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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod160

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod160 Module size 40 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 254065 BRWD3 bromodomain and WD repeat domain containing 3 80167 C4orf29 abhydrolase domain containing 18 55871 CBWD1 COBW domain containing 1 150472 CBWD2 COBW domain containing 2 445571 CBWD3 COBW domain containing 3 220869 CBWD5 COBW domain containing 5 644019 CBWD6 COBW domain containing 6 644019 CBWD7 COBW domain containing 6 29894 CPSF1 cleavage and polyadenylation specific factor 1 54973 CPSF3L integrator complex subunit 11 10898 CPSF4 cleavage and polyadenylation specific factor 4 642843 CPSF4L cleavage and polyadenylation specific factor 4 like 23283 CSTF2T cleavage stimulation factor subunit 2 tau variant 1762 DMWD DM1 locus, WD repeat containing 27436 EML4 echinoderm microtubule associated protein like 4 400954 EML6 echinoderm microtubule associated protein like 6 59271 EVA1C eva-1 homolog C 81608 FIP1L1 factor interacting with PAPOLA and CPSF1 3167 HMX2 H6 family homeobox 2 55764 IFT122 intraflagellar transport 122 57560 IFT80 intraflagellar transport 80 57495 KIAA1239 NACHT and WD repeat domain containing 2 23609 MKRN2 makorin ring finger protein 2 284434 NWD1 NACHT and WD repeat domain containing 1 56903 PAPOLB poly(A) polymerase beta 64895 PAPOLG poly(A) polymerase gamma 23398 PPWD1 peptidylprolyl isomerase domain and WD repeat containing 1 5930 RBBP6 RB binding protein 6, ubiquitin ligase 29101 SSU72 SSU72 homolog, RNA polymerase II CTD phosphatase 8189 SYMPK symplekin 57558 USP35 ubiquitin specific peptidase 35 84640 USP38 ubiquitin specific peptidase 38 57590 WDFY1 WD repeat and FYVE domain containing 1 115825 WDFY2 WD repeat and FYVE domain containing 2 91833 WDR20 WD repeat domain 20 55339 WDR33 WD repeat domain 33 23144 ZC3H3 zinc finger CCCH-type containing 3 23211 ZC3H4 zinc finger CCCH-type containing 4 376940 ZC3H6 zinc finger CCCH-type containing 6 84524 ZC3H8 zinc finger CCCH-type containing 8

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 1.98e-01 2.02e-16 GO mRNA cleavage and polyadenylation specificity factor complex cellular_component 1.22e-01 5.15e-07 GO RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding molecular_function 9.92e-02 7.49e-12 Reactome Transport of Mature mRNA Derived from an Intronless Transcript Metabolism of RNA 7.99e-02 1.31e-16 GO mRNA polyadenylation biological_process 1.72e-02 1.22e-11 Reactome Transport of Mature mRNAs Derived from Intronless Transcripts Metabolism of RNA

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 3'-end processing 0.00e+00 0.00e+00 mRNA 3'-end processing 0.00e+00 0.00e+00 RNA polyadenylation 0.00e+00 0.00e+00 mRNA processing 0.00e+00 0.00e+00 mRNA polyadenylation 0.00e+00 0.00e+00 mRNA cleavage and polyadenylation specificity factor complex 0.00e+00 0.00e+00 mRNA cleavage factor complex 4.19e-11 3.60e-08 pre-mRNA cleavage required for polyadenylation 5.53e-11 4.71e-08 mRNA cleavage 2.37e-10 1.89e-07 mRNA metabolic process 4.83e-10 3.73e-07 termination of RNA polymerase II transcription 1.01e-09 7.53e-07 DNA-templated transcription, termination 2.58e-09 1.82e-06 RNA phosphodiester bond hydrolysis 1.31e-07 7.25e-05 mRNA export from nucleus 2.09e-07 1.12e-04 ribonucleoprotein complex export from nucleus 2.28e-07 1.21e-04 ribonucleoprotein complex localization 2.36e-07 1.25e-04 nucleic acid phosphodiester bond hydrolysis 2.59e-07 1.36e-04 RNA export from nucleus 3.36e-07 1.74e-04 protein export from nucleus 3.89e-07 1.99e-04 RNA splicing

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 5.16e-03 4.69e-01 TRANSPORT OF MATURE MRNA DERIVED FROM AN INTRONLESS TRANSCRIPT 1.87e-02 1.00e+00 PROCESSING OF INTRONLESS PRE MRNAS 1.87e-02 1.00e+00 PROCESSING OF CAPPED INTRONLESS PRE MRNA 2.89e-02 1.00e+00 TRANSPORT OF MATURE TRANSCRIPT TO CYTOPLASM 4.20e-02 1.00e+00 MRNA 3 END PROCESSING 4.20e-02 1.00e+00 CLEAVAGE OF GROWING TRANSCRIPT IN THE TERMINATION REGION 4.40e-02 1.00e+00 MRNA SPLICING 4.42e-02 1.00e+00 PROCESSING OF CAPPED INTRON CONTAINING PRE MRNA 4.90e-02 1.00e+00 MRNA PROCESSING

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 2.41e-05 8.83e-02 preaxial polydactyly 1.87e-03 1.00e+00 absent semicircular canals 3.74e-03 1.00e+00 abnormal inner ear canal fusion 3.75e-03 1.00e+00 abnormal crista ampullaris morphology 3.75e-03 1.00e+00 abnormal inner ear vestibule morphology 3.75e-03 1.00e+00 abnormal ear development 5.61e-03 1.00e+00 abnormal motile primary cilium morphology 5.63e-03 1.00e+00 abnormal pharyngeal arch morphology 7.48e-03 1.00e+00 disorganized long bone epiphyseal plate 7.50e-03 1.00e+00 abnormal pelvic girdle bone morphology 7.57e-03 1.00e+00 small tail bud 1.12e-02 1.00e+00 abnormal thoracic cage shape 1.12e-02 1.00e+00 decreased width of hypertrophic chondrocyte zone 1.12e-02 1.00e+00 head tilt 1.13e-02 1.00e+00 abnormal inner ear morphology 1.31e-02 1.00e+00 abnormal long bone hypertrophic chondrocyte zone 1.32e-02 1.00e+00 small cranium 1.67e-02 1.00e+00 abnormal spermiation 1.69e-02 1.00e+00 abnormal spinal cord morphology 2.05e-02 1.00e+00 abnormal left-right axis patterning

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

²FDR corrected p-value (Benjamini-Hochberg)