Back to main page

DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod306

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod306 Module size 28 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 91304 C19orf6 transmembrane protein 259 84536 C21orf67 long intergenic non-protein coding RNA 1547 10241 CALCOCO2 calcium binding and coiled-coil domain 2 29965 CDIP1 cell death inducing p53 target 1 300235 DAZAP2 DAZ associated protein 2 54932 EXD3 exonuclease 3'-5' domain containing 3 90268 FAM105B OTU deubiquitinase with linear linkage specificity 92689 FAM114A1 family with sequence similarity 114 member A1 55603 FAM46A terminal nucleotidyltransferase 5A 60493 FASTKD5 FAST kinase domains 5 25758 KIAA1549L KIAA1549 like 115004 MB21D1 cyclic GMP-AMP synthase 9683 N4BP1 NEDD4 binding protein 1 84166 NLRC5 NLR family CARD domain containing 5 729240 PRR20C proline rich 20C 152138 PYDC2 pyrin domain containing 2 22864 R3HDM2 R3H domain containing 2 6036 RNASE2 ribonuclease A family member 2 92014 SLC25A51 solute carrier family 25 member 51 200931 SLC51A solute carrier family 51 alpha subunit 123264 SLC51B solute carrier family 51 beta subunit 83985 SPIN1 sphingolipid transporter 1 (putative) 342667 STAC2 SH3 and cysteine rich domain 2 340061 TMEM173 transmembrane protein 173 9537 TP53I11 tumor protein p53 inducible protein 11 81844 TRIM56 tripartite motif containing 56 7105 TSPAN6 tetraspanin 6 23060 ZNF609 zinc finger protein 609

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 1.66e-02 2.97e-03 Reactome STAT6-mediated induction of chemokines Immune System 1.35e-02 6.05e-05 GO bile acid transmembrane transporter activity molecular_function 1.03e-02 2.97e-03 Reactome IRF3-mediated induction of type I IFN Immune System 8.77e-03 6.05e-05 GO regulation of type I interferon production 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 3.82e-06 1.62e-03 regulation of cytokine production 7.46e-06 2.97e-03 regulation of type I interferon production 1.48e-05 5.49e-03 defense response to other organism 2.21e-05 7.84e-03 innate immune response 2.30e-05 8.13e-03 defense response to virus 2.63e-05 9.14e-03 cellular response to exogenous dsRNA 2.98e-05 1.02e-02 interferon-beta production 3.11e-05 1.06e-02 regulation of protein targeting 7.49e-05 2.28e-02 type I interferon production 7.97e-05 2.40e-02 response to virus 9.94e-05 2.91e-02 regulation of intracellular protein transport 1.05e-04 3.04e-02 regulation of defense response to virus 2.08e-04 5.41e-02 bile acid and bile salt transport 2.10e-04 5.46e-02 response to exogenous dsRNA 2.83e-04 7.01e-02 positive regulation of defense response to virus by host 2.91e-04 7.17e-02 cellular response to dsRNA 2.99e-04 7.34e-02 response to other organism 3.18e-04 7.72e-02 regulation of innate immune response 3.61e-04 8.58e-02 response to biotic stimulus 4.91e-04 1.10e-01 regulation of defense response to virus by host

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 2.15e-03 2.27e-01 NEGATIVE REGULATORS OF RIG I MDA5 SIGNALING 3.24e-03 3.21e-01 RIG I MDA5 MEDIATED INDUCTION OF IFN ALPHA BETA PATHWAYS 2.57e-02 1.00e+00 INNATE IMMUNE SYSTEM

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 2.04e-05 7.68e-02 decreased circulating interferon-alpha level 3.12e-05 1.05e-01 decreased circulating interferon-beta level 4.48e-05 1.32e-01 abnormal plasmacytoid dendritic cell physiology 4.76e-05 1.38e-01 abnormal immune cell physiology 4.50e-04 5.69e-01 increased susceptibility to viral infection induced morbidity/mortality 1.73e-03 1.00e+00 increased susceptibility to viral infection 2.25e-03 1.00e+00 abnormal dendritic cell physiology 3.75e-03 1.00e+00 decreased interferon-beta secretion 5.38e-03 1.00e+00 abnormal macrophage physiology 7.47e-03 1.00e+00 abnormal cholesterol level 7.53e-03 1.00e+00 abnormal female meiosis I arrest 1.30e-02 1.00e+00 abnormal bile salt level 1.68e-02 1.00e+00 abnormal small intestine morphology 2.05e-02 1.00e+00 decreased circulating interleukin-6 level 2.23e-02 1.00e+00 increased carbon dioxide production 2.43e-02 1.00e+00 abnormal coat/hair pigmentation 2.59e-02 1.00e+00 abnormal innate immunity 2.77e-02 1.00e+00 abnormal feces composition 2.95e-02 1.00e+00 abnormal bile salt homeostasis 2.97e-02 1.00e+00 abnormal vocalization

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

²FDR corrected p-value (Benjamini-Hochberg)