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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod63

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod63 Module size 64 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 23394 ADNP activity dependent neuroprotector homeobox 22850 ADNP2 ADNP homeobox 2 27245 AHDC1 AT-hook DNA binding motif containing 1 84159 ARID5B AT-rich interaction domain 5B 26053 AUTS2 AUTS2, activator of transcription and developmental regulator 22893 BAHD1 bromo adjacent homology domain containing 1 84312 BRMS1L BRMS1 like transcriptional repressor 84458 C10orf12 ligand dependent nuclear receptor corepressor 56946 C11orf30 EMSY, BRCA2 interacting transcriptional repressor 10263 CDK2AP2 cyclin dependent kinase 2 associated protein 2 306007 DBC1 cell cycle and apoptosis regulator 2 29947 DNMT3L DNA methyltransferase 3 like 116092 DNTTIP1 deoxynucleotidyltransferase terminal interacting protein 1 2130 EWSR1 EWS RNA binding protein 1 54478 FAM64A PICALM interacting mitotic regulator 57798 GATAD1 GATA zinc finger domain containing 1 57459 GATAD2B GATA zinc finger domain containing 2B 55105 GPATCH2 G-patch domain containing 2 341567 H1FNT H1 histone family member N, testis specific 25988 HINFP histone H4 transcription factor 3094 HINT1 histidine triad nucleotide binding protein 1 340784 HMX3 H6 family homeobox 3 3720 JARID2 jumonji and AT-rich interaction domain containing 2 23028 KDM1A lysine demethylase 1A 9813 KIAA0494 EF-hand calcium binding domain 14 1800 MBD1 dipeptidase 1 57708 MIER1 MIER1 transcriptional regulator 4335 MNT MAX network transcriptional repressor 4084 MXD1 MAX dimerization protein 1 4610 MYCL1 MYCL proto-oncogene, bHLH transcription factor 4613 MYCN MYCN proto-oncogene, bHLH transcription factor 91942 NDUFAF2 NADH:ubiquinone oxidoreductase complex assembly factor 2 579 NKX3-2 NK3 homeobox 2 23469 PHF3 PHD finger protein 3 5371 PML promyelocytic leukemia 84106 PRAM1 PML-RARA regulated adaptor molecule 1 639 PRDM1 PR/SET domain 1 84726 PRRC2B proline rich coiled-coil 2B 23215 PRRC2C proline rich coiled-coil 2C 64783 RBM15 RNA binding motif protein 15 23186 RCOR1 REST corepressor 1 55758 RCOR3 REST corepressor 3 5994 RFXAP regulatory factor X associated protein 100316904 SAP25 Sin3A associated protein 25 6304 SATB1 SATB homeobox 1 10924 SMPDL3A sphingomyelin phosphodiesterase acid like 3A 6615 SNAI1 snail family transcriptional repressor 1 6657 SOX2 SRY-box 2 6706 SPRR2G small proline rich protein 2G 90665 TBL1Y transducin beta like 1 Y-linked 57215 THAP11 THAP domain containing 11 80764 THAP7 THAP domain containing 7 134285 TMEM171 transmembrane protein 171 137835 TMEM71 transmembrane protein 71 5987 TRIM27 tripartite motif containing 27 54887 UHRF1BP1 UHRF1 binding protein 1 7391 USF1 upstream transcription factor 1 9839 ZEB2 zinc finger E-box binding homeobox 2 23051 ZHX3 zinc fingers and homeoboxes 3 7750 ZMYM2 zinc finger MYM-type containing 2 9203 ZMYM3 zinc finger MYM-type containing 3 9202 ZMYM4 zinc finger MYM-type containing 4 10771 ZMYND11 zinc finger MYND-type containing 11 55893 ZNF395 zinc finger protein 395

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 1.18e-01 5.47e-03 Reactome Regulation of TP53 Expression Gene expression (Transcription) 2.95e-02 3.25e-04 GO fibroblast migration biological_process 1.38e-02 4.18e-06 GO histone deacetylase activity molecular_function 9.82e-03 4.78e-05 GO regulation of cell morphogenesis biological_process 8.27e-03 4.78e-05 GO histone demethylase activity molecular_function 3.47e-03 4.75e-04 GO trophoblast giant cell differentiation biological_process

