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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod367

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod367 Module size 43 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 53335 BCL11A B cell CLL/lymphoma 11A 255877 BCL6B B cell CLL/lymphoma 6B 1877 E4F1 E4F transcription factor 1 1960 EGR3 early growth response 3 2672 GFI1 growth factor independent 1 transcriptional repressor 8328 GFI1B growth factor independent 1B transcriptional repressor 3090 HIC1 HIC ZBTB transcriptional repressor 1 10661 KLF1 Kruppel like factor 1 7071 KLF10 Kruppel like factor 10 8462 KLF11 Kruppel like factor 11 51621 KLF13 Kruppel like factor 13 10365 KLF2 Kruppel like factor 2 51274 KLF3 Kruppel like factor 3 11279 KLF8 Kruppel like factor 8 687 KLF9 Kruppel like factor 9 112939 NACC1 nucleus accumbens associated 1 138151 NACC2 NACC family member 2 23598 PATZ1 POZ/BTB and AT hook containing zinc finger 1 11108 PRDM4 PR/SET domain 4 11107 PRDM5 PR/SET domain 5 29803 REPIN1 replication initiator 1 5978 REST RE1 silencing transcription factor 6671 SP4 Sp4 transcription factor 126248 WDR88 WD repeat domain 88 7709 ZBTB17 zinc finger and BTB domain containing 17 27033 ZBTB32 zinc finger and BTB domain containing 32 51341 ZBTB7A zinc finger and BTB domain containing 7A 51043 ZBTB7B zinc finger and BTB domain containing 7B 7541 ZFP161 zinc finger and BTB domain containing 14 7545 ZIC1 Zic family member 1 7690 ZNF131 zinc finger protein 131 129025 ZNF280A zinc finger protein 280A 140883 ZNF280B zinc finger protein 280B 55609 ZNF280C zinc finger protein 280C 54816 ZNF280D zinc finger protein 280D 49854 ZNF295 zinc finger and BTB domain containing 21 149076 ZNF362 zinc finger protein 362 171017 ZNF384 zinc finger protein 384 23090 ZNF423 zinc finger protein 423 51710 ZNF44 zinc finger protein 44 57592 ZNF687 zinc finger protein 687 7629 ZNF76 zinc finger protein 76 152485 ZNF827 zinc finger protein 827

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 2.70e-01 6.26e-12 GO cellular response to peptide biological_process 1.33e-02 2.06e-04 GO ectoderm development 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 RNA polymerase II transcription factor activity, sequence-specific DNA binding 2.84e-11 2.48e-08 negative regulation of transcription from RNA polymerase II promoter 4.28e-10 2.42e-07 transcription regulatory region DNA binding 4.32e-10 2.44e-07 regulatory region DNA binding 2.01e-08 8.74e-06 transcription regulatory region sequence-specific DNA binding 6.27e-08 2.48e-05 double-stranded DNA binding 1.67e-07 6.17e-05 transcriptional repressor activity, RNA polymerase II transcription regulatory region sequence-specific binding 4.63e-07 1.56e-04 transcription factor activity, RNA polymerase II core promoter proximal region sequence-specific binding 1.92e-06 8.66e-04 transcription from RNA polymerase II promoter 3.45e-06 9.87e-04 transcriptional repressor activity, RNA polymerase II core promoter proximal region sequence-specific binding 5.11e-06 1.41e-03 core promoter proximal region sequence-specific DNA binding 5.12e-06 1.41e-03 core promoter proximal region DNA binding 7.64e-06 2.04e-03 RNA polymerase II regulatory region sequence-specific DNA binding 7.73e-06 2.06e-03 RNA polymerase II regulatory region DNA binding 3.25e-05 7.67e-03 RNA polymerase II core promoter proximal region sequence-specific DNA binding 6.33e-05 1.97e-02 cellular response to organonitrogen compound 7.24e-05 2.21e-02 hemopoiesis 9.57e-05 2.81e-02 cellular response to peptide 1.39e-04 3.86e-02 histone deacetylation 1.64e-04 4.44e-02 protein deacetylation

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 5.00e-03 4.11e-01 REGULATION OF THE FANCONI ANEMIA PATHWAY 6.14e-03 5.41e-01 REGULATION OF THE FANCONI ANEMIA PATHWAY 9.73e-03 7.16e-01 P75 NTR RECEPTOR MEDIATED SIGNALLING 1.46e-02 9.94e-01 SIGNALLING BY NGF 1.60e-02 1.00e+00 FANCONI ANEMIA PATHWAY 2.11e-02 1.00e+00 P75 NTR RECEPTOR MEDIATED SIGNALLING 2.64e-02 1.00e+00 FANCONI ANEMIA PATHWAY 2.73e-02 1.00e+00 SIGNALLING BY NGF 2.80e-02 1.00e+00 DNA REPAIR 3.94e-02 1.00e+00 ACTIVATION OF CHAPERONE GENES BY XBP1S 4.53e-02 1.00e+00 UNFOLDED PROTEIN RESPONSE

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 8.44e-04 8.19e-01 abnormal embryonic erythrocyte morphology 1.07e-03 9.34e-01 absent CD4-positive, alpha beta T cells 1.08e-03 9.40e-01 abnormal erythropoiesis 1.39e-03 1.00e+00 complete lethality throughout fetal growth and development 2.31e-03 1.00e+00 cerebellum hypoplasia 2.43e-03 1.00e+00 abnormal cerebellum vermis morphology 8.01e-03 1.00e+00 abnormal cerebellum development 8.89e-03 1.00e+00 abnormal choroid plexus morphology 8.91e-03 1.00e+00 abnormal CD4-positive, alpha beta T cell morphology 9.28e-03 1.00e+00 abnormal T cell differentiation 9.33e-03 1.00e+00 increased red blood cell distribution width 9.34e-03 1.00e+00 abnormal descending aorta morphology 9.58e-03 1.00e+00 decreased trabecular bone volume 1.08e-02 1.00e+00 ataxia 1.11e-02 1.00e+00 decreased thymocyte number 1.11e-02 1.00e+00 impaired contextual conditioning behavior 1.49e-02 1.00e+00 decreased presacral vertebrae number 1.55e-02 1.00e+00 impaired hematopoiesis 1.59e-02 1.00e+00 increased nucleated erythrocyte cell number 1.67e-02 1.00e+00 absent erythrocytes

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

²FDR corrected p-value (Benjamini-Hochberg)