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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod54

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod54 Module size 52 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 22794 CASC3 CASC3, exon junction complex subunit 4736 RPL10A ribosomal protein L10a 6136 RPL12 ribosomal protein L12 28998 RPL13 mitochondrial ribosomal protein L13 9045 RPL14 ribosomal protein L14 6141 RPL18 ribosomal protein L18 6142 RPL18A ribosomal protein L18a 6143 RPL19 ribosomal protein L19 6144 RPL21 ribosomal protein L21 6146 RPL22 ribosomal protein L22 6147 RPL23A ribosomal protein L23a 51187 RPL24 ribosomal L24 domain containing 1 6154 RPL26 ribosomal protein L26 51121 RPL26L1 ribosomal protein L26 like 1 6155 RPL27 ribosomal protein L27 6158 RPL28 ribosomal protein L28 6159 RPL29 ribosomal protein L29 6156 RPL30 ribosomal protein L30 6160 RPL31 ribosomal protein L31 6161 RPL32 ribosomal protein L32 6164 RPL34 ribosomal protein L34 6165 RPL35A ribosomal protein L35a 25873 RPL36 ribosomal protein L36 6167 RPL37 ribosomal protein L37 6168 RPL37A ribosomal protein L37a 6169 RPL38 ribosomal protein L38 6170 RPL39 ribosomal protein L39 6171 RPL41 ribosomal protein L41 6128 RPL6 ribosomal protein L6 6175 RPLP0 ribosomal protein lateral stalk subunit P0 6176 RPLP1 ribosomal protein lateral stalk subunit P1 6181 RPLP2 ribosomal protein lateral stalk subunit P2 6204 RPS10 ribosomal protein S10 6183 RPS12 mitochondrial ribosomal protein S12 6208 RPS14 ribosomal protein S14 6210 RPS15A ribosomal protein S15a 6223 RPS19 ribosomal protein S19 6227 RPS21 ribosomal protein S21 6229 RPS24 ribosomal protein S24 6231 RPS26 ribosomal protein S26 6232 RPS27 ribosomal protein S27 6234 RPS28 ribosomal protein S28 6235 RPS29 ribosomal protein S29 6189 RPS3A ribosomal protein S3A 6191 RPS4X ribosomal protein S4 X-linked 6192 RPS4Y1 ribosomal protein S4 Y-linked 1 6201 RPS7 ribosomal protein S7 23381 SMG5 SMG5, nonsense mediated mRNA decay factor 23293 SMG6 SMG6, nonsense mediated mRNA decay factor 9887 SMG7 SMG7, nonsense mediated mRNA decay factor 55181 SMG8 SMG8, nonsense mediated mRNA decay factor 56006 SMG9 SMG9, nonsense mediated mRNA decay factor

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 1.36e-01 3.16e-50 GO cytoplasmic translation biological_process 1.05e-01 2.32e-101 GO SRP-dependent cotranslational protein targeting to membrane biological_process 8.94e-02 4.25e-115 GO nuclear-transcribed mRNA catabolic process, nonsense-mediated decay biological_process 5.09e-02 1.76e-119 Reactome Nonsense-Mediated Decay (NMD) Metabolism of RNA 5.08e-02 1.76e-119 Reactome Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) Metabolism of RNA 4.85e-02 2.06e-36 GO polysomal ribosome cellular_component 4.48e-02 1.86e-104 Reactome Peptide chain elongation Metabolism of proteins 3.47e-02 9.67e-65 GO cytosolic large ribosomal subunit cellular_component 2.77e-02 2.91e-103 Reactome Selenocysteine synthesis Metabolism 2.05e-02 1.08e-102 Reactome Viral mRNA Translation Disease 1.34e-02 5.64e-103 Reactome Eukaryotic Translation Elongation Metabolism of proteins 2.82e-03 2.88e-05 GO telomerase holoenzyme complex cellular_component 2.41e-05 4.48e-101 Reactome Formation of a pool of free 40S subunits Metabolism of proteins

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 INFLUENZA LIFE CYCLE 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 FORMATION OF THE TERNARY COMPLEX AND SUBSEQUENTLY THE 43S COMPLEX 0e+00 0e+00 INFLUENZA LIFE CYCLE 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 3 UTR MEDIATED TRANSLATIONAL REGULATION 0e+00 0e+00 TRANSLATION

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 8.05e-06 4.02e-02 decreased caudal vertebrae number 1.31e-05 5.70e-02 belly spot 3.01e-05 1.03e-01 delayed optic fissure closure 1.26e-04 2.62e-01 abnormal vertebral transverse process morphology 1.39e-04 2.82e-01 caudal vertebral fusion 2.83e-04 4.36e-01 kinked tail 3.62e-04 5.01e-01 abnormal sternebra morphology 5.72e-04 6.58e-01 asymmetric rib-sternum attachment 6.35e-04 6.96e-01 lumbar vertebral transformation 1.37e-03 1.00e+00 abnormal vertebral arch morphology 1.45e-03 1.00e+00 increased rib number 1.52e-03 1.00e+00 vertebral fusion 1.88e-03 1.00e+00 abnormal nucleolus morphology 1.95e-03 1.00e+00 curly tail 3.11e-03 1.00e+00 complete prenatal lethality 3.54e-03 1.00e+00 abnormal digit morphology 3.74e-03 1.00e+00 retina hypoplasia 3.75e-03 1.00e+00 caudal vertebral transformation 3.76e-03 1.00e+00 partial embryonic lethality at implantation 4.11e-03 1.00e+00 polydactyly

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

²FDR corrected p-value (Benjamini-Hochberg)