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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod354

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod354 Module size 67 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 1961 EGR4 early growth response 4 84662 GLIS2 GLIS family zinc finger 2 11278 KLF12 Kruppel like factor 12 80320 KLF14 Sp6 transcription factor 63976 PRDM16 PR/SET domain 16 3093 UBE2K ubiquitin conjugating enzyme E2 K 26137 ZBTB20 zinc finger and BTB domain containing 20 9880 ZBTB39 zinc finger and BTB domain containing 39 9923 ZBTB40 zinc finger and BTB domain containing 40 360023 ZBTB41 zinc finger and BTB domain containing 41 29068 ZBTB44 zinc finger and BTB domain containing 44 221504 ZBTB9 zinc finger and BTB domain containing 9 57623 ZFAT zinc finger and AT-hook domain containing 64397 ZFP106 zinc finger protein 106 22835 ZFP30 ZFP30 zinc finger protein 7539 ZFP37 ZFP37 zinc finger protein 146198 ZFP90 ZFP90 zinc finger protein 7556 ZNF10 zinc finger protein 10 7559 ZNF12 zinc finger protein 12 7733 ZNF180 zinc finger protein 180 7748 ZNF195 zinc finger protein 195 7755 ZNF205 zinc finger protein 205 7570 ZNF22 zinc finger protein 22 8187 ZNF239 zinc finger protein 239 113835 ZNF257 zinc finger protein 257 91975 ZNF300 zinc finger protein 300 55900 ZNF302 zinc finger protein 302 57693 ZNF317 zinc finger protein 317 64288 ZNF323 zinc finger and SCAN domain containing 31 55713 ZNF334 zinc finger protein 334 59348 ZNF350 zinc finger protein 350 167465 ZNF366 zinc finger protein 366 346157 ZNF391 zinc finger protein 391 79744 ZNF419 zinc finger protein 419 80818 ZNF436 zinc finger protein 436 79973 ZNF442 zinc finger protein 442 58499 ZNF462 zinc finger protein 462 170958 ZNF525 zinc finger protein 525 162972 ZNF550 zinc finger protein 550 163081 ZNF567 zinc finger protein 567 79177 ZNF576 zinc finger protein 576 201514 ZNF584 zinc finger protein 584 89887 ZNF628 zinc finger protein 628 84146 ZNF644 zinc finger protein 644 65251 ZNF649 zinc finger protein 649 144348 ZNF664 zinc finger protein 664 93474 ZNF670 zinc finger protein 670 342926 ZNF677 zinc finger protein 677 57116 ZNF695 zinc finger protein 695 374879 ZNF699 zinc finger protein 699 7562 ZNF708 zinc finger protein 708 7552 ZNF711 zinc finger protein 711 100131827 ZNF717 zinc finger protein 717 654254 ZNF732 zinc finger protein 732 126208 ZNF787 zinc finger protein 787 285989 ZNF789 zinc finger protein 789 90576 ZNF799 zinc finger protein 799 7554 ZNF8 zinc finger protein 8 7634 ZNF80 zinc finger protein 80 125893 ZNF816 zinc finger protein 816 55552 ZNF823 zinc finger protein 823 284391 ZNF844 zinc finger protein 844 643641 ZNF862 zinc finger protein 862 7643 ZNF90 zinc finger protein 90 79149 ZSCAN5A zinc finger and SCAN domain containing 5A 342933 ZSCAN5B zinc finger and SCAN domain containing 5B 649137 ZSCAN5C zinc finger and SCAN domain containing 5C

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 9.21e-03 7.12e-26 Reactome Generic Transcription Pathway Gene expression (Transcription)

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 negative regulation of transcription from RNA polymerase II promoter 2.42e-09 1.21e-06 RNA polymerase II transcription factor activity, sequence-specific DNA binding 3.41e-05 8.02e-03 transcriptional repressor activity, RNA polymerase II transcription regulatory region sequence-specific binding 1.41e-04 3.91e-02 negative regulation of DNA binding 1.41e-04 2.78e-02 transcription factor activity, RNA polymerase II core promoter proximal region sequence-specific binding 1.77e-04 4.74e-02 regulation of DNA binding 3.56e-04 6.26e-02 transcription regulatory region DNA binding 3.57e-04 6.04e-02 transcriptional repressor complex 3.62e-04 6.35e-02 regulatory region DNA binding 8.47e-04 1.73e-01 negative regulation of binding 1.45e-03 2.00e-01 filopodium tip 1.95e-03 3.34e-01 positive regulation of peptidyl-threonine phosphorylation 1.96e-03 3.36e-01 positive regulation of tumor necrosis factor production 2.81e-03 4.48e-01 regulation of binding 3.89e-03 5.71e-01 free ubiquitin chain polymerization 3.90e-03 5.71e-01 spongiotrophoblast layer development 3.90e-03 5.71e-01 response to interferon-beta 3.90e-03 5.71e-01 cellular response to interferon-beta 4.82e-03 5.95e-01 transcriptional repressor activity, RNA polymerase II core promoter proximal region sequence-specific binding 5.84e-03 7.72e-01 regulation of cellular respiration

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 0.00e+00 0.00e+00 GENERIC TRANSCRIPTION PATHWAY 9.02e-03 7.37e-01 NEGATIVE REGULATORS OF RIG I MDA5 SIGNALING 1.19e-02 9.15e-01 RIG I MDA5 MEDIATED INDUCTION OF IFN ALPHA BETA PATHWAYS 3.75e-02 1.00e+00 INNATE IMMUNE SYSTEM

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 1.32e-03 1e+00 micrognathia 3.64e-03 1e+00 short snout 3.74e-03 1e+00 premature bone ossification 3.74e-03 1e+00 submandibular gland hypoplasia 3.74e-03 1e+00 abnormal submandibular duct morphology 4.04e-03 1e+00 increased blood urea nitrogen level 5.61e-03 1e+00 eye hemorrhage 5.61e-03 1e+00 abnormal sublingual gland morphology 7.47e-03 1e+00 abnormal Ammon gyrus morphology 7.47e-03 1e+00 decreased dentate gyrus size 7.47e-03 1e+00 small maxilla 7.47e-03 1e+00 abnormal palatal shelf elevation 9.33e-03 1e+00 renal glomerulus atrophy 9.34e-03 1e+00 detached sperm flagellum 9.36e-03 1e+00 abnormal Meckel's cartilage morphology 1.12e-02 1e+00 kidney medulla atrophy 1.31e-02 1e+00 mandible hypoplasia 1.49e-02 1e+00 abnormal glycogen homeostasis 1.68e-02 1e+00 abnormal tongue morphology 1.68e-02 1e+00 small mandible

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

²FDR corrected p-value (Benjamini-Hochberg)