From 4381ccdb7b539c73af51c98386a7ef60f78617ab Mon Sep 17 00:00:00 2001 From: OganM Date: Wed, 9 Oct 2024 16:18:15 -0700 Subject: [PATCH] readme style fix --- README.md | 121 +++++++++++++++++++++++++++-------------------------- README.rmd | 2 +- 2 files changed, 62 insertions(+), 61 deletions(-) diff --git a/README.md b/README.md index 876ce45..0d017d9 100644 --- a/README.md +++ b/README.md @@ -1,5 +1,5 @@ -# ErmineR +# ErmineR This is an R wrapper for Pavlidis Lab’s [ermineJ](http://erminej.msl.ubc.ca/). A tool for gene set enrichment @@ -7,17 +7,16 @@ analysis with multifunctionality correction. # Table of Contents -- [Installation](#installation) -- [Usage](#usage) - - [Replicable go terms](#replicable-go-terms) - - [Annotations](#annotations) - - [Examples](#examples) - - [Use GSR with gene scores](#use-gsr-with-gene-scores) - - [Use Precision Recall with gene - scores](#use-precision-recall-with-gene-scores) - - [Use ORA with a hitlist](#use-ora-with-a-hitlist) - - [Using your own GO - annotations](#using-your-own-go-annotations) +- [Installation](#installation) +- [Usage](#usage) + - [Replicable go terms](#replicable-go-terms) + - [Annotations](#annotations) + - [Examples](#examples) + - [Use GSR with gene scores](#use-gsr-with-gene-scores) + - [Use Precision Recall with gene + scores](#use-precision-recall-with-gene-scores) + - [Use ORA with a hitlist](#use-ora-with-a-hitlist) + - [Using your own GO annotations](#using-your-own-go-annotations) ## Installation @@ -30,9 +29,8 @@ After java is installed you can install ermineR by doing devtools::install_github('PavlidisLab/ermineR') ``` -If ermineR cannot find your java home by itself. Either install -rJava or use `Sys.setenv(JAVA_HOME=javaHome)` to point ermineR to the -right path. +If ermineR cannot find your java home by itself. Either install rJava or +use `Sys.setenv(JAVA_HOME=javaHome)` to point ermineR to the right path. Some users report that the ermineJ executable loses its exection privilage after installation. If this happens you will get an error like @@ -65,11 +63,11 @@ may get different results when you repeat the experiment later. If you want to use a specific version of GO, ermineR provides functions to deal with that. -- `goToday`: Downloads the latest version of go to a path you provide -- `getGoDates`: Lists all dates where a go version is available, from - the most recent to oldest -- `goAtDate`: Given a valid date, downloads the Go version from a - specific date to a file path you provide +- `goToday`: Downloads the latest version of go to a path you provide +- `getGoDates`: Lists all dates where a go version is available, from + the most recent to oldest +- `goAtDate`: Given a valid date, downloads the Go version from a + specific date to a file path you provide To use a specific version of GO, make sure to set `geneSetDescription` argument of all ermineR functions to the file path where you saved the @@ -89,9 +87,10 @@ also generic annotation files available that contain all genes from a species. These are typically named something like “Generic_human”. You can manually download these annotation files from - or by using the `gemma.R::get_platform_annotations` -function. ErmineR typically uses “noParents” versions of these files -since parent terms are derived using the ontology file acquired from GO. + or by using the +`gemma.R::get_platform_annotations` function. ErmineR typically uses +“noParents” versions of these files since parent terms are derived using +the ontology file acquired from GO. ### Examples @@ -134,14 +133,14 @@ gsrOut = gsr(annotation = 'GPL96', head(gsrOut$results) %>% knitr::kable() ``` -| Name | ID | NumProbes | NumGenes | RawScore | Pval | CorrectedPvalue | MFPvalue | CorrectedMFPvalue | Multifunctionality | Same as | GeneMembers | -|:--------------------------------|:-------------|----------:|---------:|---------:|-------:|----------------:|---------:|------------------:|-------------------:|:--------|:----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------| -| protein folding | | 40 | 24 | 3.198073 | 0.0000 | 0.000000 | 0.0000 | 0.0000000 | 0.214 | NA | AIP\|CALR\|CCT5\|CCT6A\|CCT8L2\|CDC37L1\|CLGN\|CLPX\|DNAJB1\|DNAJB4\|GAK\|HSP90AA1\|HSPA1A\|HSPA9\|HSPB6\|HSPD1\|NUDC\|PFDN6\|PTGES3\|RUVBL2\|ST13\|TCP1\|TOR1A\|UGGT1\| | -| unfolded protein binding | | 52 | 29 | 3.299625 | 0.0000 | 0.000000 | 0.0000 | 0.0000000 | 0.258 | NA | AIP\|CALR\|CCT5\|CCT6A\|CCT8L2\|CDC37L1\|CHAF1A\|CLGN\|CLPX\|DNAJB1\|DNAJB4\|HSP90AA1\|HSPA1A\|HSPA9\|HSPB6\|HSPD1\|HTRA2\|NUDC\|PFDN6\|PTGES3\|RUVBL2\|SHQ1\|SRSF10\|TAPBP\|TCP1\|TOMM20\|TOR1A\|TUBB4B\|UGGT1\| | -| cytosol | | 74 | 41 | 2.118055 | 0.0002 | 0.006333 | 0.0002 | 0.0063330 | 0.483 | NA | AAMP\|AIP\|ARC\|BHMT2\|CALR\|CCT5\|CCT6A\|CDC37L1\|CLPX\|CRABP1\|DNAJB1\|DNAJB4\|EPHB2\|FRS2\|GAK\|GEMIN2\|HCK\|HSP90AA1\|HSPA1A\|HSPB6\|HSPD1\|HTRA2\|NELFA\|NUDC\|OGG1\|PASK\|PEX5\|PIKFYVE\|POLR3K\|PRKCI\|PTGES3\|RUVBL2\|SHQ1\|SPHK1\|SRSF10\|ST13\|TCP1\|TOR1A\|TUBB4B\|UNC13B\|USP33\| | -| cellular component assembly | | 45 | 22 | 2.386422 | 0.0025 | 0.059375 | 0.0072 | 0.1140000 | 0.560 | NA | ARC\|CALR\|CHAF1A\|CLGN\|DDX46\|EPHB2\|GAK\|GEMIN2\|HSP90AA1\|HSPA1A\|HSPA9\|HSPD1\|PFDN6\|PIKFYVE\|PTGES3\|RUVBL2\|SHQ1\|SRSF10\|TAPBP\|TCP1\|UNC13B\|ZNF207\| | -| organelle organization | | 34 | 20 | 2.356244 | 0.0032 | 0.060800 | 0.0155 | 0.1636111 | 0.956 | NA | ARC\|CALR\|GAK\|HSP90AA1\|HSPA1A\|HSPA9\|HSPD1\|HTRA2\|NUDC\|PEX5\|PIKFYVE\|PRKCI\|PTGES3\|RUVBL2\|TOMM20\|TOR1A\|TUBB4B\|UNC13B\|VPS8\|ZNF207\| | -| cellular component organization | | 68 | 35 | 2.120207 | 0.0036 | 0.057000 | 0.0070 | 0.1662500 | 0.735 | NA | ARC\|CALR\|CHAF1A\|CLGN\|DDX46\|EPHB2\|FBLN2\|GAK\|GEMIN2\|HCK\|HSP90AA1\|HSPA1A\|HSPA9\|HSPD1\|HTRA2\|NUDC\|PEX5\|PFDN6\|PIKFYVE\|PRKCI\|PTGES3\|RUVBL2\|SEMA3B\|SHQ1\|SRSF10\|SULF1\|TAPBP\|TCP1\|TOMM20\|TOR1A\|TUBB4B\|UNC13B\|USP33\|VPS8\|ZNF207\| | +| Name | ID | NumProbes | NumGenes | RawScore | Pval | CorrectedPvalue | MFPvalue | CorrectedMFPvalue | Multifunctionality | Same as | GeneMembers | +|:----------------------------------------------|:-------------|----------:|---------:|---------:|----------:|----------------:|---------:|------------------:|-------------------:|:--------|:----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------| +| protein folding | | 40 | 24 | 3.198073 | 0.0000000 | 0.0000000 | 0.000000 | 0.0000000 | 0.145 | NA | AIP\|CALR\|CCT5\|CCT6A\|CCT8L2\|CDC37L1\|CLGN\|CLPX\|DNAJB1\|DNAJB4\|GAK\|HSP90AA1\|HSPA1A\|HSPA9\|HSPB6\|HSPD1\|NUDC\|PFDN6\|PTGES3\|RUVBL2\|ST13\|TCP1\|TOR1A\|UGGT1\| | +| unfolded protein binding | | 52 | 29 | 3.299625 | 0.0000000 | 0.0000000 | 0.000000 | 0.0000000 | 0.174 | NA | AIP\|CALR\|CCT5\|CCT6A\|CCT8L2\|CDC37L1\|CHAF1A\|CLGN\|CLPX\|DNAJB1\|DNAJB4\|HSP90AA1\|HSPA1A\|HSPA9\|HSPB6\|HSPD1\|HTRA2\|NUDC\|PFDN6\|PTGES3\|RUVBL2\|SHQ1\|SRSF10\|TAPBP\|TCP1\|TOMM20\|TOR1A\|TUBB4B\|UGGT1\| | +| cytosol | | 74 | 41 | 2.118055 | 0.0005727 | 0.0150806 | 0.000400 | 0.0105333 | 0.493 | NA | AAMP\|AIP\|ARC\|BHMT2\|CALR\|CCT5\|CCT6A\|CDC37L1\|CLPX\|CRABP1\|DNAJB1\|DNAJB4\|EPHB2\|FRS2\|GAK\|GEMIN2\|HCK\|HSP90AA1\|HSPA1A\|HSPB6\|HSPD1\|HTRA2\|NELFA\|NUDC\|OGG1\|PASK\|PEX5\|PIKFYVE\|POLR3K\|PRKCI\|PTGES3\|RUVBL2\|SHQ1\|SPHK1\|SRSF10\|ST13\|TCP1\|TOR1A\|TUBB4B\|UNC13B\|USP33\| | +| cellular component organization | | 67 | 34 | 2.146421 | 0.0024970 | 0.0493218 | 0.004267 | 0.0842792 | 0.829 | NA | ARC\|CALR\|CHAF1A\|CLGN\|DDX46\|EPHB2\|GAK\|GEMIN2\|HCK\|HSP90AA1\|HSPA1A\|HSPA9\|HSPD1\|HTRA2\|NUDC\|PEX5\|PFDN6\|PIKFYVE\|PRKCI\|PTGES3\|RUVBL2\|SEMA3B\|SHQ1\|SRSF10\|SULF1\|TAPBP\|TCP1\|TOMM20\|TOR1A\|TUBB4B\|UNC13B\|USP33\|VPS8\|ZNF207\| | +| cellular component organization or biogenesis | | 67 | 34 | 2.146421 | 0.0024970 | 0.0394574 | 0.004267 | 0.0674234 | 0.828 | NA | ARC\|CALR\|CHAF1A\|CLGN\|DDX46\|EPHB2\|GAK\|GEMIN2\|HCK\|HSP90AA1\|HSPA1A\|HSPA9\|HSPD1\|HTRA2\|NUDC\|PEX5\|PFDN6\|PIKFYVE\|PRKCI\|PTGES3\|RUVBL2\|SEMA3B\|SHQ1\|SRSF10\|SULF1\|TAPBP\|TCP1\|TOMM20\|TOR1A\|TUBB4B\|UNC13B\|USP33\|VPS8\|ZNF207\| | +| cellular component assembly | | 45 | 22 | 2.386422 | 0.0032000 | 0.0421333 | 0.004500 | 0.0592500 | 0.556 | NA | ARC\|CALR\|CHAF1A\|CLGN\|DDX46\|EPHB2\|GAK\|GEMIN2\|HSP90AA1\|HSPA1A\|HSPA9\|HSPD1\|PFDN6\|PIKFYVE\|PTGES3\|RUVBL2\|SHQ1\|SRSF10\|TAPBP\|TCP1\|UNC13B\|ZNF207\| | #### Use