|SOCS_box'}, ['E', 'A']]],\n",
       " 4: [3, ['CRKL|1', 'CRK|1', {'SH2|SH3_domain|SH3_domain'}, ['E', 0]]],\n",
       " 5: [3,\n",
       "  ['BCAR3|1', 'SH2D3A|1', 'SH2D3C|1', {'SH2|RASGEF_cat_dom'}, [0, 0, 0]]],\n",
       " 6: [4,\n",
       "  ['SH2B1|1', 'SH2B2|1', 'SH2B3|1', {'Phe_ZIP|PH_domain|SH2'}, [0, 0, 0]]],\n",
       " 7: [5,\n",
       "  ['SHC1|1',\n",
       "   'SHC2|1',\n",
       "   'SHC3|1',\n",
       "   'SHC4|1',\n",
       "   {'PID_Shc-like|SH2'},\n",
       "   [0, 0, 0, 0]]],\n",
       " 8: [5,\n",
       "  ['FER|1',\n",
       "   'FES|1',\n",
       "   {'FCH_dom|Fer_F-BAR|SH2|Prot_kinase_dom', 'FCH_dom|SH2|Prot_kinase_dom'},\n",
       "   ['A', 'E']]],\n",
       " 9: [6, ['BLNK|1', 'SH2D6|1', {'SH2'}, [0, 0]]],\n",
       " 10: [6, ['CLNK|1', 'LCP2|1', {'SAM|SH2', 'SH2'}, [0, 0]]],\n",
       " 11: [7,\n",
       "  ['VAV1|1',\n",
       "   'VAV2|1',\n",
       "   'VAV3|1',\n",
       "   {'CH_dom|DH-domain|PH_domain|PE/DAG-bd|SH3_domain|SH2|SH3_domain'},\n",
       "   [0, 0, 0]]],\n",
       " 12: [8,\n",
       "  ['GRB10|1',\n",
       "   'GRB14|1',\n",
       "   'GRB7|1',\n",
       "   {'RA_dom|PH_domain|BPS-dom|SH2'},\n",
       "   ['A', 'A', 'A']]],\n",
       " 13: [9, ['INPP5D|1', 'INPPL1|1', {'SH2|IPPc', 'SH2|IPPc|SAM'}, [0, 0]]],\n",
       " 14: [9, ['SH2D1A|1', 'SH2D1B|1', {'SH2'}, [0, 0]]],\n",
       " 15: [10,\n",
       "  ['NCK1|1', 'NCK2|1', {'SH3_domain|SH3_domain|SH3_domain|SH2'}, [0, 0]]],\n",
       " 16: [10,\n",
       "  ['GRAP2|1',\n",
       "   'GRAPL|1',\n",
       "   'GRAP|1',\n",
       "   'GRB2|1',\n",
       "   {'SH3_domain|SH2', 'SH3_domain|SH2|SH3_domain'},\n",
       "   [0, 0, 0, 'E']]],\n",
       " 17: [10, ['SH2D5|1', {'PTB/PI_dom|SH2'}, ['A']]],\n",
       " 18: [11, ['DAPP1', {'SH2|PH_domain'}, [0]]],\n",
       " 19: [12, ['HSH2D|1', 'SH2D2A|1', 'SH2D7|1', {'SH2'}, [0, 0, 0]]],\n",
       " 20: [12, ['SH2D4A|1', 'SH2D4B|1', {'SH2'}, [0, 0]]],\n",
       " 21: [13, ['SH3BP2|1', {'PH_domain|SH2'}, [0]]],\n",
       " 22: [13,\n",
       "  ['ABL1|1',\n",
       "   'ABL2|1',\n",
       "   {'SH3_domain|SH2|Prot_kinase_dom|F-actin-binding'},\n",
       "   ['E', 'A']]],\n",
       " 23: [13, ['PTK6|1', 'SRMS|1', {'SH3_domain|SH2|Prot_kinase_dom'}, [0, 0]]],\n",
       " 24: [13, ['CSK|1', 'MATK|1', {'SH3_domain|SH2|Prot_kinase_dom'}, [0, 'A']]],\n",
       " 25: [13,\n",
       "  ['RASA1|1', {'SH2|SH3_domain|SH2|PH_domain|C2_dom|RasGAP_dom'}, [0]]],\n",
       " 26: [14,\n",
       "  ['ITK|1', 'TEC|1', {'PH_domain|SH3_domain|SH2|Prot_kinase_dom'}, [0, 0]]],\n",
       " 27: [14,\n",
       "  ['BMX|1',\n",
       "   'BTK|1',\n",
       "   'TXK|1',\n",
       "   {'PH_domain|SH2|Prot_kinase_dom',\n",
       "    'PH_domain|SH3_domain|SH2|Prot_kinase_dom',\n",
       "    'SH3_domain|SH2|Prot_kinase_dom'},\n",
       "   [0, 0, 0]]],\n",
       " 28: [15, ['RIN2|1', 'RIN3|1', 'RIN1|1', {'SH2|VPS9|RA_dom'}, [0, 0, 0]]],\n",
       " 29: [16,\n",
       "  ['STAT1|1',\n",
       "   'STAT3|1',\n",
       "   'STAT4|1',\n",
       "   {'STAT_TF_prot_interaction|STAT_TF_alpha|STAT_TF_DNA-bd|STAT_linker|SH2',\n",
       "    'STAT_TF_prot_interaction|STAT_TF_alpha|STAT_TF_DNA-bd|STAT_linker|SH2|STAT1_TAZ2-bd_C'},\n",
       "   ['E', 'E', 'A']]],\n",
       " 30: [16,\n",
       "  ['STAT2|1',\n",
       "   {'STAT_TF_prot_interaction|STAT_TF_alpha|STAT_TF_DNA-bd|STAT_linker|SH2|STAT2_C'},\n",
       "   ['E']]],\n",
       " 31: [17,\n",
