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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod7

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod7 Module size 89 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 140690 CTCFL CCCTC-binding factor like 6018 RLF rearranged L-myc fusion 65986 ZBTB10 zinc finger and BTB domain containing 10 57621 ZBTB2 zinc finger and BTB domain containing 2 10009 ZBTB33 zinc finger and BTB domain containing 33 403341 ZBTB34 zinc finger and BTB domain containing 34 80108 ZFP2 ZFP2 zinc finger protein 139735 ZFP92 ZFP92 zinc finger protein 284307 ZIK1 zinc finger protein interacting with K protein 1 163227 ZNF100 zinc finger protein 100 51427 ZNF107 zinc finger protein 107 7692 ZNF133 zinc finger protein 133 7699 ZNF140 zinc finger protein 140 7700 ZNF141 zinc finger protein 141 7705 ZNF146 zinc finger protein 146 7711 ZNF155 zinc finger protein 155 7712 ZNF157 zinc finger protein 157 90338 ZNF160 zinc finger protein 160 7743 ZNF189 zinc finger protein 189 7752 ZNF200 zinc finger protein 200 7988 ZNF212 zinc finger protein 212 7761 ZNF214 zinc finger protein 214 7770 ZNF227 zinc finger protein 227 7551 ZNF3 zinc finger protein 3 57343 ZNF304 zinc finger protein 304 150 ZNF32 adrenoceptor alpha 2A 79175 ZNF343 zinc finger protein 343 7584 ZNF35 zinc finger protein 35 57541 ZNF398 zinc finger protein 398 84330 ZNF414 zinc finger protein 414 55786 ZNF415 zinc finger protein 415 79088 ZNF426 zinc finger protein 426 353088 ZNF429 zinc finger protein 429 220929 ZNF438 zinc finger protein 438 126070 ZNF440 zinc finger protein 440 388566 ZNF470 zinc finger protein 470 220992 ZNF485 zinc finger protein 485 26048 ZNF500 zinc finger protein 500 440515 ZNF506 zinc finger protein 506 84450 ZNF512 zinc finger protein 512 9658 ZNF516 zinc finger protein 516 340385 ZNF517 zinc finger protein 517 348327 ZNF530 zinc finger protein 530 284306 ZNF547 zinc finger protein 547 79818 ZNF552 zinc finger protein 552 84527 ZNF559 zinc finger protein 559 100529215 ZNF559-ZNF177 ZNF559-ZNF177 readthrough 126295 ZNF57 zinc finger protein 57 163033 ZNF579 zinc finger protein 579 84914 ZNF587 zinc finger protein 587 152687 ZNF595 zinc finger protein 595 169270 ZNF596 zinc finger protein 596 148103 ZNF599 zinc finger protein 599 84775 ZNF607 zinc finger protein 607 90317 ZNF616 zinc finger protein 616 57547 ZNF624 zinc finger protein 624 90589 ZNF625 zinc finger protein 625 51193 ZNF639 zinc finger protein 639 9726 ZNF646 zinc finger protein 646 55279 ZNF654 zinc finger protein 654 79027 ZNF655 zinc finger protein 655 285349 ZNF660 zinc finger protein 660 79894 ZNF672 zinc finger protein 672 641339 ZNF674 zinc finger protein 674 168417 ZNF679 zinc finger protein 679 340252 ZNF680 zinc finger protein 680 127396 ZNF684 zinc finger protein 684 146542 ZNF688 zinc finger protein 688 55657 ZNF692 zinc finger protein 692 124411 ZNF720 zinc finger protein 720 170960 ZNF721 zinc finger protein 721 388523 ZNF728 zinc finger protein 728 148203 ZNF738 zinc finger protein 738 7625 ZNF74 zinc finger protein 74 7627 ZNF75A zinc finger protein 75a 91661 ZNF765 zinc finger protein 765 79724 ZNF768 zinc finger protein 768 58492 ZNF77 zinc finger protein 77 284323 ZNF780A zinc finger protein 780A 136051 ZNF786 zinc finger protein 786 388536 ZNF790 zinc finger protein 790 126375 ZNF792 zinc finger protein 792 390980 ZNF805 zinc finger protein 805 388558 ZNF808 zinc finger protein 808 55769 ZNF83 zinc finger protein 83 7637 ZNF84 zinc finger protein 84 7639 ZNF85 zinc finger protein 85 168374 ZNF92 zinc finger protein 92 222696 ZSCAN23 zinc finger and SCAN domain containing 23

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 3.01e-02 1.30e-57 Reactome Generic Transcription Pathway Gene expression (Transcription) 4.41e-03 6.27e-55 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 3.87e-04 9.09e-02 regulation of histone methylation 4.25e-04 9.81e-02 transcription from RNA polymerase II promoter 5.67e-04 1.24e-01 regulation of histone modification 9.07e-04 1.82e-01 histone methylation 9.23e-04 1.85e-01 regulation of chromatin organization 1.91e-03 3.33e-01 covalent chromatin modification 1.95e-03 3.34e-01 positive regulation of histone H3-K9 trimethylation 1.95e-03 3.34e-01 positive regulation of histone H3-K9 methylation 1.95e-03 3.34e-01 regulation of methylation-dependent chromatin silencing 1.95e-03 3.34e-01 positive regulation of methylation-dependent chromatin silencing 2.71e-03 4.36e-01 protein methylation 3.89e-03 5.71e-01 positive regulation of chromatin silencing 3.90e-03 5.71e-01 negative regulation by host of viral transcription 3.90e-03 5.71e-01 regulation of histone H3-K9 trimethylation 4.29e-03 6.15e-01 regulation of chromosome organization 5.35e-03 7.33e-01 chromatin organization 5.84e-03 7.72e-01 positive regulation by host of viral transcription 5.84e-03 7.72e-01 regulation of histone H3-K9 methylation 7.53e-03 8.56e-01 core promoter proximal region sequence-specific DNA binding 7.53e-03 8.56e-01 core promoter proximal region DNA binding

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 2.99e-04 4.47e-01 abnormal spermatogenesis 3.75e-03 1.00e+00 testis hypoplasia 3.77e-03 1.00e+00 abnormal testis morphology 1.47e-02 1.00e+00 abnormal male meiosis 1.53e-02 1.00e+00 small testis 1.62e-02 1.00e+00 postnatal lethality 1.89e-02 1.00e+00 abnormal male germ cell apoptosis 3.16e-02 1.00e+00 reduced male fertility

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

²FDR corrected p-value (Benjamini-Hochberg)