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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod286

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod286 Module size 41 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 8852 AKAP4 A-kinase anchoring protein 4 55729 ATF7IP activating transcription factor 7 interacting protein 80129 CCDC170 coiled-coil domain containing 170 902 CCNH cyclin H 8812 CCNK cyclin K 81669 CCNL2 cyclin L2 728642 CDK11A cyclin dependent kinase 11A 984 CDK11B cyclin dependent kinase 11B 23552 CDK20 cyclin dependent kinase 20 1022 CDK7 cyclin dependent kinase 7 23085 ERC1 ELKS/RAB6-interacting/CAST family member 1 2068 ERCC2 ERCC excision repair 2, TFIIH core complex helicase subunit 2071 ERCC3 ERCC excision repair 3, TFIIH core complex helicase subunit 84191 FAM96A cytosolic iron-sulfur assembly component 2A 51647 FAM96B cytosolic iron-sulfur assembly component 2B 161835 FSIP1 fibrous sheath interacting protein 1 401024 FSIP2 fibrous sheath interacting protein 2 2958 GTF2A2 general transcription factor IIA subunit 2 2960 GTF2E1 general transcription factor IIE subunit 1 2961 GTF2E2 general transcription factor IIE subunit 2 2965 GTF2H1 general transcription factor IIH subunit 1 2966 GTF2H2 general transcription factor IIH subunit 2 728340 GTF2H2C GTF2H2 family member C 2967 GTF2H3 general transcription factor IIH subunit 3 2968 GTF2H4 general transcription factor IIH subunit 4 404672 GTF2H5 general transcription factor IIH subunit 5 10614 HEXIM1 hexamethylene bisacetamide inducible 1 10489 LRRC41 leucine rich repeat containing 41 64210 MMS19 MMS19 homolog, cytosolic iron-sulfur assembly component 4331 MNAT1 MNAT1, CDK activating kinase assembly factor 79684 MSANTD2 Myb/SANT DNA binding domain containing 2 79664 NARG2 interactor of little elongation complex ELL subunit 2 5256 PHKA2 phosphorylase kinase regulatory subunit alpha 2 5261 PHKG2 phosphorylase kinase catalytic subunit gamma 2 284119 PTRF caveolae associated protein 1 260434 PYDC1 pyrin domain containing 1 91607 SLFN11 schlafen family member 11 6921 TCEB1 elongin C 6923 TCEB2 elongin B 162699 TCEB3C elongin A3 57654 UVSSA UV stimulated scaffold protein 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 5.57e-01 2.42e-30 GO holo TFIIH complex cellular_component 1.18e-01 1.20e-24 GO RNA polymerase II carboxy-terminal domain kinase activity molecular_function 4.99e-02 3.57e-05 GO CIA complex cellular_component 2.68e-02 3.81e-23 Reactome RNA Polymerase I Transcription Termination Gene expression (Transcription) 2.16e-02 1.95e-04 GO IkappaB kinase complex cellular_component 1.36e-02 2.83e-17 GO transcription factor TFIID complex cellular_component 1.27e-02 2.33e-04 GO regulation of mRNA processing biological_process 1.06e-02 4.29e-26 Reactome RNA Polymerase II Transcription Initiation Gene expression (Transcription) 1.02e-02 4.29e-26 Reactome RNA Polymerase II Transcription Initiation And Promoter Clearance Gene expression (Transcription) 9.14e-03 4.29e-26 Reactome RNA Polymerase II Promoter Escape Gene expression (Transcription) 8.17e-03 4.29e-26 Reactome RNA Polymerase II Transcription Pre-Initiation And Promoter Opening Gene expression (Transcription) 7.56e-03 7.96e-09 GO cyclin-dependent protein serine/threonine kinase activity molecular_function 6.98e-03 4.29e-26 Reactome RNA Polymerase II HIV Promoter Escape Disease 6.82e-03 4.29e-26 Reactome HIV Transcription Initiation 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 0e+00 0e+00 nucleotide-excision repair, DNA duplex unwinding 0e+00 0e+00 transcription initiation from RNA polymerase I promoter 0e+00 0e+00 nucleotide-excision repair, DNA incision 0e+00 0e+00 7-methylguanosine RNA capping 0e+00 0e+00 transcription elongation from RNA polymerase I promoter 0e+00 0e+00 transcription from RNA polymerase I promoter 0e+00 0e+00 transcription-coupled nucleotide-excision repair 0e+00 0e+00 nucleotide-excision repair 0e+00 0e+00 termination of RNA polymerase I transcription 0e+00 0e+00 transcription initiation from RNA polymerase II promoter 0e+00 0e+00 transcription elongation from RNA polymerase II promoter 0e+00 0e+00 nucleotide-excision repair, DNA incision, 3'-to lesion 0e+00 0e+00 protein-DNA complex assembly 0e+00 0e+00 nucleotide-excision repair, DNA incision, 5'-to lesion 0e+00 0e+00 7-methylguanosine mRNA capping 0e+00 0e+00 nucleotide-excision repair, preincision complex stabilization 0e+00 0e+00 nucleotide-excision repair, preincision complex assembly 0e+00 0e+00 DNA-templated transcription, elongation 0e+00 0e+00 DNA-templated transcription, initiation 0e+00 0e+00 DNA-templated transcription, termination

