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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod154

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod154 Module size 51 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 10384 BTF3 butyrophilin subfamily 3 member A3 91408 BTF3L4 basic transcription factor 3 like 4 8562 DENR density regulated re-initiation and release factor 1915 EEF1A1 eukaryotic translation elongation factor 1 alpha 1 1917 EEF1A2 eukaryotic translation elongation factor 1 alpha 2 1933 EEF1B2 eukaryotic translation elongation factor 1 beta 2 1936 EEF1D eukaryotic translation elongation factor 1 delta 1984 EIF5A eukaryotic translation initiation factor 5A 56648 EIF5A2 eukaryotic translation initiation factor 5A2 143244 EIF5AL1 eukaryotic translation initiation factor 5A-like 1 2197 FAU FAU, ubiquitin like and ribosomal protein S30 fusion 10399 GNB2L1 receptor for activated C kinase 1 149281 METTL11B methyltransferase like 11B 4666 NACA nascent polypeptide associated complex subunit alpha 342538 NACA2 nascent polypeptide associated complex subunit alpha 2 23148 NACAD NAC alpha domain containing 5339 PLEC plectin 23521 RPL13A ribosomal protein L13a 6138 RPL15 ribosomal protein L15 200916 RPL22L1 ribosomal protein L22 like 1 6122 RPL3 ribosomal protein L3 11224 RPL35 ribosomal protein L35 6166 RPL36A ribosomal protein L36a like 6166 RPL36AL ribosomal protein L36a like 116832 RPL39L ribosomal protein L39 like 6123 RPL3L ribosomal protein L3 like 6125 RPL5 ribosomal protein L5 6129 RPL7 ribosomal protein L7 6130 RPL7A ribosomal protein L7a 6132 RPL8 ribosomal protein L8 6205 RPS11 ribosomal protein S11 6207 RPS13 ribosomal protein S13 6209 RPS15 ribosomal protein S15 6217 RPS16 ribosomal protein S16 6218 RPS17 ribosomal protein S17 6218 RPS17L ribosomal protein S17 6187 RPS2 ribosomal protein S2 6224 RPS20 ribosomal protein S20 6228 RPS23 ribosomal protein S23 6230 RPS25 ribosomal protein S25 51065 RPS27L ribosomal protein S27 like 6188 RPS3 ribosomal protein S3 NA RPS4XP21 140032 RPS4Y2 ribosomal protein S4 Y-linked 2 6193 RPS5 ribosomal protein S5 6202 RPS8 ribosomal protein S8 3921 RPSA ribosomal protein SA 51319 RSRC1 arginine and serine rich coiled-coil 1 26135 SERBP1 SERPINE1 mRNA binding protein 1 7178 TPT1 tumor protein, translationally-controlled 1 114987 WDR31 WD repeat domain 31

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 2.05e-01 2.59e-69 Reactome Eukaryotic Translation Elongation Metabolism of proteins 1.56e-01 3.49e-05 Reactome Hypusine synthesis from eIF5A-lysine Metabolism of proteins 1.40e-01 2.34e-14 GO translation elongation factor activity molecular_function 5.26e-02 6.02e-31 Reactome Formation of the ternary complex, and subsequently, the 43S complex Metabolism of proteins 4.00e-02 1.74e-61 Reactome Peptide chain elongation Metabolism of proteins 2.04e-02 3.98e-19 GO ribosome cellular_component 1.39e-02 5.82e-29 GO cytosolic small ribosomal subunit 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 0e+00 0e+00 amide biosynthetic process 0e+00 0e+00 cellular amide metabolic process 0e+00 0e+00 aromatic compound catabolic process 0e+00 0e+00 nuclear-transcribed mRNA catabolic process 0e+00 0e+00 ribosome biogenesis 0e+00 0e+00 protein targeting to ER 0e+00 0e+00 rRNA processing 0e+00 0e+00 mRNA catabolic process 0e+00 0e+00 establishment of protein localization to membrane 0e+00 0e+00 RNA catabolic process 0e+00 0e+00 viral transcription 0e+00 0e+00 cotranslational protein targeting to membrane 0e+00 0e+00 SRP-dependent cotranslational protein targeting to membrane 0e+00 0e+00 mRNA metabolic process 0e+00 0e+00 rRNA metabolic process 0e+00 0e+00 nuclear-transcribed mRNA catabolic process, nonsense-mediated decay 0e+00 0e+00 peptide metabolic process 0e+00 0e+00 ribonucleoprotein complex biogenesis 0e+00 0e+00 translational initiation 0e+00 0e+00 protein targeting to membrane

