Back to main page

DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod333

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod333 Module size 23 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 303617 DDT bromodomain PHD finger transcription factor 100037417 DDTL D-dopachrome tautomerase like 27000 DNAJC2 DnaJ heat shock protein family (Hsp40) member C2 1797 DOM3Z decapping exoribonuclease 9521 EEF1E1 eukaryotic translation elongation factor 1 epsilon 1 1937 EEF1G eukaryotic translation elongation factor 1 gamma 2935 GSPT1 G1 to S phase transition 1 23708 GSPT2 G1 to S phase transition 2 2953 GSTT2 glutathione S-transferase theta 2 (gene/pseudogene) 2954 GSTZ1 glutathione S-transferase zeta 1 22927 HABP4 hyaluronan binding protein 4 10767 HBS1L HBS1 like translational GTPase 26151 NAT9 N-acetyltransferase 9 (putative) 27250 PDCD4 programmed cell death 4 53918 PELO pelota mRNA surveillance and ribosome rescue factor 138716 RPP25L ribonuclease P/MRP subunit p25 like 2030 SLC29A1 solute carrier family 29 member 1 (Augustine blood group) 3177 SLC29A2 solute carrier family 29 member 2 55315 SLC29A3 solute carrier family 29 member 3 222962 SLC29A4 solute carrier family 29 member 4 163589 TDRD5 tudor domain containing 5 221400 TDRD6 tudor domain containing 6 9652 TTC37 tetratricopeptide repeat domain 37

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 1.77e-01 4.67e-11 GO nucleoside transmembrane transporter activity molecular_function 1.76e-01 4.67e-11 Reactome Transport of nucleosides and free purine and pyrimidine bases across the plasma membrane Transport of small molecules 7.42e-03 9.97e-05 GO chromatoid body cellular_component

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 1.70e-11 1.11e-08 nucleoside transmembrane transporter activity 9.49e-09 6.19e-06 nucleoside transmembrane transport 9.49e-09 6.19e-06 nucleoside transport 2.77e-08 1.17e-05 nucleobase-containing compound transmembrane transporter activity 2.56e-06 1.12e-03 peptide metabolic process 3.17e-06 1.37e-03 carbohydrate derivative transport 5.27e-06 2.17e-03 translation 6.85e-06 1.84e-03 translation factor activity, RNA binding 7.83e-06 3.11e-03 peptide biosynthetic process 8.13e-06 3.22e-03 nuclear-transcribed mRNA catabolic process 1.11e-05 4.26e-03 mRNA catabolic process 1.36e-05 5.09e-03 aromatic compound catabolic process 1.43e-05 5.33e-03 cellular amide metabolic process 1.70e-05 6.22e-03 RNA catabolic process 2.10e-05 7.49e-03 amide biosynthetic process 3.62e-05 7.92e-03 chromatoid body 6.37e-05 1.40e-02 translation release factor activity 6.37e-05 1.40e-02 translation termination factor activity 1.95e-04 5.13e-02 nucleobase-containing compound transport 3.26e-04 5.80e-02 glutathione transferase activity

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 1.02e-06 2.31e-04 TRANSPORT OF VITAMINS NUCLEOSIDES AND RELATED MOLECULES 1.34e-06 2.28e-04 TRANSPORT OF VITAMINS NUCLEOSIDES AND RELATED MOLECULES 3.59e-04 4.03e-02 SLC MEDIATED TRANSMEMBRANE TRANSPORT 4.22e-04 5.56e-02 SLC MEDIATED TRANSMEMBRANE TRANSPORT 2.55e-03 2.62e-01 TRANSMEMBRANE TRANSPORT OF SMALL MOLECULES 2.77e-03 2.81e-01 TRANSLATION 3.29e-03 2.87e-01 NONSENSE MEDIATED DECAY ENHANCED BY THE EXON JUNCTION COMPLEX 7.08e-03 5.53e-01 TRANSLATION 4.24e-02 1.00e+00 NONSENSE MEDIATED DECAY ENHANCED BY THE EXON JUNCTION COMPLEX 4.59e-02 1.00e+00 METABOLISM OF MRNA 4.66e-02 1.00e+00 RESPONSE TO ELEVATED PLATELET CYTOSOLIC CA2

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 3.74e-03 1e+00 cellular necrosis 3.75e-03 1e+00 dystrophic cardiac calcinosis 4.32e-03 1e+00 arrest of spermatogenesis 5.61e-03 1e+00 preneoplasia 5.61e-03 1e+00 decreased splenocyte apoptosis 5.61e-03 1e+00 renal necrosis 5.61e-03 1e+00 increased macrophage apoptosis 7.47e-03 1e+00 absent extraembryonic coelom 9.33e-03 1e+00 impaired behavioral response to alcohol 9.34e-03 1e+00 increased splenocyte proliferation 1.12e-02 1e+00 increased circulating total protein level 1.12e-02 1e+00 increased kidney apoptosis 1.12e-02 1e+00 ketoaciduria 1.26e-02 1e+00 abnormal male germ cell apoptosis 1.30e-02 1e+00 increased papilloma incidence 1.30e-02 1e+00 increased alcohol consumption 1.49e-02 1e+00 increased histiocytic sarcoma incidence 1.65e-02 1e+00 abnormal choroid plexus morphology 1.67e-02 1e+00 absent ectoplacental cavity 1.68e-02 1e+00 abnormal lumbar vertebrae morphology

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

²FDR corrected p-value (Benjamini-Hochberg)