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 0e+00 0e+00 FORMATION OF TRANSCRIPTION COUPLED NER TC NER REPAIR COMPLEX 0e+00 0e+00 RNA POL I TRANSCRIPTION 0e+00 0e+00 RNA POL I TRANSCRIPTION TERMINATION 0e+00 0e+00 FORMATION OF RNA POL II ELONGATION COMPLEX 0e+00 0e+00 RNA POL II TRANSCRIPTION PRE INITIATION AND PROMOTER OPENING 0e+00 0e+00 RNA POL II PRE TRANSCRIPTION EVENTS 0e+00 0e+00 TRANSCRIPTION 0e+00 0e+00 HIV LIFE CYCLE 0e+00 0e+00 RNA POL II TRANSCRIPTION 0e+00 0e+00 LATE PHASE OF HIV LIFE CYCLE 0e+00 0e+00 RNA POL I TRANSCRIPTION INITIATION 0e+00 0e+00 RNA POL I RNA POL III AND MITOCHONDRIAL TRANSCRIPTION 0e+00 0e+00 FORMATION OF INCISION COMPLEX IN GG NER 0e+00 0e+00 RNA POL I TRANSCRIPTION TERMINATION 0e+00 0e+00 FORMATION OF RNA POL II ELONGATION COMPLEX 0e+00 0e+00 RNA POL II TRANSCRIPTION PRE INITIATION AND PROMOTER OPENING 0e+00 0e+00 RNA POL II PRE TRANSCRIPTION EVENTS 0e+00 0e+00 TRANSCRIPTION 0e+00 0e+00 HIV LIFE CYCLE 0e+00 0e+00 RNA POL II TRANSCRIPTION

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 5.30e-04 6.30e-01 increased cellular sensitivity to ultraviolet irradiation 8.79e-04 8.36e-01 acanthosis 1.19e-03 9.96e-01 complete embryonic lethality before implantation 3.74e-03 1.00e+00 impaired contractility of urinary bladder detrusor smooth muscle 3.74e-03 1.00e+00 increased right ventricle systolic pressure 3.74e-03 1.00e+00 increased urinary bladder weight 3.74e-03 1.00e+00 reduced activated sperm motility 3.75e-03 1.00e+00 abnormal urinary bladder detrusor smooth muscle morphology 3.75e-03 1.00e+00 increased heart right ventricle weight 3.75e-03 1.00e+00 absent caveolae 4.41e-03 1.00e+00 increased embryonic tissue cell apoptosis 5.62e-03 1.00e+00 increased incidence of tumors by UV-induction 5.63e-03 1.00e+00 focal dorsal hair loss 5.63e-03 1.00e+00 atrium hypoplasia 5.64e-03 1.00e+00 enlarged hair follicles 7.48e-03 1.00e+00 skin photosensitivity 9.34e-03 1.00e+00 abnormal sperm principal piece morphology 9.37e-03 1.00e+00 pulmonary hypertension 1.12e-02 1.00e+00 reduced hyperactivated sperm motility 1.31e-02 1.00e+00 brittle hair

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

²FDR corrected p-value (Benjamini-Hochberg)