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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod177

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod177 Module size 31 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 26469 BDP1 protein tyrosine phosphatase, non-receptor type 18 27297 CRCP CGRP receptor component 2975 GTF3C1 general transcription factor IIIC subunit 1 2976 GTF3C2 general transcription factor IIIC subunit 2 9330 GTF3C3 general transcription factor IIIC subunit 3 9329 GTF3C4 general transcription factor IIIC subunit 4 9328 GTF3C5 general transcription factor IIIC subunit 5 112495 GTF3C6 general transcription factor IIIC subunit 6 11178 LZTS1 leucine zipper tumor suppressor 1 4337 MOCS1 molybdenum cofactor synthesis 1 4774 NFIA nuclear factor I A 4781 NFIB nuclear factor I B 4782 NFIC nuclear factor I C 4784 NFIX nuclear factor I X 318 NUDT2 nudix hydrolase 2 51082 POLR1D RNA polymerase I and III subunit D 548644 POLR2J2 RNA polymerase II subunit J3 548644 POLR2J3 RNA polymerase II subunit J3 11128 POLR3A RNA polymerase III subunit A 55703 POLR3B RNA polymerase III subunit B 661 POLR3D RNA polymerase III subunit D 55718 POLR3E RNA polymerase III subunit E 10621 POLR3F RNA polymerase III subunit F 10622 POLR3G RNA polymerase III subunit G 84265 POLR3GL RNA polymerase III subunit G like 171568 POLR3H RNA polymerase III subunit H 51728 POLR3K RNA polymerase III subunit K 6617 SNAPC1 small nuclear RNA activating complex polypeptide 1 6618 SNAPC2 small nuclear RNA activating complex polypeptide 2 6619 SNAPC3 small nuclear RNA activating complex polypeptide 3 10302 SNAPC5 small nuclear RNA activating complex polypeptide 5

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 3.04e-01 2.07e-17 GO transcription factor TFIIIC complex cellular_component 1.16e-01 5.88e-56 Reactome RNA Polymerase III Transcription Gene expression (Transcription) 1.16e-01 5.88e-56 Reactome RNA Polymerase III Transcription Initiation Gene expression (Transcription) 1.15e-01 5.88e-56 Reactome RNA Polymerase III Abortive And Retractive Initiation Gene expression (Transcription) 1.07e-01 3.67e-46 Reactome RNA Polymerase III Transcription Initiation From Type 2 Promoter Gene expression (Transcription) 5.33e-02 1.67e-23 GO DNA-directed 5'-3' RNA polymerase activity molecular_function 4.20e-02 3.32e-39 Reactome RNA Polymerase III Transcription Initiation From Type 3 Promoter Gene expression (Transcription)

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 transcription from RNA polymerase III promoter 0.00e+00 0.00e+00 positive regulation of type I interferon production 0.00e+00 0.00e+00 defense response to virus 0.00e+00 0.00e+00 regulation of cytokine production 0.00e+00 0.00e+00 response to virus 0.00e+00 0.00e+00 positive regulation of cytokine production 0.00e+00 0.00e+00 regulation of type I interferon production 0.00e+00 0.00e+00 transcription initiation from RNA polymerase III promoter 0.00e+00 0.00e+00 5S class rRNA transcription from RNA polymerase III type 1 promoter 0.00e+00 0.00e+00 ncRNA transcription 0.00e+00 0.00e+00 tRNA transcription from RNA polymerase III promoter 0.00e+00 0.00e+00 tRNA transcription 0.00e+00 0.00e+00 DNA-directed RNA polymerase III complex 0.00e+00 0.00e+00 transcription factor TFIIIC complex 0.00e+00 0.00e+00 RNA polymerase III activity 0.00e+00 0.00e+00 nucleotidyltransferase activity 0.00e+00 0.00e+00 5'-3' RNA polymerase activity 0.00e+00 0.00e+00 DNA-directed 5'-3' RNA polymerase activity 4.03e-11 3.48e-08 defense response to other organism 4.07e-11 3.51e-08 regulation of transcription from RNA polymerase III promoter

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 0.00e+00 0e+00 RNA POL III CHAIN ELONGATION 0.00e+00 0e+00 RNA POL III TRANSCRIPTION 0.00e+00 0e+00 RNA POL III TRANSCRIPTION INITIATION FROM TYPE 2 PROMOTER 0.00e+00 0e+00 TRANSCRIPTION 0.00e+00 0e+00 RNA POL III TRANSCRIPTION TERMINATION 0.00e+00 0e+00 RNA POL III TRANSCRIPTION INITIATION FROM TYPE 3 PROMOTER 0.00e+00 0e+00 RNA POL I RNA POL III AND MITOCHONDRIAL TRANSCRIPTION 0.00e+00 0e+00 RNA POL III CHAIN ELONGATION 0.00e+00 0e+00 RNA POL III TRANSCRIPTION 0.00e+00 0e+00 RNA POL III TRANSCRIPTION INITIATION FROM TYPE 2 PROMOTER 0.00e+00 0e+00 TRANSCRIPTION 0.00e+00 0e+00 RNA POL III TRANSCRIPTION TERMINATION 0.00e+00 0e+00 RNA POL III TRANSCRIPTION INITIATION FROM TYPE 3 PROMOTER 0.00e+00 0e+00 RNA POL I RNA POL III AND MITOCHONDRIAL TRANSCRIPTION 4.69e-02 1e+00 RNA POL I TRANSCRIPTION INITIATION 4.81e-02 1e+00 RNA POL I TRANSCRIPTION TERMINATION 4.96e-02 1e+00 RNA POL I TRANSCRIPTION TERMINATION

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 5.40e-05 1.51e-01 abnormal corpus callosum morphology 1.16e-04 2.49e-01 abnormal glial cell morphology 2.85e-04 4.37e-01 abnormal cerebellar granule cell morphology 7.15e-04 7.46e-01 absent corpus callosum 7.77e-04 7.77e-01 dilated third ventricle 2.15e-03 1.00e+00 preweaning lethality 2.47e-03 1.00e+00 dilated lateral ventricles 3.74e-03 1.00e+00 decreased submandibular gland size 3.74e-03 1.00e+00 abnormal submandibular gland development 3.74e-03 1.00e+00 double ureter 3.74e-03 1.00e+00 dilated ureter 3.74e-03 1.00e+00 abnormal inner ear canal morphology 5.61e-03 1.00e+00 increased wet-to-dry lung weight ratio 5.61e-03 1.00e+00 small lung saccule 5.61e-03 1.00e+00 intervertebral disk degeneration 7.21e-03 1.00e+00 abnormal hippocampus morphology 7.47e-03 1.00e+00 absent dentate gyrus 7.47e-03 1.00e+00 submandibular gland hypoplasia 7.47e-03 1.00e+00 long incisors 8.91e-03 1.00e+00 hydroencephaly

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

²FDR corrected p-value (Benjamini-Hochberg)