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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod124

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod124 Module size 33 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 10209 EIF1 eukaryotic translation initiation factor 1 107984923 EIF1AX eukaryotic translation initiation factor 1A, X-chromosomal 10289 EIF1B eukaryotic translation initiation factor 1B 1965 EIF2A eukaryotic translation initiation factor 2 subunit alpha 1965 EIF2S1 eukaryotic translation initiation factor 2 subunit alpha 8894 EIF2S2 eukaryotic translation initiation factor 2 subunit beta 1968 EIF2S3 eukaryotic translation initiation factor 2 subunit gamma 3692 EIF3A eukaryotic translation initiation factor 6 8662 EIF3B eukaryotic translation initiation factor 3 subunit B 8663 EIF3C eukaryotic translation initiation factor 3 subunit C 8664 EIF3D eukaryotic translation initiation factor 3 subunit D 3646 EIF3E eukaryotic translation initiation factor 3 subunit E 8665 EIF3F eukaryotic translation initiation factor 3 subunit F 8666 EIF3G eukaryotic translation initiation factor 3 subunit G 8667 EIF3H eukaryotic translation initiation factor 3 subunit H 8668 EIF3I eukaryotic translation initiation factor 3 subunit I 8669 EIF3J eukaryotic translation initiation factor 3 subunit J 27335 EIF3K eukaryotic translation initiation factor 3 subunit K 51386 EIF3L eukaryotic translation initiation factor 3 subunit L 10480 EIF3M eukaryotic translation initiation factor 3 subunit M 1973 EIF4A1 eukaryotic translation initiation factor 4A1 1974 EIF4A2 eukaryotic translation initiation factor 4A2 9775 EIF4A3 eukaryotic translation initiation factor 4A3 1975 EIF4B eukaryotic translation initiation factor 4B 1977 EIF4E eukaryotic translation initiation factor 4E 1983 EIF5 eukaryotic translation initiation factor 5 9669 EIF5B eukaryotic translation initiation factor 5B 2107 ETF1 eukaryotic translation termination factor 1 26986 PABPC1 poly(A) binding protein cytoplasmic 1 158471 PRUNE2 prune homolog 2 6194 RPS6 ribosomal protein S6 94107 TMEM203 transmembrane protein 203 5976 UPF1 UPF1, RNA helicase and ATPase

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 2.86e-01 1.07e-34 GO eukaryotic translation initiation factor 3 complex cellular_component 2.44e-01 7.14e-64 GO translation initiation factor activity molecular_function 6.96e-02 4.12e-52 Reactome Translation initiation complex formation Metabolism of proteins 5.37e-02 6.68e-52 Reactome Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S Metabolism of proteins 4.46e-02 4.12e-52 Reactome Ribosomal scanning and start codon recognition Metabolism of proteins 4.17e-02 4.39e-12 Reactome Deadenylation of mRNA Metabolism of RNA 2.41e-02 8.69e-22 GO regulation of translational initiation 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 amide biosynthetic process 0.00e+00 0.00e+00 regulation of translation 0.00e+00 0.00e+00 posttranscriptional regulation of gene expression 0.00e+00 0.00e+00 cellular amide metabolic process 0.00e+00 0.00e+00 peptide metabolic process 0.00e+00 0.00e+00 peptide biosynthetic process 0.00e+00 0.00e+00 translational initiation 0.00e+00 0.00e+00 regulation of translational initiation 0.00e+00 0.00e+00 translation 0.00e+00 0.00e+00 mRNA catabolic process 0.00e+00 0.00e+00 RNA catabolic process 0.00e+00 0.00e+00 nuclear-transcribed mRNA catabolic process 0.00e+00 0.00e+00 cytoplasmic translational initiation 0.00e+00 0.00e+00 viral translation 0.00e+00 0.00e+00 eukaryotic translation initiation factor 3 complex, eIF3m 0.00e+00 0.00e+00 eukaryotic translation initiation factor 3 complex 0.00e+00 0.00e+00 translation initiation factor activity 0.00e+00 0.00e+00 translation factor activity, RNA binding 1.50e-12 1.39e-09 cytoplasmic translation 1.19e-11 1.07e-08 viral translational termination-reinitiation

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 0.00e+00 0.00e+00 ACTIVATION OF THE MRNA UPON BINDING OF THE CAP BINDING COMPLEX AND EIFS AND SUBSEQUENT BINDING TO 43S 0.00e+00 0.00e+00 FORMATION OF THE TERNARY COMPLEX AND SUBSEQUENTLY THE 43S COMPLEX 0.00e+00 0.00e+00 TRANSLATION 0.00e+00 0.00e+00 3 UTR MEDIATED TRANSLATIONAL REGULATION 0.00e+00 0.00e+00 ACTIVATION OF THE MRNA UPON BINDING OF THE CAP BINDING COMPLEX AND EIFS AND SUBSEQUENT BINDING TO 43S 0.00e+00 0.00e+00 FORMATION OF THE TERNARY COMPLEX AND SUBSEQUENTLY THE 43S COMPLEX 0.00e+00 0.00e+00 3 UTR MEDIATED TRANSLATIONAL REGULATION 0.00e+00 0.00e+00 TRANSLATION 1.86e-10 6.62e-08 DEADENYLATION OF MRNA 2.58e-08 7.20e-06 DEADENYLATION DEPENDENT MRNA DECAY 2.99e-07 5.55e-05 DEADENYLATION OF MRNA 3.47e-06 7.14e-04 METABOLISM OF MRNA 9.53e-06 1.83e-03 METABOLISM OF RNA 1.47e-05 2.73e-03 MTORC1 MEDIATED SIGNALLING 2.26e-05 3.20e-03 MTORC1 MEDIATED SIGNALLING 2.81e-05 3.91e-03 DEADENYLATION DEPENDENT MRNA DECAY 1.47e-04 2.19e-02 ANTIVIRAL MECHANISM BY IFN STIMULATED GENES 1.95e-04 2.32e-02 METABOLISM OF MRNA 3.64e-04 4.86e-02 PKB MEDIATED EVENTS 3.69e-04 4.13e-02 METABOLISM OF RNA

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 1.12e-03 9.61e-01 decreased insulin secretion 1.87e-03 1.00e+00 abnormal hallux morphology 1.87e-03 1.00e+00 head spot 1.88e-03 1.00e+00 abnormal outer ear morphology 1.88e-03 1.00e+00 white spotting 5.50e-03 1.00e+00 decreased circulating insulin level 7.47e-03 1.00e+00 empty decidua capsularis 7.48e-03 1.00e+00 decreased total fat pad weight 9.33e-03 1.00e+00 abnormal primordial germ cell proliferation 9.36e-03 1.00e+00 belly spot 9.41e-03 1.00e+00 abnormal limb morphology 9.42e-03 1.00e+00 complete lethality 1.12e-02 1.00e+00 decreased incidence of induced tumors 1.49e-02 1.00e+00 abnormal pancreatic beta cell morphology 1.50e-02 1.00e+00 abnormal thoracic vertebrae morphology 1.50e-02 1.00e+00 abnormal pancreatic islet morphology 1.50e-02 1.00e+00 decreased kidney weight 1.56e-02 1.00e+00 abnormal cell physiology 1.69e-02 1.00e+00 polydactyly 3.52e-02 1.00e+00 decreased liver weight

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

²FDR corrected p-value (Benjamini-Hochberg)