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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod305

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod305 Module size 69 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 286 ANK1 ankyrin 1 287 ANK2 ankyrin 2 288 ANK3 ankyrin 3 51479 ANKFY1 ankyrin repeat and FYVE domain containing 1 63926 ANKRD5 ankyrin repeat and EF-hand domain containing 1 79998 ANKRD53 ankyrin repeat domain 53 140731 ANKRD60 ankyrin repeat domain 60 374569 ASPG asparaginase 467 ATF3 activating transcription factor 3 11016 ATF7 activating transcription factor 7 10538 BATF basic leucine zipper ATF-like transcription factor 116071 BATF2 basic leucine zipper ATF-like transcription factor 2 55509 BATF3 basic leucine zipper ATF-like transcription factor 3 585 BBS4 Bardet-Biedl syndrome 4 9586 CREB5 cAMP responsive element binding protein 5 140850 DEFB127 defensin beta 127 27294 DHDH dihydrodiol dehydrogenase 161582 DYX1C1 dynein axonemal assembly factor 4 54620 FBXL19 F-box and leucine rich repeat protein 19 63943 FKBPL FK506 binding protein like 2354 FOSB FosB proto-oncogene, AP-1 transcription factor subunit 8061 FOSL1 FOS like 1, AP-1 transcription factor subunit 2355 FOSL2 FOS like 2, AP-1 transcription factor subunit 3297 HSF1 heat shock transcription factor 1 3298 HSF2 heat shock transcription factor 2 3299 HSF4 heat shock transcription factor 4 100506164 HSFX1 heat shock transcription factor family, X-linked 1 100130086 HSFX2 heat shock transcription factor family, X-linked 2 86614 HSFY1 heat shock transcription factor Y-linked 1 159119 HSFY2 heat shock transcription factor Y-linked 2 3434 IFIT1 interferon induced protein with tetratricopeptide repeats 1 439996 IFIT1B interferon induced protein with tetratricopeptide repeats 1B 3433 IFIT2 interferon induced protein with tetratricopeptide repeats 2 3437 IFIT3 interferon induced protein with tetratricopeptide repeats 3 24138 IFIT5 interferon induced protein with tetratricopeptide repeats 5 122953 JDP2 Jun dimerization protein 2 10535 JUNB ribonuclease H2 subunit A 3727 JUND JunD proto-oncogene, AP-1 transcription factor subunit 22992 KDM2A lysine demethylase 2A 84678 KDM2B lysine demethylase 2B 164832 LONRF2 LON peptidase N-terminal domain and ring finger 2 79836 LONRF3 LON peptidase N-terminal domain and ring finger 3 4286 MITF melanogenesis associated transcription factor 54737 MPHOSPH8 M-phase phosphoprotein 8 4800 NFYA nuclear transcription factor Y subunit alpha 5307 PITX1 paired like homeodomain 1 5308 PITX2 paired like homeodomain 2 5309 PITX3 paired like homeodomain 3 4864 POGZ NPC intracellular cholesterol transporter 1 5565 PRKAB2 protein kinase AMP-activated non-catalytic subunit beta 2 6041 RNASEL ribonuclease L 6674 SPAG1 sperm associated antigen 1 7003 TEAD1 TEA domain transcription factor 1 8463 TEAD2 TEA domain transcription factor 2 7005 TEAD3 TEA domain transcription factor 3 7004 TEAD4 TEA domain transcription factor 4 22797 TFEC transcription factor EC 83857 TMTC1 transmembrane and tetratricopeptide repeat containing 1 160418 TMTC3 transmembrane and tetratricopeptide repeat containing 3 10953 TOMM34 translocase of outer mitochondrial membrane 34 84231 TRAF7 TNF receptor associated factor 7 158248 TTC16 tetratricopeptide repeat domain 16 164118 TTC24 tetratricopeptide repeat domain 24 130502 TTC32 tetratricopeptide repeat domain 32 319089 TTC6 tetratricopeptide repeat domain 6 51442 VGLL1 vestigial like family member 1 197335 WDR90 WD repeat domain 90 58189 WFDC1 WAP four-disulfide core domain 1 100125288 ZGLP1 zinc finger, GATA-like protein 1

Functional annotation

Modules were tested for enrichment in functional and pathway annotations using two complementary approaches:
1. To select a small number of specific / non-redundant annotations for each module, a regression-based approach was used;
2. To obtain the complete set of enriched annotations, an extension of Fisher’s exact test that takes annotation bias into account was employed (Wallenius’ non-central hypergeometric distribution).

Most specific annotations for this module

Coeff.1 P-value.2 Source.3 Term.4 Class.5 4.09e-01 1.55e-11 GO positive regulation of transcription from RNA polymerase II promoter in response to heat stress biological_process 3.16e-01 3.27e-09 Reactome RUNX3 regulates YAP1-mediated transcription Gene expression (Transcription) 3.81e-02 2.45e-05 GO axon initial segment cellular_component 3.70e-02 2.45e-05 GO myeloid dendritic cell differentiation biological_process 3.04e-02 4.46e-04 GO cellular response to interferon-alpha biological_process 3.04e-02 4.46e-04 GO histone H3-K36 demethylation biological_process 2.86e-02 3.66e-10 GO RNA polymerase II transcription factor binding molecular_function 1.95e-02 3.05e-08 Reactome YAP1- and WWTR1 (TAZ)-stimulated gene expression Gene expression (Transcription) 8.90e-03 1.16e-05 GO response to cAMP biological_process 2.95e-03 1.07e-04 GO response to radiation biological_process 2.10e-03 8.61e-05 GO spectrin binding molecular_function

