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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod97

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod97 Module size 37 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 4299 AFF1 AF4/FMR2 family member 1 27125 AFF4 AF4/FMR2 family member 4 222389 BEND7 BEN domain containing 7 904 CCNT1 cyclin T1 905 CCNT2 cyclin T2 304832 CDC73 cell division cycle 73 1025 CDK9 cyclin dependent kinase 9 311796 COBRA1 negative elongation factor complex member B 9150 CTDP1 CTD phosphatase subunit 1 9646 CTR9 CTR9 homolog, Paf1/RNA polymerase II complex component 85403 EAF1 ELL associated factor 1 55929 EAF2 DNA methyltransferase 1 associated protein 1 306347 ELL elongation factor for RNA polymerase II 22936 ELL2 elongation factor for RNA polymerase II 2 80237 ELL3 elongation factor for RNA polymerase II 3 55250 ELP2 elongator acetyltransferase complex subunit 2 26610 ELP4 elongator acetyltransferase complex subunit 4 23587 ELP5 elongator acetyltransferase complex subunit 5 54859 ELP6 elongator acetyltransferase complex subunit 6 2074 ERCC6 ERCC excision repair 6, chromatin remodeling factor 8518 IKBKAP elongator complex protein 1 25275 KTI12 2',3'-cyclic nucleotide 3' phosphodiesterase 364430 NUFIP1 NUFIP1, FMR1 interacting protein 1 54623 PAF1 PAF1 homolog, Paf1/RNA polymerase II complex component 5828 PEX2 peroxisomal biogenesis factor 2 7936 RDBP negative elongation factor complex member E 23168 RTF1 RTF1 homolog, Paf1/RNA polymerase II complex component 6827 SUPT4H1 SPT4 homolog, DSIF elongation factor subunit 6829 SUPT5H SPT5 homolog, DSIF elongation factor subunit 6917 TCEA1 transcription elongation factor A1 6919 TCEA2 transcription elongation factor A2 6924 TCEB3 elongin A 51497 TH1L negative elongation factor complex member C/D 85014 TMEM141 transmembrane protein 141 8458 TTF2 transcription termination factor 2 80349 WDR61 WD repeat domain 61 7469 WHSC2 negative elongation factor complex member A

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 4.56e-01 3.72e-16 GO Cdc73/Paf1 complex cellular_component 3.30e-01 1.54e-34 GO transcription elongation factor complex cellular_component 1.98e-01 9.80e-11 GO Elongator holoenzyme complex cellular_component 1.58e-01 4.38e-12 GO positive regulation of DNA-templated transcription, elongation biological_process 1.38e-01 8.25e-06 Reactome Interactions of Tat with host cellular proteins Disease 6.91e-02 2.41e-07 GO cyclin/CDK positive transcription elongation factor complex cellular_component 3.11e-02 4.89e-33 Reactome Formation of RNA Pol II elongation complex Gene expression (Transcription) 3.04e-02 4.89e-33 Reactome RNA Polymerase II Transcription Elongation Gene expression (Transcription) 2.45e-02 2.06e-42 GO transcription elongation from RNA polymerase II promoter biological_process 9.72e-04 6.72e-16 Reactome Pausing and recovery of HIV elongation Disease 5.27e-05 6.72e-16 Reactome HIV elongation arrest and recovery Disease