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 0.00e+00 0.00e+00 transcription regulatory region DNA binding 0.00e+00 0.00e+00 regulatory region DNA binding 4.35e-11 3.74e-08 negative regulation of transcription from RNA polymerase II promoter 9.51e-10 5.07e-07 transcriptional repressor activity, RNA polymerase II transcription regulatory region sequence-specific binding 9.16e-09 4.20e-06 double-stranded DNA binding 9.60e-09 4.40e-06 chromatin binding 2.63e-08 1.12e-05 RNA polymerase II transcription factor activity, sequence-specific DNA binding 1.01e-07 3.88e-05 transcription regulatory region sequence-specific DNA binding 1.36e-07 4.52e-05 chromatin 4.07e-07 2.08e-04 chromatin organization 4.56e-07 1.41e-04 nuclear chromatin 1.50e-06 4.62e-04 RNA polymerase II regulatory region sequence-specific DNA binding 1.51e-06 4.65e-04 RNA polymerase II regulatory region DNA binding 2.25e-06 6.21e-04 nuclear chromosome 2.39e-06 7.04e-04 transcription cofactor activity 2.99e-06 8.02e-04 nuclear body 6.34e-06 1.72e-03 transcription factor activity, transcription factor binding 6.96e-06 1.87e-03 transcription factor activity, protein binding 1.15e-05 4.40e-03 covalent chromatin modification 1.61e-05 4.04e-03 transcription corepressor activity

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 9.50e-03 7.70e-01 FACTORS INVOLVED IN MEGAKARYOCYTE DEVELOPMENT AND PLATELET PRODUCTION 9.66e-03 7.14e-01 SIGNALING BY FGFR1 FUSION MUTANTS 9.68e-03 7.14e-01 SIGNALING BY FGFR1 MUTANTS 9.71e-03 7.15e-01 SIGNALING BY FGFR MUTANTS 1.10e-02 7.90e-01 FACTORS INVOLVED IN MEGAKARYOCYTE DEVELOPMENT AND PLATELET PRODUCTION 1.31e-02 9.12e-01 SIGNALING BY FGFR IN DISEASE 2.13e-02 1.00e+00 SIGNALING BY FGFR1 FUSION MUTANTS 2.14e-02 1.00e+00 SIGNALING BY FGFR1 MUTANTS 2.48e-02 1.00e+00 SIGNALING BY FGFR MUTANTS 2.59e-02 1.00e+00 APOPTOTIC CLEAVAGE OF CELLULAR PROTEINS 3.14e-02 1.00e+00 APOPTOTIC CLEAVAGE OF CELLULAR PROTEINS 3.18e-02 1.00e+00 SIGNALING BY FGFR IN DISEASE 4.03e-02 1.00e+00 INTERFERON GAMMA SIGNALING 4.06e-02 1.00e+00 APOPTOTIC EXECUTION PHASE 4.50e-02 1.00e+00 APOPTOTIC EXECUTION PHASE 4.87e-02 1.00e+00 INTERFERON GAMMA SIGNALING

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 6.96e-04 7.33e-01 abnormal vertebral body development 1.36e-03 1.00e+00 increased trophoblast giant cell number 1.88e-03 1.00e+00 absent plasma cells 2.77e-03 1.00e+00 failure to form egg cylinders 3.05e-03 1.00e+00 abnormal embryogenesis/ development 5.36e-03 1.00e+00 abnormal fetal cardiomyocyte proliferation 6.23e-03 1.00e+00 abnormal palate morphology 6.79e-03 1.00e+00 abnormal stomach morphology 9.34e-03 1.00e+00 abnormal neural crest cell delamination 9.60e-03 1.00e+00 abnormal neural plate morphology 9.78e-03 1.00e+00 abnormal vestibular saccule morphology 9.90e-03 1.00e+00 abnormal neurocranium morphology 9.92e-03 1.00e+00 increased fibroblast proliferation 1.12e-02 1.00e+00 abnormal whisker trimming behavior 1.31e-02 1.00e+00 small occipital bone 1.58e-02 1.00e+00 abnormal semicircular canal morphology 1.59e-02 1.00e+00 embryonic growth arrest 1.67e-02 1.00e+00 abnormal circadian persistence 1.68e-02 1.00e+00 absent first pharyngeal arch 1.68e-02 1.00e+00 abnormal guard hair morphology

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

²FDR corrected p-value (Benjamini-Hochberg)