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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod366

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod366 Module size 63 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 389549 FEZF1 FEZ family zinc finger 1 55079 FEZF2 FEZ family zinc finger 2 2738 GLI4 GLI family zinc finger 4 148979 GLIS1 GLIS family zinc finger 1 169792 GLIS3 GLIS family zinc finger 3 64412 GZF1 GDNF inducible zinc finger protein 1 23119 HIC2 HIC ZBTB transcriptional repressor 2 3097 HIVEP2 human immunodeficiency virus type I enhancer binding protein 2 59269 HIVEP3 human immunodeficiency virus type I enhancer binding protein 3 28999 KLF15 Kruppel like factor 15 1316 KLF6 Kruppel like factor 6 8609 KLF7 Kruppel like factor 7 4150 MAZ MYC associated zinc finger protein 4241 MTF1 melanotransferrin 55892 MYNN myoneurin 55922 NKRF NFKB repressing factor 116039 OSR2 odd-skipped related transciption factor 2 5325 PLAGL1 PLAG1 like zinc finger 1 5326 PLAGL2 PLAG1 like zinc finger 2 93166 PRDM6 PR/SET domain 6 56978 PRDM8 PR/SET domain 8 6239 RREB1 ras responsive element binding protein 1 389058 SP5 Sp5 transcription factor 121340 SP7 Sp7 transcription factor 221833 SP8 Sp8 transcription factor 100131390 SP9 Sp9 transcription factor 9841 ZBTB24 zinc finger and BTB domain containing 24 57684 ZBTB26 zinc finger and BTB domain containing 26 79842 ZBTB3 zinc finger and BTB domain containing 3 253461 ZBTB38 zinc finger and BTB domain containing 38 57659 ZBTB4 zinc finger and BTB domain containing 4 23099 ZBTB43 zinc finger and BTB domain containing 43 9925 ZBTB5 zinc finger and BTB domain containing 5 10773 ZBTB6 zinc finger and BTB domain containing 6 653121 ZBTB8A zinc finger and BTB domain containing 8A 132625 ZFP42 ZFP42 zinc finger protein 284406 ZFP82 ZFP82 zinc finger protein 80829 ZFP91 ZFP91 zinc finger protein 84107 ZIC4 Zic family member 4 85416 ZIC5 Zic family member 5 7694 ZNF135 zinc finger protein 135 7707 ZNF148 zinc finger protein 148 7757 ZNF208 zinc finger protein 208 51222 ZNF219 zinc finger protein 219 10793 ZNF273 zinc finger protein 273 23528 ZNF281 zinc finger protein 281 63925 ZNF335 zinc finger protein 335 6940 ZNF354A zinc finger protein 354A 10224 ZNF443 zinc finger protein 443 57573 ZNF471 zinc finger protein 471 57474 ZNF490 zinc finger protein 490 57473 ZNF512B zinc finger protein 512B 130557 ZNF513 zinc finger protein 513 162655 ZNF519 zinc finger protein 519 51385 ZNF589 zinc finger protein 589 22834 ZNF652 zinc finger protein 652 65988 ZNF747 zinc finger protein 747 92595 ZNF764 zinc finger protein 764 374928 ZNF773 zinc finger protein 773 54753 ZNF853 zinc finger protein 853 7644 ZNF91 zinc finger protein 91 7789 ZXDA zinc finger X-linked duplicated A 79364 ZXDC ZXD family zinc finger C

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 2.75e-02 8.19e-03 Reactome MTF1 activates gene expression Cellular responses to external stimuli 3.73e-03 3.74e-07 GO transcriptional repressor activity, RNA polymerase II transcription regulatory region sequence-specific DNA 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 0.00e+00 0.00e+00 RNA polymerase II regulatory region DNA binding 0.00e+00 0.00e+00 double-stranded DNA binding 0.00e+00 0.00e+00 RNA polymerase II regulatory region sequence-specific DNA binding 0.00e+00 0.00e+00 transcription regulatory region DNA binding 0.00e+00 0.00e+00 transcription regulatory region sequence-specific DNA binding 0.00e+00 0.00e+00 regulatory region DNA binding 0.00e+00 0.00e+00 RNA polymerase II transcription factor activity, sequence-specific DNA binding 2.62e-10 2.09e-07 transcription from RNA polymerase II promoter 1.82e-08 1.14e-05 negative regulation of transcription from RNA polymerase II promoter 3.78e-07 1.30e-04 transcriptional activator activity, RNA polymerase II transcription regulatory region sequence-specific binding 4.88e-07 1.63e-04 RNA polymerase II core promoter proximal region sequence-specific DNA binding 5.83e-07 1.93e-04 transcription factor activity, RNA polymerase II core promoter proximal region sequence-specific binding 6.02e-07 1.98e-04 core promoter proximal region sequence-specific DNA binding 7.04e-07 2.29e-04 core promoter proximal region DNA binding 1.97e-06 5.91e-04 transcriptional repressor activity, RNA polymerase II transcription regulatory region sequence-specific binding 5.92e-06 2.41e-03 forebrain anterior/posterior pattern specification 5.69e-05 1.27e-02 RNA polymerase II core promoter sequence-specific DNA binding 7.43e-05 1.60e-02 core promoter binding 9.71e-05 2.85e-02 kidney development 1.21e-04 3.44e-02 renal system development

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 2.52e-07 6.19e-05 GENERIC TRANSCRIPTION PATHWAY

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 6.98e-04 7.34e-01 abnormal axon guidance 2.49e-03 1.00e+00 abnormal caudal vertebrae morphology 4.31e-03 1.00e+00 absent corpus callosum 4.49e-03 1.00e+00 muscular ventricular septal defect 4.79e-03 1.00e+00 increased circulating ketone body level 4.81e-03 1.00e+00 abnormal thalamus morphology 4.83e-03 1.00e+00 decreased single-positive T cell number 5.61e-03 1.00e+00 adactyly 5.62e-03 1.00e+00 absent radius 6.44e-03 1.00e+00 small olfactory bulb 6.68e-03 1.00e+00 abnormal vitelline vasculature morphology 7.40e-03 1.00e+00 abnormal cerebral cortex morphology 7.48e-03 1.00e+00 hypopnea 7.48e-03 1.00e+00 small vomeronasal organ 7.48e-03 1.00e+00 increased teratoma incidence 7.86e-03 1.00e+00 partial embryonic lethality 8.57e-03 1.00e+00 abnormal incisor morphology 8.93e-03 1.00e+00 abnormal telencephalon development 9.34e-03 1.00e+00 abnormal genital tubercle morphology 9.34e-03 1.00e+00 absent caudal vertebrae

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

²FDR corrected p-value (Benjamini-Hochberg)