Back to main page

DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod307

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod307 Module size 33 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 6310 ATXN1 ataxin 1 342371 ATXN1L ataxin 1 like 79870 BAALC BAALC, MAP3K1 and KLF4 binding 139105 BEND2 BEN domain containing 2 283551 C14orf182 long intergenic non-protein coding RNA 1588 84970 C1orf94 chromosome 1 open reading frame 94 408029 C2orf27B chromosome 2 open reading frame 27B 10658 CELF1 CUGBP Elav-like family member 1 10659 CELF2 CUGBP Elav-like family member 2 11189 CELF3 CUGBP Elav-like family member 3 56853 CELF4 CUGBP Elav-like family member 4 60680 CELF5 CUGBP Elav-like family member 5 60677 CELF6 CUGBP Elav-like family member 6 23152 CIC capicua transcriptional repressor 165530 CLEC4F C-type lectin domain family 4 member F 25763 CXorf27 huntingtin interacting protein M 1993 ELAVL2 ELAV like RNA binding protein 2 1995 ELAVL3 ELAV like RNA binding protein 3 1996 ELAVL4 ELAV like RNA binding protein 4 23201 FAM168A family with sequence similarity 168 member A 729262 FAM22B NUT family member 2B 115572 FAM46B terminal nucleotidyltransferase 5B 169966 FAM46D terminal nucleotidyltransferase 5D 122183 PRR20A proline rich 20A 54715 RBFOX1 RNA binding fox-1 homolog 1 11030 RBPMS RNA binding protein, mRNA processing factor 348093 RBPMS2 RNA binding protein, mRNA processing factor 2 6988 TCTA T cell leukemia translocation altered 200523 TEX37 testis expressed 37 23074 UHRF1BP1L UHRF1 binding protein 1 like 84058 WDR54 WD repeat domain 54 84872 ZC3H10 zinc finger CCCH-type containing 10 91752 ZNF804A zinc finger protein 804A

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 1.24e-01 3.71e-12 GO pre-mRNA binding molecular_function 1.23e-01 4.18e-14 GO mRNA splice site selection biological_process 1.27e-02 2.20e-15 GO regulation of alternative mRNA splicing, via spliceosome 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 mRNA processing 2.50e-11 1.61e-08 mRNA binding 3.89e-11 3.36e-08 mRNA metabolic process 5.02e-09 3.39e-06 regulation of alternative mRNA splicing, via spliceosome 1.57e-08 9.97e-06 regulation of RNA splicing 1.03e-07 5.81e-05 regulation of mRNA splicing, via spliceosome 2.69e-07 1.41e-04 regulation of mRNA processing 2.32e-06 1.03e-03 RNA splicing 6.12e-06 2.48e-03 mRNA splicing, via spliceosome 6.76e-06 2.72e-03 RNA splicing, via transesterification reactions 2.65e-05 9.21e-03 positive regulation of mRNA splicing, via spliceosome 2.66e-05 6.40e-03 translation repressor activity, nucleic acid binding 4.27e-05 1.40e-02 positive regulation of RNA splicing 6.89e-05 1.50e-02 poly-purine tract binding 1.38e-04 3.84e-02 mRNA splice site selection 1.49e-04 2.92e-02 translation repressor activity 1.93e-04 3.66e-02 AU-rich element binding 3.22e-04 5.74e-02 snRNA binding 3.90e-04 9.13e-02 spliceosomal complex assembly 4.87e-04 8.21e-02 translation regulator activity

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 2.25e-04 3.75e-01 cachexia 7.24e-04 7.53e-01 abnormal pulmonary alveolus morphology 8.51e-04 8.22e-01 impaired coordination 1.49e-03 1.00e+00 kyphosis 2.56e-03 1.00e+00 limb grasping 3.81e-03 1.00e+00 abnormal macrophage cytokine production 5.61e-03 1.00e+00 abnormal pulmonary alveolar sac morphology 5.62e-03 1.00e+00 dilated brain ventricles 7.33e-03 1.00e+00 partial neonatal lethality 7.47e-03 1.00e+00 neuronal intranuclear inclusions 9.35e-03 1.00e+00 abnormal spike wave discharge 9.40e-03 1.00e+00 absence seizures 1.12e-02 1.00e+00 enlarged third ventricle 1.31e-02 1.00e+00 nonconvulsive seizures 1.45e-02 1.00e+00 hypoactivity 1.49e-02 1.00e+00 decreased paired-pulse facilitation 1.50e-02 1.00e+00 abnormal seizure response to electrical stimulation 1.68e-02 1.00e+00 muscle degeneration 1.87e-02 1.00e+00 decreased Purkinje cell number 1.99e-02 1.00e+00 abnormal Purkinje cell dendrite morphology

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

²FDR corrected p-value (Benjamini-Hochberg)