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 DNA-templated transcription, elongation 0.00e+00 0.00e+00 transcription from RNA polymerase II promoter 0.00e+00 0.00e+00 transcription elongation from RNA polymerase II promoter 0.00e+00 0.00e+00 positive regulation of transcription elongation from RNA polymerase II promoter 0.00e+00 0.00e+00 regulation of DNA-templated transcription, elongation 0.00e+00 0.00e+00 positive regulation of DNA-templated transcription, elongation 0.00e+00 0.00e+00 regulation of transcription elongation from RNA polymerase II promoter 0.00e+00 0.00e+00 transcription elongation factor complex 0.00e+00 0.00e+00 Cdc73/Paf1 complex 0.00e+00 0.00e+00 RNA polymerase binding 0.00e+00 0.00e+00 basal RNA polymerase II transcription machinery binding 0.00e+00 0.00e+00 RNA polymerase core enzyme binding 0.00e+00 0.00e+00 RNA polymerase II core binding 3.27e-11 1.75e-08 Elongator holoenzyme complex 4.19e-11 3.60e-08 regulation of mRNA 3'-end processing 2.52e-10 1.23e-07 DNA-directed RNA polymerase II, holoenzyme 2.46e-09 1.06e-06 transferase complex 6.73e-09 4.47e-06 negative regulation of mRNA polyadenylation 7.14e-09 4.72e-06 snRNA transcription from RNA polymerase II promoter 7.14e-09 4.72e-06 snRNA transcription

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 RNA POL II PRE TRANSCRIPTION EVENTS 0.00e+00 0.00e+00 ABORTIVE ELONGATION OF HIV1 TRANSCRIPT IN THE ABSENCE OF TAT 0.00e+00 0.00e+00 TRANSCRIPTION 0.00e+00 0.00e+00 FORMATION OF THE HIV1 EARLY ELONGATION COMPLEX 0.00e+00 0.00e+00 HIV LIFE CYCLE 0.00e+00 0.00e+00 RNA POL II TRANSCRIPTION 0.00e+00 0.00e+00 LATE PHASE OF HIV LIFE CYCLE 0.00e+00 0.00e+00 HIV INFECTION 0.00e+00 0.00e+00 ELONGATION ARREST AND RECOVERY 0.00e+00 0.00e+00 FORMATION OF RNA POL II ELONGATION COMPLEX 0.00e+00 0.00e+00 RNA POL II PRE TRANSCRIPTION EVENTS 0.00e+00 0.00e+00 TRANSCRIPTION 0.00e+00 0.00e+00 HIV LIFE CYCLE 0.00e+00 0.00e+00 RNA POL II TRANSCRIPTION 0.00e+00 0.00e+00 LATE PHASE OF HIV LIFE CYCLE 0.00e+00 0.00e+00 HIV INFECTION 0.00e+00 0.00e+00 ELONGATION ARREST AND RECOVERY 0.00e+00 0.00e+00 FORMATION OF RNA POL II ELONGATION COMPLEX 3.56e-10 9.18e-08 ABORTIVE ELONGATION OF HIV1 TRANSCRIPT IN THE ABSENCE OF TAT 2.64e-09 6.13e-07 FORMATION OF THE HIV1 EARLY ELONGATION COMPLEX

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 2.43e-04 3.95e-01 impaired balance 1.87e-03 1.00e+00 photophobia 1.87e-03 1.00e+00 pillar cell degeneration 5.61e-03 1.00e+00 cholestasis 5.61e-03 1.00e+00 increased seminal vesicle weight 7.24e-03 1.00e+00 abnormal cerebellum morphology 7.47e-03 1.00e+00 absent limb buds 7.47e-03 1.00e+00 absent trophectoderm cell proliferation 7.47e-03 1.00e+00 increased prostate intraepithelial neoplasia incidence 7.48e-03 1.00e+00 absent pharyngeal arches 7.48e-03 1.00e+00 abnormal head movements 7.48e-03 1.00e+00 abnormal interparietal bone morphology 9.34e-03 1.00e+00 absent optic vesicle 9.34e-03 1.00e+00 increased prostate gland weight 1.12e-02 1.00e+00 absent second pharyngeal arch 1.12e-02 1.00e+00 abnormal circulating free fatty acids level 1.12e-02 1.00e+00 delayed hepatic development 1.12e-02 1.00e+00 delayed brain development 1.12e-02 1.00e+00 photosensitivity 1.12e-02 1.00e+00 skin photosensitivity

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

²FDR corrected p-value (Benjamini-Hochberg)