Precision Recall with gene scores @@ -164,12 +163,12 @@ head(precRecallOut$results) %>% knitr::kable() | Name | ID | NumProbes | NumGenes | RawScore | Pval | CorrectedPvalue | MFPvalue | CorrectedMFPvalue | Multifunctionality | Same as | GeneMembers | |:---------------------------|:-------------|----------:|---------:|----------:|-------:|----------------:|---------:|------------------:|-------------------:|:--------|:------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------| -| binding | | 143 | 81 | 0.9992282 | 0.0000 | 0.0000000 | 0.0000 | 0.0000000 | 0.486 | NA | AAMP\|AIP\|ARC\|ARF3\|BHMT2\|C5AR2\|CACNA1F\|CALR\|CCNG1\|CCT5\|CCT6A\|CCT8L2\|CDC37L1\|CHAF1A\|CLGN\|CLPX\|CPT1A\|CRABP1\|DDX46\|DMBT1\|DNAJB1\|DNAJB4\|DZIP3\|EPHB2\|FBLN2\|FOXB1\|FPR3\|FRS2\|GAK\|GEMIN2\|GPR17\|HCK\|HMGCR\|HSP90AA1\|HSPA1A\|HSPA9\|HSPB6\|HSPD1\|HTRA2\|ITIH2\|KCNJ1\|LIPF\|MAN1B1\|NELFA\|NR2E3\|NUDC\|OGG1\|PASK\|PEX5\|PFDN6\|PIKFYVE\|PLCH1\|POLR3K\|PPARA\|PRKCI\|PRPSAP1\|PTGES3\|RUVBL2\|SEMA3B\|SHOX2\|SHQ1\|SLC22A14\|SLC24A1\|SPHK1\|SRSF10\|ST13\|SULF1\|TAPBP\|TBKBP1\|TCP1\|TNFRSF12A\|TOMM20\|TOR1A\|TUBB4B\|UGGT1\|UNC13B\|USP33\|VPS8\|YIPF2\|ZCCHC8\|ZNF207\| | -| protein folding | | 40 | 24 | 0.7176581 | 0.0000 | 0.0000000 | 0.0000 | 0.0000000 | 0.214 | NA | AIP\|CALR\|CCT5\|CCT6A\|CCT8L2\|CDC37L1\|CLGN\|CLPX\|DNAJB1\|DNAJB4\|GAK\|HSP90AA1\|HSPA1A\|HSPA9\|HSPB6\|HSPD1\|NUDC\|PFDN6\|PTGES3\|RUVBL2\|ST13\|TCP1\|TOR1A\|UGGT1\| | -| unfolded protein binding | | 52 | 29 | 0.8507590 | 0.0000 | 0.0000000 | 0.0000 | 0.0000000 | 0.258 | NA | AIP\|CALR\|CCT5\|CCT6A\|CCT8L2\|CDC37L1\|CHAF1A\|CLGN\|CLPX\|DNAJB1\|DNAJB4\|HSP90AA1\|HSPA1A\|HSPA9\|HSPB6\|HSPD1\|HTRA2\|NUDC\|PFDN6\|PTGES3\|RUVBL2\|SHQ1\|SRSF10\|TAPBP\|TCP1\|TOMM20\|TOR1A\|TUBB4B\|UGGT1\| | -| cytosol | | 74 | 41 | 0.7108333 | 0.0003 | 0.0071250 | 0.0005 | 0.0118750 | 0.483 | NA | AAMP\|AIP\|ARC\|BHMT2\|CALR\|CCT5\|CCT6A\|CDC37L1\|CLPX\|CRABP1\|DNAJB1\|DNAJB4\|EPHB2\|FRS2\|GAK\|GEMIN2\|HCK\|HSP90AA1\|HSPA1A\|HSPB6\|HSPD1\|HTRA2\|NELFA\|NUDC\|OGG1\|PASK\|PEX5\|PIKFYVE\|POLR3K\|PRKCI\|PTGES3\|RUVBL2\|SHQ1\|SPHK1\|SRSF10\|ST13\|TCP1\|TOR1A\|TUBB4B\|UNC13B\|USP33\| | -| protein binding | | 127 | 73 | 0.9569410 | 0.0005 | 0.0095000 | 0.0006 | 0.0114000 | 0.369 | NA | AAMP\|AIP\|ARC\|ARF3\|C5AR2\|CALR\|CCNG1\|CCT5\|CCT6A\|CCT8L2\|CDC37L1\|CHAF1A\|CLGN\|CLPX\|CPT1A\|CRABP1\|DDX46\|DMBT1\|DNAJB1\|DNAJB4\|DZIP3\|EPHB2\|FBLN2\|FOXB1\|FPR3\|FRS2\|GAK\|GEMIN2\|GPR17\|HCK\|HMGCR\|HSP90AA1\|HSPA1A\|HSPA9\|HSPB6\|HSPD1\|HTRA2\|ITIH2\|NELFA\|NR2E3\|NUDC\|OGG1\|PASK\|PEX5\|PFDN6\|PIKFYVE\|POLR3K\|PPARA\|PRKCI\|PRPSAP1\|PTGES3\|RUVBL2\|SEMA3B\|SHQ1\|SLC22A14\|SLC24A1\|SPHK1\|SRSF10\|ST13\|TAPBP\|TBKBP1\|TCP1\|TNFRSF12A\|TOMM20\|TOR1A\|TUBB4B\|UGGT1\|UNC13B\|USP33\|VPS8\|YIPF2\|ZCCHC8\|ZNF207\| | -| cellular anatomical entity | | 142 | 80 | 0.9860952 | 0.0011 | 0.0174167 | 0.0014 | 0.0221667 | 0.442 | NA | AAMP\|AIP\|ARC\|ARF3\|BHMT2\|C5AR2\|CACNA1F\|CALR\|CCNG1\|CCT5\|CCT6A\|CDC37L1\|CHAF1A\|CLGN\|CLPX\|CPT1A\|CRABP1\|DDX46\|DMBT1\|DNAJB1\|DNAJB4\|DZIP3\|EPHB2\|FBLN2\|FOXB1\|FPR3\|FRS2\|GAK\|GEMIN2\|GPR17\|HCK\|HMGCR\|HSP90AA1\|HSPA1A\|HSPA9\|HSPB6\|HSPD1\|HTRA2\|ITIH2\|KCNJ1\|LIPF\|MAN1B1\|NELFA\|NR2E3\|NUDC\|OGG1\|PASK\|PEX5\|PFDN6\|PIKFYVE\|PLCH1\|POLR3K\|PPARA\|PRKCI\|PRPSAP1\|PTGES3\|RUVBL2\|SEMA3B\|SHOX2\|SHQ1\|SLC22A14\|SLC24A1\|SPHK1\|SRSF10\|ST13\|SULF1\|TAPBP\|TBKBP1\|TCP1\|TNFRSF12A\|TOMM20\|TOR1A\|TUBB4B\|UGGT1\|UNC13B\|USP33\|VPS8\|YIPF2\|ZCCHC8\|ZNF207\| | +| binding | | 143 | 81 | 0.9992282 | 0.0000 | 0.0000000 | 0.0000 | 0.0000000 | 0.479 | NA | AAMP\|AIP\|ARC\|ARF3\|BHMT2\|C5AR2\|CACNA1F\|CALR\|CCNG1\|CCT5\|CCT6A\|CCT8L2\|CDC37L1\|CHAF1A\|CLGN\|CLPX\|CPT1A\|CRABP1\|DDX46\|DMBT1\|DNAJB1\|DNAJB4\|DZIP3\|EPHB2\|FBLN2\|FOXB1\|FPR3\|FRS2\|GAK\|GEMIN2\|GPR17\|HCK\|HMGCR\|HSP90AA1\|HSPA1A\|HSPA9\|HSPB6\|HSPD1\|HTRA2\|ITIH2\|KCNJ1\|LIPF\|MAN1B1\|NELFA\|NR2E3\|NUDC\|OGG1\|PASK\|PEX5\|PFDN6\|PIKFYVE\|PLCH1\|POLR3K\|PPARA\|PRKCI\|PRPSAP1\|PTGES3\|RUVBL2\|SEMA3B\|SHOX2\|SHQ1\|SLC22A14\|SLC24A1\|SPHK1\|SRSF10\|ST13\|SULF1\|TAPBP\|TBKBP1\|TCP1\|TNFRSF12A\|TOMM20\|TOR1A\|TUBB4B\|UGGT1\|UNC13B\|USP33\|VPS8\|YIPF2\|ZCCHC8\|ZNF207\| | +| protein folding | | 40 | 24 | 0.7176581 | 0.0000 | 0.0000000 | 0.0000 | 0.0000000 | 0.145 | NA | AIP\|CALR\|CCT5\|CCT6A\|CCT8L2\|CDC37L1\|CLGN\|CLPX\|DNAJB1\|DNAJB4\|GAK\|HSP90AA1\|HSPA1A\|HSPA9\|HSPB6\|HSPD1\|NUDC\|PFDN6\|PTGES3\|RUVBL2\|ST13\|TCP1\|TOR1A\|UGGT1\| | +| unfolded protein binding | | 52 | 29 | 0.8507590 | 0.0000 | 0.0000000 | 0.0000 | 0.0000000 | 0.174 | NA | AIP\|CALR\|CCT5\|CCT6A\|CCT8L2\|CDC37L1\|CHAF1A\|CLGN\|CLPX\|DNAJB1\|DNAJB4\|HSP90AA1\|HSPA1A\|HSPA9\|HSPB6\|HSPD1\|HTRA2\|NUDC\|PFDN6\|PTGES3\|RUVBL2\|SHQ1\|SRSF10\|TAPBP\|TCP1\|TOMM20\|TOR1A\|TUBB4B\|UGGT1\| | +| protein binding | | 127 | 73 | 0.9569410 | 0.0002 | 0.0039500 | 0.0001 | 0.0019750 | 0.267 | NA | AAMP\|AIP\|ARC\|ARF3\|C5AR2\|CALR\|CCNG1\|CCT5\|CCT6A\|CCT8L2\|CDC37L1\|CHAF1A\|CLGN\|CLPX\|CPT1A\|CRABP1\|DDX46\|DMBT1\|DNAJB1\|DNAJB4\|DZIP3\|EPHB2\|FBLN2\|FOXB1\|FPR3\|FRS2\|GAK\|GEMIN2\|GPR17\|HCK\|HMGCR\|HSP90AA1\|HSPA1A\|HSPA9\|HSPB6\|HSPD1\|HTRA2\|ITIH2\|NELFA\|NR2E3\|NUDC\|OGG1\|PASK\|PEX5\|PFDN6\|PIKFYVE\|POLR3K\|PPARA\|PRKCI\|PRPSAP1\|PTGES3\|RUVBL2\|SEMA3B\|SHQ1\|SLC22A14\|SLC24A1\|SPHK1\|SRSF10\|ST13\|TAPBP\|TBKBP1\|TCP1\|TNFRSF12A\|TOMM20\|TOR1A\|TUBB4B\|UGGT1\|UNC13B\|USP33\|VPS8\|YIPF2\|ZCCHC8\|ZNF207\| | +| cytosol | | 74 | 41 | 0.7108333 | 0.0013 | 0.0205400 | 0.0011 | 0.0144833 | 0.493 | NA | AAMP\|AIP\|ARC\|BHMT2\|CALR\|CCT5\|CCT6A\|CDC37L1\|CLPX\|CRABP1\|DNAJB1\|DNAJB4\|EPHB2\|FRS2\|GAK\|GEMIN2\|HCK\|HSP90AA1\|HSPA1A\|HSPB6\|HSPD1\|HTRA2\|NELFA\|NUDC\|OGG1\|PASK\|PEX5\|PIKFYVE\|POLR3K\|PRKCI\|PTGES3\|RUVBL2\|SHQ1\|SPHK1\|SRSF10\|ST13\|TCP1\|TOR1A\|TUBB4B\|UNC13B\|USP33\| | +| cellular anatomical entity | | 142 | 80 | 0.9860952 | 0.0020 | 0.0263333 | 0.0011 | 0.0173800 | 0.366 | NA | AAMP\|AIP\|ARC\|ARF3\|BHMT2\|C5AR2\|CACNA1F\|CALR\|CCNG1\|CCT5\|CCT6A\|CDC37L1\|CHAF1A\|CLGN\|CLPX\|CPT1A\|CRABP1\|DDX46\|DMBT1\|DNAJB1\|DNAJB4\|DZIP3\|EPHB2\|FBLN2\|FOXB1\|FPR3\|FRS2\|GAK\|GEMIN2\|GPR17\|HCK\|HMGCR\|HSP90AA1\|HSPA1A\|HSPA9\|HSPB6\|HSPD1\|HTRA2\|ITIH2\|KCNJ1\|LIPF\|MAN1B1\|NELFA\|NR2E3\|NUDC\|OGG1\|PASK\|PEX5\|PFDN6\|PIKFYVE\|PLCH1\|POLR3K\|PPARA\|PRKCI\|PRPSAP1\|PTGES3\|RUVBL2\|SEMA3B\|SHOX2\|SHQ1\|SLC22A14\|SLC24A1\|SPHK1\|SRSF10\|ST13\|SULF1\|TAPBP\|TBKBP1\|TCP1\|TNFRSF12A\|TOMM20\|TOR1A\|TUBB4B\|UGGT1\|UNC13B\|USP33\|VPS8\|YIPF2\|ZCCHC8\|ZNF207\| | #### Use ORA with a hitlist @@ -201,14 +200,14 @@ oraOut = ora(annotation = 'Generic_human', head(oraOut$results) %>% knitr::kable() ``` -| Name | ID | NumProbes | NumGenes | RawScore | Pval | CorrectedPvalue | MFPvalue | CorrectedMFPvalue | Multifunctionality | Same as | GeneMembers | -|:----------------------------------------|:-------------|----------:|---------:|---------:|-----:|----------------:|---------:|------------------:|-------------------:|:--------|:-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------| -| unfolded protein binding | | 124 | 124 | 105 | 0 | 0 | 0 | 0 | 0.674 | NA | AFG3L2\|AHSP\|AIP\|AIPL1\|APCS\|CALR\|CALR3\|CANX\|CCDC115\|CCT2\|CCT3\|CCT4\|CCT5\|CCT6A\|CCT6B\|CCT7\|CCT8\|CCT8L1P\|CCT8L2\|CDC37\|CDC37L1\|CHAF1A\|CHAF1B\|CLGN\|CLPX\|CLU\|CRYAA\|CRYAB\|DNAJA1\|DNAJA2\|DNAJA3\|DNAJA4\|DNAJB1\|DNAJB11\|DNAJB13\|DNAJB2\|DNAJB3\|DNAJB4\|DNAJB5\|DNAJB6\|DNAJB7\|DNAJB8\|DNAJC4\|ERLEC1\|ERN1\|ERN2\|ERO1B\|GRPEL1\|GRPEL2\|HEATR3\|HSP90AA1\|HSP90AA2P\|HSP90AA4P\|HSP90AA5P\|HSP90AB1\|HSP90AB2P\|HSP90AB3P\|HSP90AB4P\|HSP90B1\|HSP90B2P\|HSPA13\|HSPA14\|HSPA1A\|HSPA1B\|HSPA1L\|HSPA2\|HSPA5\|HSPA6\|HSPA7\|HSPA8\|HSPA9\|HSPB1\|HSPB2\|HSPB6\|HSPD1\|HSPE1\|HTRA2\|HYOU1\|LMAN1\|MKKS\|NACA\|NACA2\|NACA4P\|NACAD\|NAP1L4\|NDUFAF1\|NPM1\|NUDC\|NUDCD2\|NUDCD3\|PDRG1\|PET100\|PFDN1\|PFDN2\|PFDN4\|PFDN5\|PFDN6\|PPIA\|PPIB\|PTGES3\|RP2\|RUVBL2\|SCAP\|SCG5\|SERPINH1\|SHQ1\|SIL1\|SPG7\|SRSF10\|SRSF12\|SSUH2\|SYVN1\|TAPBP\|TCP1\|TIMM10B\|TMEM67\|TOMM20\|TOR1A\|TRAP1\|TTC1\|TUBB4B\|UGGT1\|UGGT2\|VBP1\| | -| protein folding chaperone | | 52 | 52 | 33 | 0 | 0 | 0 | 0 | 0.640 | NA | CALR\|CALR3\|CCDC47\|CCT2\|CCT3\|CCT4\|CCT5\|CCT6A\|CCT6B\|CCT7\|CCT8\|CCT8L1P\|CCT8L2\|CD74\|CLGN\|CLPX\|DFFA\|DNAJB1\|DNAJB3\|DNAJB6\|DNAJB7\|DNAJB8\|FKBP8\|HSP90AA1\|HSP90AB1\|HSPA13\|HSPA14\|HSPA1A\|HSPA1B\|HSPA1L\|HSPA2\|HSPA4\|HSPA4L\|HSPA5\|HSPA6\|HSPA7\|HSPA8\|HSPA9\|HSPB1\|HSPD1\|HSPE1\|HSPH1\|HYOU1\|LYRM7\|PDCL3\|PFDN1\|PFDN2\|RIC3\|TCP1\|TOR1A\|WDR83OS\|ZMYND10\| | -| chaperone-mediated