¹Regression coefficient

²Fisher’s exact test nominal P-value

³Annotation source (Reactome, GO biological process (BP), molecular function (MF) and cellular component (CC))

⁴GO category or Reactome pathway

⁵High-level branch of annotation tree

Gene membership

All enriched annotations

Gene Ontology

P-value1 FDR2 Term 1.46e-12 1.35e-09 transcription from RNA polymerase II promoter 1.26e-09 6.58e-07 transcription regulatory region DNA binding 1.27e-09 6.62e-07 regulatory region DNA binding 1.03e-08 4.68e-06 RNA polymerase II transcription factor activity, sequence-specific DNA binding 2.70e-08 1.01e-05 transcription factor complex 1.77e-07 6.51e-05 transcription regulatory region sequence-specific DNA binding 2.05e-07 7.45e-05 RNA polymerase II regulatory region sequence-specific DNA binding 2.15e-07 7.78e-05 RNA polymerase II regulatory region DNA binding 4.27e-07 1.46e-04 core promoter proximal region DNA binding 4.35e-07 1.48e-04 transcription factor activity, RNA polymerase II core promoter proximal region sequence-specific binding 9.11e-07 2.91e-04 double-stranded DNA binding 1.15e-06 3.61e-04 transcriptional activator activity, RNA polymerase II transcription regulatory region sequence-specific binding 1.78e-06 8.07e-04 response to other organism 1.79e-06 5.41e-04 RNA polymerase II core promoter proximal region sequence-specific DNA binding 2.56e-06 7.50e-04 core promoter proximal region sequence-specific DNA binding 2.68e-06 1.17e-03 response to biotic stimulus 4.84e-06 2.01e-03 hippo signaling 1.15e-05 4.40e-03 response to virus 1.17e-05 3.02e-03 RNA polymerase II transcription factor binding 1.35e-05 5.06e-03 defense response to other organism

¹1Nominal enrichment p-value (Wallenius’ noncentral hypergeometric distribution)

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 8.91e-07 1.56e-04 YAP1 AND WWTR1 TAZ STIMULATED GENE EXPRESSION 1.48e-06 3.25e-04 YAP1 AND WWTR1 TAZ STIMULATED GENE EXPRESSION 8.86e-06 1.33e-03 FATTY ACID TRIACYLGLYCEROL AND KETONE BODY METABOLISM 3.72e-05 6.41e-03 FATTY ACID TRIACYLGLYCEROL AND KETONE BODY METABOLISM 4.34e-05 7.37e-03 PPARA ACTIVATES GENE EXPRESSION 5.81e-05 7.72e-03 PPARA ACTIVATES GENE EXPRESSION 7.02e-05 1.13e-02 INTERFERON ALPHA BETA SIGNALING 7.07e-05 9.25e-03 INTERFERON ALPHA BETA SIGNALING 2.68e-04 3.09e-02 ACTIVATION OF GENES BY ATF4 7.42e-04 7.69e-02 PERK REGULATED GENE EXPRESSION 8.14e-04 9.83e-02 INTERFERON SIGNALING 1.14e-03 1.13e-01 INTERFERON SIGNALING 3.06e-03 3.06e-01 CYTOKINE SIGNALING IN IMMUNE SYSTEM 3.72e-03 3.57e-01 GENERIC TRANSCRIPTION PATHWAY 3.78e-03 3.24e-01 CYTOKINE SIGNALING IN IMMUNE SYSTEM 4.28e-03 4.02e-01 ACTIVATION OF GENES BY ATF4 4.71e-03 4.35e-01 INTERACTION BETWEEN L1 AND ANKYRINS 4.90e-03 4.50e-01 PERK REGULATED GENE EXPRESSION 6.07e-03 4.83e-01 INTERACTION BETWEEN L1 AND ANKYRINS 1.44e-02 9.84e-01 ACTIVATION OF CHAPERONE GENES BY ATF6 ALPHA

¹1Nominal enrichment p-value (Wallenius’ noncentral hypergeometric distribution)

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 9.73e-06 4.64e-02 abnormal optic fissure closure 5.37e-05 1.50e-01 abnormal posterior eye segment morphology 2.43e-04 3.95e-01 abnormal ocular fundus morphology 4.08e-04 5.37e-01 decreased thyrotroph cell number 1.84e-03 1.00e+00 increased circulating magnesium level 2.61e-03 1.00e+00 right atrial isomerism 2.81e-03 1.00e+00 abnormal synaptonemal complex 2.99e-03 1.00e+00 abnormal eye distance/ position 3.46e-03 1.00e+00 abnormal iris pigmentation 3.81e-03 1.00e+00 abnormal photoreceptor inner segment morphology 4.38e-03 1.00e+00 double outlet right ventricle with atrioventricular septal defect 4.74e-03 1.00e+00 abnormal osteoclast morphology 4.93e-03 1.00e+00 enlarged third ventricle 6.29e-03 1.00e+00 partial prenatal lethality 6.78e-03 1.00e+00 abnormal lens development 6.79e-03 1.00e+00 enhanced wound healing 8.12e-03 1.00e+00 increased anxiety-related response 8.22e-03 1.00e+00 abnormal lens morphology 9.78e-03 1.00e+00 eyelids fail to open 9.82e-03 1.00e+00 abnormal nursing

¹1Nominal enrichment p-value (Wallenius’ noncentral hypergeometric distribution)

²FDR corrected p-value (Benjamini-Hochberg)