       "  ['STAT6|1',\n",
       "   {'STAT_TF_prot_interaction|STAT_TF_alpha|STAT_TF_DNA-bd|STAT_linker|SH2|STAT6_C'},\n",
       "   ['E']]],\n",
       " 32: [18,\n",
       "  ['TNS1|1',\n",
       "   'TNS2|1',\n",
       "   'TNS3|1',\n",
       "   'TNS4|1',\n",
       "   {'PE/DAG-bd|Tensin_phosphatase|Tensin_C2-dom|SH2|PTB/PI_dom',\n",
       "    'PE/DAG-bd|Tyr_Pase_cat|Tensin_C2-dom|SH2|PTB/PI_dom',\n",
       "    'SH2|PTB/PI_dom',\n",
       "    'Tyr_Pase_dom|Tensin_C2-dom|SH2|PTB/PI_dom'},\n",
       "   [0, 0, 0, 0]]],\n",
       " 33: [19, ['CHN2|1', 'CHN1|1', {'SH2|PE/DAG-bd|RhoGAP_dom'}, ['E', 'E']]],\n",
       " 34: [20,\n",
       "  ['JAK1|1',\n",
       "   'JAK2|1',\n",
       "   'JAK3|1',\n",
       "   'TYK2|1',\n",
       "   {'FERM_domain|SH2|Prot_kinase_dom|Prot_kinase_dom'},\n",
       "   ['A', 'A', 'A', 'A']]],\n",
       " 35: [21,\n",
       "  ['STAT5B|1',\n",
       "   'STAT5A|1',\n",
       "   {'STAT_TF_prot_interaction|STAT_TF_alpha|STAT_TF_DNA-bd|STAT_linker|SH2'},\n",
       "   ['E', 'E']]],\n",
       " 36: [22, ['STAP2|1', 'STAP1|1', {'PH_domain|SH2', 'SH2'}, [0, 0]]],\n",
       " 37: [23,\n",
       "  ['SUPT6H|1',\n",
       "   {'Spt6_acidic_N_dom|Spt6_HTH_DNA-bd_dom|YqgF/RNaseH-like_dom|Spt6_HHH|HHH_9|S1_domain|SH2|Spt6_SH2_C'},\n",
       "   [0]]],\n",
       " 38: [24, ['SLA2|1', 'SLA|1', {'SH3_domain|SH2'}, ['E', 'A']]],\n",
       " 39: [24,\n",
       "  ['BLK|1',\n",
       "   'FRK|1',\n",
       "   'HCK|1',\n",
       "   'LCK|1',\n",
       "   'LYN|1',\n",
       "   {'SH3_domain|SH2|Prot_kinase_dom'},\n",
       "   [0, 0, 'A', 'A', 'A']]],\n",
       " 40: [24,\n",
       "  ['FGR|1',\n",
       "   'FYN|1',\n",
       "   'SRC|1',\n",
       "   'YES1|1',\n",
       "   {'SH3_domain|SH2|Prot_kinase_dom'},\n",
       "   ['A', 'A', 'E', 'A']]],\n",
       " 41: [25, ['SHB|1', 'SHF|1', {'SH2'}, [0, 0]]],\n",
       " 42: [25, ['SHE|1', 'SHD|1', {'SH2'}, [0, 0]]],\n",
       " 43: [26, ['PTPN11|1', 'PTPN11|2', {'SH2|SH2|PTP_cat'}, ['E', 'E']]],\n",
       " 44: [27, ['PTPN6|1', 'PTPN6|2', {'SH2|SH2|PTP_cat'}, ['E', 'E']]],\n",
       " 45: [28,\n",
       "  ['PLCG1|1',\n",
       "   'PLCG1|2',\n",
       "   {'PH_domain|EF_hand_dom|PLipase_C_PInositol-sp_X_dom|SH2|SH2|SH3_domain|PH_domain|PLipase_C_Pinositol-sp_Y|C2_dom'},\n",
       "   [0, 'A']]],\n",
       " 46: [29,\n",
       "  ['PLCG2|1',\n",
       "   'PLCG2|2',\n",
       "   {'PH_domain|PLipase_C_PInositol-sp_X_dom|SH2|SH2|SH3_domain|PH_domain|PLipase_C_Pinositol-sp_Y|C2_dom'},\n",
       "   [0, 0]]],\n",
       " 47: [30, ['PIK3R1|1', 'PIK3R1|2', {'SH3_domain|RhoGAP_dom|SH2|SH2'}, [0, 0]]],\n",
       " 48: [31, ['PIK3R2|1', 'PIK3R2|2', {'SH3_domain|RhoGAP_dom|SH2|SH2'}, [0, 0]]],\n",
       " 49: [32, ['PIK3R3|1', 'PIK3R3|2', {'SH2|SH2'}, [0, 0]]],\n",
       " 50: [33,\n",
       "  ['RASA1|1',\n",
       "   'RASA1|2',\n",
       "   {'SH2|SH3_domain|SH2|PH_domain|C2_dom|RasGAP_dom'},\n",
       "   [0, 0]]],\n",
       " 51: [34, ['SYK|1', 'SYK|2', {'SH2|SH2|Prot_kinase_dom'}, ['E', 'A']]],\n",
       " 52: [35, ['ZAP70|1', 'ZAP70|2', {'SH2|SH2|Prot_kinase_dom'}, [0, 0]]]}"
      ]
     },
     "execution_count": 18,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "cluster_dict"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "f7d8c01a-5841-4f7e-bef9-f0c8320c1923",
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
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