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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod338

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod338 Module size 87 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 128209 KLF17 Kruppel like factor 17 59336 PRDM13 PR/SET domain 13 221527 ZBTB12 zinc finger and BTB domain containing 12 346171 ZFP57 ZFP57 zinc finger protein 386607 ZFP91-CNTF ZFP91-CNTF readthrough (NMD candidate) 114026 ZIM3 zinc finger imprinted 3 80317 ZKSCAN3 zinc finger with KRAB and SCAN domains 3 7675 ZNF121 zinc finger protein 121 7693 ZNF134 zinc finger protein 134 7565 ZNF17 zinc finger protein 17 339318 ZNF181 zinc finger protein 181 7988 ZNF182 zinc finger protein 212 7738 ZNF184 zinc finger protein 184 105379427 ZNF2 zinc finger protein 73 7638 ZNF221 zinc finger protein 221 7766 ZNF223 zinc finger protein 223 353355 ZNF233 zinc finger protein 233 57209 ZNF248 zinc finger protein 248 342909 ZNF284 zinc finger protein 284 729288 ZNF286B zinc finger protein 286B 90075 ZNF30 zinc finger protein 30 282890 ZNF311 zinc finger protein 311 162967 ZNF320 zinc finger protein 320 399669 ZNF321P zinc finger protein 321, pseudogene 25799 ZNF324 zinc finger protein 324 342908 ZNF404 zinc finger protein 404 55659 ZNF416 zinc finger protein 416 147686 ZNF418 zinc finger protein 418 9668 ZNF432 zinc finger protein 432 163059 ZNF433 zinc finger protein 433 353274 ZNF445 zinc finger protein 445 203523 ZNF449 zinc finger protein 449 197407 ZNF48 zinc finger protein 48 642819 ZNF487P zinc finger protein 487 118738 ZNF488 zinc finger protein 488 126069 ZNF491 zinc finger protein 491 91392 ZNF502 zinc finger protein 502 116115 ZNF526 zinc finger protein 526 84503 ZNF527 zinc finger protein 527 57711 ZNF529 zinc finger protein 529 55205 ZNF532 zinc finger protein 532 147658 ZNF534 zinc finger protein 534 84215 ZNF541 zinc finger protein 541 147694 ZNF548 zinc finger protein 548 79230 ZNF557 zinc finger protein 557 147837 ZNF563 zinc finger protein 563 163050 ZNF564 zinc finger protein 564 84924 ZNF566 zinc finger protein 566 148268 ZNF570 zinc finger protein 570 284346 ZNF575 zinc finger protein 575 147949 ZNF583 zinc finger protein 583 54807 ZNF586 zinc finger protein 586 285267 ZNF619 zinc finger protein 619 199692 ZNF627 zinc finger protein 627 65243 ZNF643 ZFP69 zinc finger protein B 115950 ZNF653 zinc finger protein 653 79759 ZNF668 zinc finger protein 668 79891 ZNF671 zinc finger protein 671 163223 ZNF676 zinc finger protein 676 148213 ZNF681 zinc finger protein 681 79943 ZNF696 zinc finger protein 696 90874 ZNF697 zinc finger protein 697 55762 ZNF701 zinc finger protein 701 349075 ZNF713 zinc finger protein 713 728927 ZNF736 zinc finger protein 736 388567 ZNF749 zinc finger protein 749 90321 ZNF766 zinc finger protein 766 285971 ZNF775 zinc finger protein 775 284309 ZNF776 zinc finger protein 776 197320 ZNF778 zinc finger protein 778 163131 ZNF780B zinc finger protein 780B 163115 ZNF781 zinc finger protein 781 158431 ZNF782 zinc finger protein 782 147808 ZNF784 zinc finger protein 784 388507 ZNF788 zinc finger family member 788, pseudogene 168850 ZNF800 zinc finger protein 800 374899 ZNF829 zinc finger protein 829 128611 ZNF831 zinc finger protein 831 90485 ZNF835 zinc finger protein 835 116412 ZNF837 zinc finger protein 837 285346 ZNF852 zinc finger protein 852 729747 ZNF878 zinc finger protein 878 400713 ZNF880 zinc finger protein 880 101060200 ZNF891 zinc finger protein 891 148198 ZNF98 zinc finger protein 98 65982 ZSCAN18 zinc finger and SCAN domain containing 18 146050 ZSCAN29 zinc finger and SCAN domain containing 29

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 1.90e-02 3.37e-45 Reactome Generic Transcription Pathway Gene expression (Transcription) 1.74e-03 3.80e-43 Reactome RNA Polymerase II Transcription 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 2.07e-07 1.11e-04 negative regulation of transcription from RNA polymerase II promoter 1.57e-04 3.06e-02 transcription regulatory region DNA binding 1.59e-04 3.09e-02 regulatory region DNA binding 1.64e-04 3.18e-02 RNA polymerase II transcription factor activity, sequence-specific DNA binding 4.97e-04 8.36e-02 transcriptional repressor activity, RNA polymerase II transcription regulatory region sequence-specific binding 1.95e-03 3.34e-01 regulation of oligodendrocyte differentiation 1.95e-03 3.34e-01 positive regulation of oligodendrocyte differentiation 1.95e-03 3.34e-01 regulation of viral release from host cell 1.95e-03 3.34e-01 positive regulation by host of viral release from host cell 1.95e-03 3.34e-01 positive regulation of viral release from host cell 1.95e-03 3.34e-01 positive regulation by host of viral process 3.89e-03 5.71e-01 negative regulation of cellular senescence 3.90e-03 5.71e-01 positive regulation of gliogenesis 3.90e-03 5.71e-01 oligodendrocyte development 3.90e-03 5.71e-01 positive regulation of glial cell differentiation 3.90e-03 5.71e-01 regulation of gene expression by genetic imprinting 3.90e-03 5.71e-01 negative regulation of cell aging 3.91e-03 5.73e-01 regulation of glial cell differentiation 3.92e-03 5.74e-01 regulation of gliogenesis 3.92e-03 5.74e-01 positive regulation of viral life cycle

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 0e+00 0e+00 GENERIC TRANSCRIPTION PATHWAY

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 1.87e-03 1e+00 decreased mean platelet volume 1.87e-03 1e+00 abnormal imprinting 3.77e-03 1e+00 abnormal lens morphology 1.13e-02 1e+00 cataract 1.52e-02 1e+00 partial lethality throughout fetal growth and development 1.68e-02 1e+00 maternal effect 3.72e-02 1e+00 other phenotype

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

²FDR corrected p-value (Benjamini-Hochberg)