protein folding | | 70 | 70 | 30 | 0 | 0 | 0 | 0 | 0.676 | NA | BAG1\|CCT2\|CCT3\|CCT4\|CCT5\|CCT6A\|CCT7\|CCT8\|CD74\|CHORDC1\|CLU\|CRTAP\|CSNK2A1\|DFFA\|DNAJB1\|DNAJB12\|DNAJB13\|DNAJB14\|DNAJB2\|DNAJB3\|DNAJB4\|DNAJB5\|DNAJB6\|DNAJB7\|DNAJB8\|DNAJC18\|DNAJC24\|DNAJC5\|DNAJC7\|ERO1A\|FKBP11\|FKBP1A\|FKBP1B\|FKBP2\|FKBP4\|FKBP5\|GAK\|HSPA13\|HSPA14\|HSPA1A\|HSPA1B\|HSPA1L\|HSPA2\|HSPA5\|HSPA6\|HSPA7\|HSPA8\|HSPA9\|HSPB1\|HSPB6\|HSPE1\|HSPH1\|P3H1\|PDCL3\|PDIA4\|PEX19\|PPIB\|PPID\|PTGES3\|SDF2\|SDF2L1\|ST13\|TCP1\|TOR1A\|TOR1B\|TOR2A\|TRAP1\|UMOD\|UNC45A\|UNC45B\| | -| ATP-dependent protein folding chaperone | | 30 | 30 | 23 | 0 | 0 | 0 | 0 | 0.612 | NA | CCT2\|CCT3\|CCT4\|CCT5\|CCT6A\|CCT6B\|CCT7\|CCT8\|CCT8L1P\|CCT8L2\|CLPX\|HSPA13\|HSPA14\|HSPA1A\|HSPA1B\|HSPA1L\|HSPA2\|HSPA4\|HSPA4L\|HSPA5\|HSPA6\|HSPA7\|HSPA8\|HSPA9\|HSPD1\|HSPE1\|HSPH1\|HYOU1\|TCP1\|TOR1A\| | -| chaperone complex | | 42 | 42 | 20 | 0 | 0 | 0 | 0 | 0.526 | NA | BAG2\|BAG3\|CCDC47\|CCT2\|CCT3\|CCT4\|CCT5\|CCT6A\|CCT6B\|CCT7\|CCT8\|CCT8L1P\|CCT8L2\|CDC37\|DNAAF2\|DNAJB11\|DNAJC9\|HSF1\|HSP90AB1\|HSPA8\|HSPB8\|PDRG1\|PFDN2\|PFDN6\|PIH1D2\|PPP5C\|PSMG1\|PSMG2\|PTGES3\|RPAP3\|RUVBL1\|RUVBL2\|SDF2\|SDF2L1\|SPAG1\|STIP1\|STUB1\|TCP1\|TSC1\|URI1\|UXT\|WDR83OS\| | -| chaperone binding | | 106 | 106 | 25 | 0 | 0 | 0 | 0 | 0.927 | NA | AHSA1\|AHSA2P\|ALB\|AMFR\|ATP1A1\|ATP1A2\|ATP1A3\|ATP7A\|BAG1\|BAG2\|BAG3\|BAG4\|BAG5\|BAK1\|BAX\|BIN1\|BIRC2\|BIRC5\|CALR\|CDC25A\|CDC37\|CDC37L1\|CDKN1B\|CFTR\|CLU\|CP\|CTSC\|DNAAF6\|DNAJA1\|DNAJA2\|DNAJA4\|DNAJB1\|DNAJB13\|DNAJB2\|DNAJB3\|DNAJB4\|DNAJB5\|DNAJB6\|DNAJB7\|DNAJB8\|DNAJB9\|DNAJC1\|DNAJC10\|DNAJC3\|DNAJC9\|DNLZ\|ERP29\|FGB\|FICD\|FN1\|FNIP1\|FNIP2\|GAK\|GET4\|GNB5\|GRN\|GRPEL1\|GRPEL2\|HES1\|HLA-B\|HSCB\|HSPA2\|HSPA5\|HSPA8\|HSPB6\|HSPD1\|HSPE1\|HYOU1\|LRP2\|MAPT\|OGDH\|PACRG\|PDPN\|PFDN4\|PFDN6\|PLG\|PRKN\|PRNP\|PTGES3\|PTGES3L\|RNF207\|SACS\|SCARB2\|SDF2L1\|SLC12A2\|SLC25A17\|SOD1\|STUB1\|SUGT1\|SYVN1\|TBCA\|TBCC\|TBCD\|TBCE\|TERT\|TFRC\|TIMM10\|TIMM44\|TIMM9\|TP53\|TSACC\|TSC1\|UBL4A\|USP13\|VWF\|WRAP53\| | +| Name | ID | NumProbes | NumGenes | RawScore | Pval | CorrectedPvalue | MFPvalue | CorrectedMFPvalue | Multifunctionality | Same as | GeneMembers | +|:----------------------------------------|:-------------|----------:|---------:|---------:|-----:|----------------:|---------:|------------------:|-------------------:|:--------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------| +| unfolded protein binding | | 116 | 116 | 99 | 0 | 0 | 0 | 0 | 0.726 | NA | AFG3L2\|AHSP\|AIP\|AIPL1\|APCS\|CALR\|CALR3\|CANX\|CCAR2\|CCDC115\|CCT2\|CCT3\|CCT4\|CCT5\|CCT6A\|CCT6B\|CCT7\|CCT8\|CCT8L2\|CDC37\|CDC37L1\|CHAF1A\|CHAF1B\|CLGN\|CLPX\|CLU\|CRYAA\|CRYAB\|DNAJA1\|DNAJA2\|DNAJA3\|DNAJA4\|DNAJB1\|DNAJB11\|DNAJB13\|DNAJB2\|DNAJB3\|DNAJB4\|DNAJB5\|DNAJB6\|DNAJB7\|DNAJB8\|DNAJC4\|ERLEC1\|ERN1\|ERN2\|ERO1B\|GRPEL1\|GRPEL2\|HEATR3\|HSP90AA1\|HSP90AB1\|HSP90AB4P\|HSP90B1\|HSP90B2P\|HSPA1A\|HSPA1B\|HSPA1L\|HSPA2\|HSPA5\|HSPA6\|HSPA8\|HSPA9\|HSPB1\|HSPB2\|HSPB6\|HSPD1\|HSPE1\|HTRA2\|HYOU1\|LMAN1\|MKKS\|NACA\|NACA2\|NACA4P\|NACAD\|NAP1L4\|NDUFAF1\|NPM1\|NUDC\|NUDCD2\|NUDCD3\|PDRG1\|PET100\|PFDN1\|PFDN2\|PFDN4\|PFDN5\|PFDN6\|PPIA\|PPIB\|PTGES3\|RP2\|RUVBL2\|SCAP\|SCG5\|SERPINH1\|SHQ1\|SIL1\|SPG7\|SRSF10\|SRSF12\|SSUH2\|SYVN1\|TAPBP\|TCP1\|TIMM10B\|TMEM67\|TOMM20\|TOR1A\|TRAP1\|TTC1\|TUBB4B\|UGGT1\|UGGT2\|VBP1\| | +| protein folding chaperone | | 60 | 60 | 37 | 0 | 0 | 0 | 0 | 0.638 | NA | ANP32E\|APLF\|CALR\|CALR3\|CCDC47\|CCT2\|CCT3\|CCT4\|CCT5\|CCT6A\|CCT6B\|CCT7\|CCT8\|CCT8L2\|CD74\|CLGN\|CLPX\|DFFA\|DNAJB1\|DNAJB6\|DNAJB7\|DNAJB8\|FKBP8\|HSP90AA1\|HSP90AB1\|HSP90AB4P\|HSP90B1\|HSP90B2P\|HSPA13\|HSPA14\|HSPA1A\|HSPA1B\|HSPA1L\|HSPA2\|HSPA4\|HSPA4L\|HSPA5\|HSPA6\|HSPA7\|HSPA8\|HSPA9\|HSPB1\|HSPB6\|HSPD1\|HSPE1\|HSPH1\|HYOU1\|HYPK\|KHSRP\|LYRM7\|PDCL3\|PFDN1\|PFDN2\|RIC3\|TCP1\|TOR1A\|TRAP1\|WDR83OS\|WIPF1\|ZMYND10\| | +| chaperone-mediated protein folding | | 74 | 74 | 35 | 0 | 0 | 0 | 0 | 0.588 | NA | BAG1\|CCT2\|CCT3\|CCT4\|CCT5\|CCT6A\|CCT7\|CCT8\|CD74\|CHORDC1\|CLU\|CRTAP\|CSNK2A1\|DFFA\|DNAJB1\|DNAJB12\|DNAJB13\|DNAJB14\|DNAJB2\|DNAJB3\|DNAJB4\|DNAJB5\|DNAJB6\|DNAJB7\|DNAJB8\|DNAJC18\|DNAJC24\|DNAJC5\|DNAJC7\|ERO1A\|FKBP11\|FKBP2\|FKBP4\|FKBP5\|GAK\|HSPA13\|HSPA14\|HSPA1A\|HSPA1B\|HSPA1L\|HSPA2\|HSPA5\|HSPA6\|HSPA7\|HSPA8\|HSPA9\|HSPB1\|HSPB6\|HSPE1\|HSPH1\|P3H1\|PDCL3\|PDIA4\|PEX19\|PFDN1\|PFDN2\|PFDN4\|PFDN5\|PFDN6\|PPIB\|PPID\|PTGES3\|SDF2\|SDF2L1\|ST13\|TCP1\|TOR1A\|TOR1B\|TOR2A\|TRAP1\|UMOD\|UNC45A\|UNC45B\|VBP1\| | +| ATP-dependent protein folding chaperone | | 34 | 34 | 27 | 0 | 0 | 0 | 0 | 0.662 | NA | CCT2\|CCT3\|CCT4\|CCT5\|CCT6A\|CCT6B\|CCT7\|CCT8\|CCT8L2\|CLPX\|HSP90AA1\|HSP90AB1\|HSP90AB4P\|HSP90B1\|HSP90B2P\|HSPA13\|HSPA14\|HSPA1A\|HSPA1B\|HSPA1L\|HSPA2\|HSPA4\|HSPA4L\|HSPA5\|HSPA6\|HSPA7\|HSPA8\|HSPA9\|HSPD1\|HSPH1\|HYOU1\|TCP1\|TOR1A\|TRAP1\| | +| protein-folding chaperone binding | | 133 | 133 | 27 | 0 | 0 | 0 | 0 | 0.928 | NA | AHSA1\|AHSA2P\|ALB\|AMFR\|ATP1A1\|ATP1A2\|ATP1A3\|ATP7A\|BAG1\|BAG2\|BAG3\|BAG4\|BAG5\|BAG6\|BAK1\|BAX\|BIN1\|BIRC2\|BIRC5\|CALR\|CDC25A\|CDC37\|CDC37L1\|CDK1\|CDKN1B\|CFTR\|CLU\|CP\|CTSC\|CYP1A1\|CYP2E1\|DNAAF6\|DNAJA1\|DNAJA2\|DNAJA3\|DNAJA4\|DNAJB1\|DNAJB12\|DNAJB13\|DNAJB14\|DNAJB2\|DNAJB3\|DNAJB4\|DNAJB5\|DNAJB6\|DNAJB7\|DNAJB8\|DNAJB9\|DNAJC1\|DNAJC10\|DNAJC18\|DNAJC2\|DNAJC3\|DNAJC8\|DNAJC9\|DNLZ\|ERN1\|ERP29\|FGB\|FGF1\|FICD\|FNIP1\|FNIP2\|GAK\|GET4\|GNB5\|GPR37\|GRN\|GRPEL1\|GRPEL2\|HDAC8\|HES1\|HIKESHI\|HLA-B\|HSCB\|HSPA2\|HSPA5\|HSPA8\|HSPB6\|HSPD1\|HSPE1\|IQCG\|LRP2\|MAPT\|METTL21A\|MVD\|NOD2\|NUP62\|PACRG\|PDPN\|PFDN4\|PFDN6\|PGLYRP1\|PLG\|PPEF2\|PPID\|PRKN\|PRNP\|PTGES3\|PTGES3L\|RNF207\|RPS3\|SACS\|SCARB2\|SDF2L1\|SGTB\|SLC12A2\|SLC25A17\|SNCA\|SOD1\|SPN\|ST13\|STAU2\|STUB1\|SUGT1\|SYVN1\|TBCA\|TBCC\|TBCD\|TBCE\|TERT\|TFRC\|TIMM10\|TIMM44\|TIMM9\|TP53\|TSACC\|TSC1\|TTC4\|UBL4A\|USP13\|VWF\|WRAP53\| | +| protein refolding | | 25 | 25 | 17 | 0 | 0 | 0 | 0 | 0.591 | NA | B2M\|CRYAA\|CRYAB\|DNAJA1\|DNAJA2\|DNAJA4\|DNAJB2\|FKBP1A\|FKBP1B\|HSP90AA1\|HSPA13\|HSPA14\|HSPA1A\|HSPA1B\|HSPA1L\|HSPA2\|HSPA5\|HSPA6\|HSPA7\|HSPA8\|HSPA9\|HSPB1\|HSPB2\|HSPB6\|HSPD1\| | #### Using your own GO annotations @@ -225,15 +224,17 @@ goAnnots %>% head ## $`1` ## [1] "GO:0008150" "GO:0005576" "GO:0005576" "GO:0005576" "GO:0005615" - ## [6] "GO:0031093" "GO:0034774" "GO:0062023" "GO:0070062" "GO:0072562" - ## [11] "GO:1904813" "GO:0003674" + ## [6] "GO:0005886" "GO:0031093" "GO:0034774" "GO:0062023" "GO:0070062" + ## [11] "GO:0072562" "GO:1904813" "GO:0003674" ## ## $`2` - ## [1] "GO:0001869" "GO:0010951" "GO:0048863" "GO:0005576" "GO:0005576" - ## [6] "GO:0005615" "GO:0031093" "GO:0062023" "GO:0070062" "GO:0072562" - ## [11] "GO:0002020" "GO:0002020" "GO:0004866" "GO:0004867" "GO:0005102" - ## [16] "GO:0005515" "GO:0019838" "GO:0019899" "GO:0019959" "GO:0019966" - ## [21] "GO:0043120" "GO:0048306" + ## [1] "GO:0001553" "GO:0001869" "GO:0002438" "GO:0006953" "GO:0007584" + ## [6] "GO:0010037" "GO:0034695" "GO:0048863" "GO:0051384" "GO:1990402" + ## [11] "GO:0005576" "GO:0005576" "GO:0005615" "GO:0031093" "GO:0062023" + ## [16] "GO:0070062" "GO:0072562" "GO:0002020" "GO:0002020" "GO:0004866" + ## [21] "GO:0004866" "GO:0004867" "GO:0005102" "GO:0005515" "GO:0019838" + ## [26] "GO:0019899" "GO:0019959" "GO:0019966" "GO:0042802" "GO:0043120" + ## [31] "GO:0048306" "GO:0048403" "GO:0048406" ## ## $`3` ## NULL @@ -298,13 +299,13 @@ oraOut = ora(annotation = annotation, head(oraOut$results) %>% knitr::kable() ``` -| Name | ID | NumProbes | NumGenes | RawScore | Pval | CorrectedPvalue | MFPvalue | CorrectedMFPvalue | Multifunctionality | Same as | GeneMembers | -|:---------------------------------------------|:-------------|----------:|---------:|:---------|:----------|:----------------|:-----------|:------------------|:-------------------|:--------|:----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------| -| unfolded protein binding | | 122 | 122 | 122.000 | 0E00 | 0E00 | 1.845E-306 | 7.861E-303 | 0.706 | NA | AFG3L2\|AHSP\|AIP\|AIPL1\|APCS\|CALR\|CALR3\|CANX\|CCDC115\|CCT2\|CCT3\|CCT4\|CCT5\|CCT6A\|CCT6B\|CCT7\|CCT8\|CCT8L1P\|CCT8L2\|CDC37\|CDC37L1\|CHAF1A\|CHAF1B\|CLGN\|CLPX\|CLU\|CRYAA\|CRYAB\|DNAJA1\|DNAJA2\|DNAJA3\|DNAJA4\|DNAJB1\|DNAJB11\|DNAJB13\|DNAJB2\|DNAJB3\|DNAJB4\|DNAJB5\|DNAJB6\|DNAJB7\|DNAJB8\|DNAJC4\|ERLEC1\|ERN1\|ERN2\|ERO1B\|GRPEL1\|GRPEL2\|HEATR3\|HSP90AA1\|HSP90AA2P\|HSP90AA4P\|HSP90AA5P\|HSP90AB1\|HSP90AB2P\|HSP90AB3P\|HSP90AB4P\|HSP90B1\|HSP90B2P\|HSPA13\|HSPA14\|HSPA1A\|HSPA1B\|HSPA1L\|HSPA2\|HSPA5\|HSPA6\|HSPA7\|HSPA8\|HSPA9\|HSPB6\|HSPD1\|HSPE1\|HTRA2\|HYOU1\|LMAN1\|MKKS\|NACA\|NACA2\|NACA4P\|NACAD\|NAP1L4\|NDUFAF1\|NPM1\|NUDC\|NUDCD2\|NUDCD3\|PDRG1\|PET100\|PFDN1\|PFDN2\|PFDN4\|PFDN5\|PFDN6\|PPIA\|PPIB\|PTGES3\|RP2\|RUVBL2\|SCAP\|SCG5\|SERPINH1\|SHQ1\|SIL1\|SPG7\|SRSF10\|SRSF12\|ST13\|SYVN1\|TAPBP\|TCP1\|TIMM10B\|TMEM67\|TOMM20\|TOR1A\|TRAP1\|TTC1\|TUBB4B\|UGGT1\|UGGT2\|VBP1\| | -| protein folding chaperone | | 40 | 40 | 31.000 | 3.213E-63 | 6.843E-60 | 1.342E-57 | 2.858E-54 | 0.613 | NA | CALR\|CALR3\|CCDC47\|CCT2\|CCT3\|CCT4\|CCT5\|CCT6A\|CCT6B\|CCT7\|CCT8\|CD74\|CLGN\|DFFA\|DNAJB1\|DNAJB3\|DNAJB6\|DNAJB7\|DNAJB8\|FKBP8\|HSP90AB1\|HSPA13\|HSPA14\|HSPA1A\|HSPA1B\|HSPA1L\|HSPA2\|HSPA5\|HSPA6\|HSPA7\|HSPA8\|HSPA9\|HSPB1\|PDCL3\|PFDN1\|PFDN2\|RIC3\|TCP1\|WDR83OS\|ZMYND10\| | -| chaperone-mediated protein folding | | 65 | 65 | 29.000 | 1.305E-48 | 1.853E-45 | 3.56E-44 | 5.055E-41 | 0.636 | NA | BAG1\|CCT2\|CD74\|CHORDC1\|CLU\|CRTAP\|CSNK2A1\|DFFA\|DNAJB1\|DNAJB12\|DNAJB13\|DNAJB14\|DNAJB2\|DNAJB3\|DNAJB4\|DNAJB5\|DNAJB6\|DNAJB7\|DNAJB8\|DNAJC18\|DNAJC24\|DNAJC5\|DNAJC7\|ERO1A\|FKBP11\|FKBP1A\|FKBP1B\|FKBP2\|FKBP4\|FKBP5\|GAK\|HSPA13\|HSPA14\|HSPA1A\|HSPA1B\|HSPA1L\|HSPA2\|HSPA5\|HSPA6\|HSPA7\|HSPA8\|HSPA9\|HSPB1\|HSPB6\|HSPE1\|HSPH1\|P3H1\|PDCL3\|PDIA4\|PEX19\|PPIB\|PPID\|PTGES3\|SDF2\|SDF2L1\|SGTA\|ST13\|ST13P4\|ST13P5\|TOR1A\|TOR1B\|TOR2A\|TRAP1\|UNC45A\|UNC45B\| | -| chaperone binding | | 107 | 107 | 30.000 | 6.258E-43 | 6.664E-40 | 4.248E-39 | 4.524E-36 | 0.928 | NA | AHSA1\|AHSA2P\|ALB\|AMFR\|ATP1A1\|ATP1A2\|ATP1A3\|ATP7A\|BAG1\|BAG2\|BAG3\|BAG4\|BAG5\|BAK1\|BAX\|BIN1\|BIRC2\|BIRC5\|CALR\|CDC25A\|CDC37\|CDC37L1\|CDKN1B\|CFTR\|CLU\|CP\|CTSC\|DNAAF6\|DNAJA1\|DNAJA2\|DNAJA4\|DNAJB1\|DNAJB13\|DNAJB2\|DNAJB3\|DNAJB4\|DNAJB5\|DNAJB6\|DNAJB7\|DNAJB8\|DNAJB9\|DNAJC1\|DNAJC10\|DNAJC3\|DNAJC9\|DNLZ\|ERP29\|FGB\|FICD\|FN1\|FNIP1\|FNIP2\|GAK\|GET4\|GNB5\|GRN\|GRPEL1\|GRPEL2\|HES1\|HLA-B\|HSCB\|HSPA2\|HSPA5\|HSPA8\|HSPB6\|HSPD1\|HSPE1\|HYOU1\|LRP2\|MAPT\|OGDH\|PACRG\|PDPN\|PFDN4\|PFDN6\|PLG\|PRKN\|PRNP\|PTGES3\|PTGES3L\|RNF207\|SACS\|SCARB2\|SDF2L1\|SLC12A2\|SLC25A17\|SOD1\|ST13\|STIP1\|STUB1\|SUGT1\|SYVN1\|TBCA\|TBCC\|TBCD\|TBCE\|TERT\|TIMM10\|TIMM44\|TIMM9\|TP53\|TSACC\|TSC1\|UBL4A\|USP13\|VWF\|WRAP53\| | -| ‘de novo’ protein folding | | 43 | 43 | 22.000 | 1.158E-38 | 9.867E-36 | 2.357E-36 | 2.008E-33 | 0.569 | NA | BAG1\|CCT2\|CD74\|CHCHD4\|DNAJB1\|DNAJB12\|DNAJB13\|DNAJB14\|DNAJB4\|DNAJB5\|DNAJC18\|DNAJC2\|DNAJC7\|ENTPD5\|ERO1A\|FKBP1A\|FKBP1B\|GAK\|HSPA13\|HSPA14\|HSPA1A\|HSPA1B\|HSPA1L\|HSPA2\|HSPA5\|HSPA6\|HSPA7\|HSPA8\|HSPA9\|HSPD1\|HSPE1\|HSPH1\|PTGES3\|SDF2\|SDF2L1\|SELENOF\|ST13\|ST13P4\|ST13P5\|TOR1A\|TOR1B\|TOR2A\|UGGT1\| | -| ‘de novo’ post-translational protein folding | | 39 | 39 | 21.000 | 1.423E-37 | 1.011E-34 | 3.171E-35 | 2.251E-32 | 0.450 | NA | BAG1\|CCT2\|CD74\|CHCHD4\|DNAJB1\|DNAJB12\|DNAJB13\|DNAJB14\|DNAJB4\|DNAJB5\|DNAJC18\|DNAJC7\|ENTPD5\|ERO1A\|GAK\|HSPA13\|HSPA14\|HSPA1A\|HSPA1B\|HSPA1L\|HSPA2\|HSPA5\|HSPA6\|HSPA7\|HSPA8\|HSPA9\|HSPE1\|HSPH1\|PTGES3\|SDF2\|SDF2L1\|SELENOF\|ST13\|ST13P4\|ST13P5\|TOR1A\|TOR1B\|TOR2A\|UGGT1\| | +| Name | ID | NumProbes | NumGenes | RawScore | Pval | CorrectedPvalue | MFPvalue | CorrectedMFPvalue | Multifunctionality | Same as | GeneMembers | +|:----------------------------------------|:-------------|----------:|---------:|:---------|:----------|:----------------|:-----------|:------------------|:-------------------|:--------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------| +| unfolded protein binding | | 122 | 122 | 122.000 | 0E00 | 0E00 | 1.226E-306 | 5.253E-303 | 0.695 | NA | AFG3L2\|AHSP\|AIP\|AIPL1\|APCS\|CALR\|CALR3\|CANX\|CCAR2\|CCDC115\|CCT2\|CCT3\|CCT4\|CCT5\|CCT6A\|CCT6B\|CCT7\|CCT8\|CCT8L1P\|CCT8L2\|CDC37\|CDC37L1\|CHAF1A\|CHAF1B\|CLGN\|CLPX\|CLU\|CRYAA\|CRYAB\|DNAJA1\|DNAJA2\|DNAJA3\|DNAJA4\|DNAJB1\|DNAJB11\|DNAJB13\|DNAJB2\|DNAJB3\|DNAJB4\|DNAJB5\|DNAJB6\|DNAJB7\|DNAJB8\|DNAJC4\|ERLEC1\|ERN1\|ERN2\|ERO1B\|GRPEL1\|GRPEL2\|HEATR3\|HSP90AA1\|HSP90AA2P\|HSP90AA4P\|HSP90AA5P\|HSP90AB1\|HSP90AB2P\|HSP90AB3P\|HSP90AB4P\|HSP90B1\|HSP90B2P\|HSPA1A\|HSPA1B\|HSPA1L\|HSPA2\|HSPA5\|HSPA6\|HSPA8\|HSPA9\|HSPB1\|HSPB2\|HSPB6\|HSPD1\|HSPE1\|HTRA2\|HYOU1\|LMAN1\|MKKS\|NACA\|NACA2\|NACA4P\|NACAD\|NAP1L4\|NDUFAF1\|NPM1\|NUDC\|NUDCD2\|NUDCD3\|PDRG1\|PET100\|PFDN1\|PFDN2\|PFDN4\|PFDN5\|PFDN6\|PPIA\|PPIB\|PTGES3\|RP2\|RUVBL2\|SCAP\|SCG5\|SERPINH1\|SHQ1\|SIL1\|SPG7\|SRSF10\|SRSF12\|SSUH2\|SYVN1\|TAPBP\|TCP1\|TIMM10B\|TMEM67\|TOMM20\|TOR1A\|TRAP1\|TTC1\|TUBB4B\|UGGT1\|UGGT2\|VBP1\| | +| protein folding chaperone | | 69 | 69 | 47.000 | 2.823E-92 | 6.049E-89 | 1.565E-89 | 3.353E-86 | 0.573 | NA | ANP32E\|APLF\|CALR\|CALR3\|CCDC47\|CCT2\|CCT3\|CCT4\|CCT5\|CCT6A\|CCT6B\|CCT7\|CCT8\|CCT8L1P\|CCT8L2\|CD74\|CDC123\|CLGN\|CLPX\|DFFA\|DNAJB1\|DNAJB6\|DNAJB7\|DNAJB8\|FKBP8\|HSP90AA1\|HSP90AA2P\|HSP90AA4P\|HSP90AA5P\|HSP90AB1\|HSP90AB2P\|HSP90AB3P\|HSP90AB4P\|HSP90B1\|HSP90B2P\|HSPA13\|HSPA14\|HSPA1A\|HSPA1B\|HSPA1L\|HSPA2\|HSPA4\|HSPA4L\|HSPA5\|HSPA6\|HSPA7\|HSPA8\|HSPA9\|HSPB1\|HSPB6\|HSPD1\|HSPE1\|HSPH1\|HYOU1\|HYPK\|KHSRP\|LYRM7\|PDCL3\|PFDN1\|PFDN2\|RIC3\|TAPBP\|TCP1\|TOR1A\|TRAP1\|WDR83OS\|WIPF1\|ZMYND10\|ZPR1\| | +| ATP-dependent protein folding chaperone | | 40 | 40 | 34.000 | 3.365E-72 | 4.807E-69 | 3.79E-69 | 5.413E-66 | 0.541 | NA | CCT2\|CCT3\|CCT4\|CCT5\|CCT6A\|CCT6B\|CCT7\|CCT8\|CCT8L1P\|CCT8L2\|CLPX\|HSP90AA1\|HSP90AA2P\|HSP90AA4P\|HSP90AA5P\|HSP90AB1\|HSP90AB2P\|HSP90AB3P\|HSP90AB4P\|HSP90B1\|HSP90B2P\|HSPA13\|HSPA14\|HSPA1A\|HSPA1B\|HSPA1L\|HSPA2\|HSPA4\|HSPA4L\|HSPA5\|HSPA6\|HSPA7\|HSPA8\|HSPA9\|HSPD1\|HSPH1\|HYOU1\|TCP1\|TOR1A\|TRAP1\| | +| chaperone-mediated protein folding | | 74 | 74 | 39.000 | 1.513E-69 | 1.621E-66 | 4.022E-67 | 4.308E-64 | 0.599 | NA | BAG1\|CCT2\|CCT3\|CCT4\|CCT5\|CCT6A\|CCT7\|CCT8\|CD74\|CHORDC1\|CLU\|CRTAP\|CSNK2A1\|DFFA\|DNAJB1\|DNAJB12\|DNAJB13\|DNAJB14\|DNAJB2\|DNAJB3\|DNAJB4\|DNAJB5\|DNAJB6\|DNAJB7\|DNAJB8\|DNAJC18\|DNAJC24\|DNAJC5\|DNAJC7\|ERO1A\|FKBP11\|FKBP2\|FKBP4\|FKBP5\|GAK\|HSPA13\|HSPA14\|HSPA1A\|HSPA1B\|HSPA1L\|HSPA2\|HSPA5\|HSPA6\|HSPA7\|HSPA8\|HSPA9\|HSPB1\|HSPB6\|HSPE1\|HSPH1\|P3H1\|PDCL3\|PDIA4\|PEX19\|PFDN1\|PFDN2\|PFDN4\|PFDN5\|PFDN6\|PPIB\|PPID\|PTGES3\|SDF2\|SDF2L1\|ST13\|TCP1\|TOR1A\|TOR1B\|TOR2A\|TRAP1\|UMOD\|UNC45A\|UNC45B\|VBP1\| | +| protein-folding chaperone binding | | 133 | 133 | 30.000 | 8.981E-40 | 7.697E-37 | 5.724E-38 | 4.906E-35 | 0.928 | NA | AHSA1\|AHSA2P\|ALB\|AMFR\|ATP1A1\|ATP1A2\|ATP1A3\|ATP7A\|BAG1\|BAG2\|BAG3\|BAG4\|BAG5\|BAG6\|BAK1\|BAX\|BIN1\|BIRC2\|BIRC5\|CALR\|CDC25A\|CDC37\|CDC37L1\|CDK1\|CDKN1B\|CFTR\|CLU\|CP\|CTSC\|CYP1A1\|CYP2E1\|DNAAF6\|DNAJA1\|DNAJA2\|DNAJA3\|DNAJA4\|DNAJB1\|DNAJB12\|DNAJB13\|DNAJB14\|DNAJB2\|DNAJB3\|DNAJB4\|DNAJB5\|DNAJB6\|DNAJB7\|DNAJB8\|DNAJB9\|DNAJC1\|DNAJC10\|DNAJC18\|DNAJC2\|DNAJC3\|DNAJC8\|DNAJC9\|DNLZ\|ERN1\|ERP29\|FGB\|FGF1\|FICD\|FNIP1\|FNIP2\|GAK\|GET4\|GNB5\|GPR37\|GRN\|GRPEL1\|GRPEL2\|HDAC8\|HES1\|HIKESHI\|HLA-B\|HSCB\|HSPA2\|HSPA5\|HSPA8\|HSPB6\|HSPD1\|HSPE1\|IQCG\|LRP2\|MAPT\|METTL21A\|MVD\|NOD2\|NUP62\|PACRG\|PDPN\|PFDN4\|PFDN6\|PGLYRP1\|PLG\|PPEF2\|PPID\|PRKN\|PRNP\|PTGES3\|PTGES3L\|RNF207\|RPS3\|SACS\|SCARB2\|SDF2L1\|SGTB\|SLC12A2\|SLC25A17\|SNCA\|SOD1\|SPN\|ST13\|STAU2\|STUB1\|SUGT1\|SYVN1\|TBCA\|TBCC\|TBCD\|TBCE\|TERT\|TFRC\|TIMM10\|TIMM44\|TIMM9\|TP53\|TSACC\|TSC1\|TTC4\|UBL4A\|USP13\|VWF\|WRAP53\| | +| protein refolding | | 25 | 25 | 19.000 | 1.628E-38 | 1.163E-35 | 8.77E-36 | 6.263E-33 | 0.574 | NA | B2M\|CRYAA\|CRYAB\|DNAJA1\|DNAJA2\|DNAJA4\|DNAJB2\|FKBP1A\|FKBP1B\|HSP90AA1\|HSPA13\|HSPA14\|HSPA1A\|HSPA1B\|HSPA1L\|HSPA2\|HSPA5\|HSPA6\|HSPA7\|HSPA8\|HSPA9\|HSPB1\|HSPB2\|HSPB6\|HSPD1\| | We can see is the top scoring hit as expected. diff --git a/README.rmd b/README.rmd index 31f1be7..dd60c09 100644 --- a/README.rmd +++ b/README.rmd @@ -6,7 +6,7 @@ knitr::opts_chunk$set(echo = TRUE) devtools::load_all() ``` -# ErmineR +# ErmineR This is an R wrapper for Pavlidis Lab's [ermineJ](http://erminej.msl.ubc.ca/). A tool for gene set enrichment analysis with multifunctionality correction.