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 0e+00 0e+00 ACTIVATION OF THE MRNA UPON BINDING OF THE CAP BINDING COMPLEX AND EIFS AND SUBSEQUENT BINDING TO 43S 0e+00 0e+00 INFLUENZA LIFE CYCLE 0e+00 0e+00 FORMATION OF THE TERNARY COMPLEX AND SUBSEQUENTLY THE 43S COMPLEX 0e+00 0e+00 INFLUENZA VIRAL RNA TRANSCRIPTION AND REPLICATION 0e+00 0e+00 METABOLISM OF RNA 0e+00 0e+00 SRP DEPENDENT COTRANSLATIONAL PROTEIN TARGETING TO MEMBRANE 0e+00 0e+00 PEPTIDE CHAIN ELONGATION 0e+00 0e+00 NONSENSE MEDIATED DECAY ENHANCED BY THE EXON JUNCTION COMPLEX 0e+00 0e+00 METABOLISM OF MRNA 0e+00 0e+00 TRANSLATION 0e+00 0e+00 3 UTR MEDIATED TRANSLATIONAL REGULATION 0e+00 0e+00 ACTIVATION OF THE MRNA UPON BINDING OF THE CAP BINDING COMPLEX AND EIFS AND SUBSEQUENT BINDING TO 43S 0e+00 0e+00 INFLUENZA LIFE CYCLE 0e+00 0e+00 FORMATION OF THE TERNARY COMPLEX AND SUBSEQUENTLY THE 43S COMPLEX 0e+00 0e+00 INFLUENZA VIRAL RNA TRANSCRIPTION AND REPLICATION 0e+00 0e+00 METABOLISM OF RNA 0e+00 0e+00 SRP DEPENDENT COTRANSLATIONAL PROTEIN TARGETING TO MEMBRANE 0e+00 0e+00 PEPTIDE CHAIN ELONGATION 0e+00 0e+00 NONSENSE MEDIATED DECAY ENHANCED BY THE EXON JUNCTION COMPLEX 0e+00 0e+00 METABOLISM OF MRNA

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 abnormal osteoid morphology 7.47e-03 1e+00 decreased plasma cell number 7.47e-03 1e+00 abnormal cell chemotaxis 7.47e-03 1e+00 impaired skeletal muscle regeneration 7.50e-03 1e+00 empty decidua capsularis 1.12e-02 1e+00 increased embryonic epiblast cell apoptosis 1.30e-02 1e+00 decreased embryonic epiblast cell proliferation 1.30e-02 1e+00 abnormal osteocyte morphology 1.31e-02 1e+00 small lymph nodes 1.31e-02 1e+00 abnormal blastocyst morphology 1.49e-02 1e+00 lymphoid hypoplasia 1.49e-02 1e+00 decreased neurotransmitter release 1.49e-02 1e+00 abnormal neurotransmitter uptake 1.49e-02 1e+00 skeletal muscle fiber necrosis 1.49e-02 1e+00 decreased fibroblast cell migration 1.49e-02 1e+00 abnormal aerobic respiration 1.49e-02 1e+00 abnormal keratinocyte morphology 1.49e-02 1e+00 abnormal bone trabecula morphology 1.67e-02 1e+00 abnormal endplate potential 1.67e-02 1e+00 complete embryonic lethality between implantation and somite formation

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

²FDR corrected p-value (Benjamini-Hochberg)