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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod134

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod134 Module size 54 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 221264 AKD1 adenylate kinase 9 1938 EEF2 eukaryotic translation elongation factor 2 79631 EFTUD1 elongation factor like GTPase 1 9086 EIF1AY eukaryotic translation initiation factor 1A Y-linked 85476 GFM1 G elongation factor mitochondrial 1 84340 GFM2 G elongation factor mitochondrial 2 85865 GTPBP10 GTP binding protein 10 26164 GTPBP5 mitochondrial ribosome associated GTPase 2 51751 HIGD1B HIG1 hypoxia inducible domain family member 1B 613227 HIGD1C HIG1 hypoxia inducible domain family member 1C 123346 HIGD2B HIG1 hypoxia inducible domain family member 2B 23173 METAP1 methionyl aminopeptidase 1 254042 METAP1D methionyl aminopeptidase type 1D, mitochondrial 10988 METAP2 methionyl aminopeptidase 2 64745 METTL17 methyltransferase like 17 65008 MRPL1 mitochondrial ribosomal protein L1 65003 MRPL11 mitochondrial ribosomal protein L11 29088 MRPL15 mitochondrial ribosomal protein L15 54948 MRPL16 mitochondrial ribosomal protein L16 51069 MRPL2 mitochondrial ribosomal protein L2 29093 MRPL22 mitochondrial ribosomal protein L22 79590 MRPL24 mitochondrial ribosomal protein L24 11222 MRPL3 mitochondrial ribosomal protein L3 9553 MRPL33 mitochondrial ribosomal protein L33 64979 MRPL36 mitochondrial ribosomal protein L36 51073 MRPL4 mitochondrial ribosomal protein L4 55173 MRPS10 mitochondrial ribosomal protein S10 64963 MRPS11 mitochondrial ribosomal protein S11 6183 MRPS12 mitochondrial ribosomal protein S12 63931 MRPS14 mitochondrial ribosomal protein S14 64960 MRPS15 mitochondrial ribosomal protein S15 51021 MRPS16 mitochondrial ribosomal protein S16 51116 MRPS2 mitochondrial ribosomal protein S2 64969 MRPS5 mitochondrial ribosomal protein S5 64968 MRPS6 mitochondrial ribosomal protein S6 51081 MRPS7 mitochondrial ribosomal protein S7 64965 MRPS9 mitochondrial ribosomal protein S9 92399 MRRF mitochondrial ribosome recycling factor NA MRRFP1 219402 MTIF3 mitochondrial translational initiation factor 3 6138 RPL10 ribosomal protein L15 140801 RPL10L ribosomal protein L10 like 6135 RPL11 ribosomal protein L11 6139 RPL17 ribosomal protein L17 9349 RPL23 ribosomal protein L23 6157 RPL27A ribosomal protein L27a 6124 RPL4 ribosomal protein L4 285855 RPL7L1 ribosomal protein L7 like 1 6133 RPL9 ribosomal protein L9 6222 RPS18 ribosomal protein S18 6203 RPS9 ribosomal protein S9 388524 RPSAP58 ribosomal protein SA pseudogene 58 10102 TSFM Ts translation elongation factor, mitochondrial 7284 TUFM Tu translation elongation factor, mitochondrial

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 1.19e-01 3.99e-53 Reactome Mitochondrial translation Metabolism of proteins 9.40e-02 9.97e-07 GO ribosome disassembly biological_process 9.17e-02 3.89e-06 GO metalloexopeptidase activity molecular_function 7.55e-02 1.66e-09 GO translation elongation factor activity molecular_function 6.70e-02 4.66e-22 GO mitochondrial small ribosomal subunit cellular_component 6.30e-02 3.46e-49 GO mitochondrial translational elongation biological_process 5.24e-02 1.48e-15 GO cytosolic large ribosomal subunit cellular_component 5.13e-02 5.88e-19 GO mitochondrial translation biological_process 2.17e-02 4.99e-16 Reactome Peptide chain elongation Metabolism of proteins 1.12e-02 9.24e-63 Reactome Translation Metabolism of proteins 1.42e-03 8.03e-10 GO rRNA binding molecular_function

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 peptide metabolic process 0e+00 0e+00 peptide biosynthetic process 0e+00 0e+00 mitochondrial translation 0e+00 0e+00 mitochondrial translational elongation 0e+00 0e+00 translational elongation 0e+00 0e+00 translation 0e+00 0e+00 translational termination 0e+00 0e+00 mitochondrial translational termination 0e+00 0e+00 ribosome biogenesis 0e+00 0e+00 ribonucleoprotein complex biogenesis 0e+00 0e+00 translational initiation 0e+00 0e+00 rRNA processing 0e+00 0e+00 rRNA metabolic process 0e+00 0e+00 mitochondrial matrix 0e+00 0e+00 mitochondrial membrane 0e+00 0e+00 intracellular ribonucleoprotein complex 0e+00 0e+00 mitochondrial ribosome 0e+00 0e+00 large ribosomal subunit

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 PEPTIDE CHAIN ELONGATION 0.00e+00 0.00e+00 PEPTIDE CHAIN ELONGATION 0.00e+00 0.00e+00 TRANSLATION 6.25e-11 2.30e-08 TRANSLATION 7.49e-10 1.86e-07 INFLUENZA VIRAL RNA TRANSCRIPTION AND REPLICATION 7.55e-10 2.52e-07 INFLUENZA VIRAL RNA TRANSCRIPTION AND REPLICATION 7.81e-10 1.93e-07 NONSENSE MEDIATED DECAY ENHANCED BY THE EXON JUNCTION COMPLEX 8.05e-10 1.99e-07 3 UTR MEDIATED TRANSLATIONAL REGULATION 9.09e-10 2.23e-07 SRP DEPENDENT COTRANSLATIONAL PROTEIN TARGETING TO MEMBRANE 1.33e-09 4.34e-07 INFLUENZA LIFE CYCLE 1.44e-09 4.67e-07 3 UTR MEDIATED TRANSLATIONAL REGULATION 1.47e-09 4.76e-07 SRP DEPENDENT COTRANSLATIONAL PROTEIN TARGETING TO MEMBRANE 1.69e-09 5.43e-07 NONSENSE MEDIATED DECAY ENHANCED BY THE EXON JUNCTION COMPLEX 3.26e-09 7.52e-07 INFLUENZA LIFE CYCLE 7.76e-09 2.31e-06 METABOLISM OF MRNA 1.12e-08 3.26e-06 METABOLISM OF RNA 1.68e-08 3.60e-06 METABOLISM OF MRNA 4.23e-08 8.65e-06 METABOLISM OF RNA 1.13e-02 8.10e-01 FORMATION OF THE TERNARY COMPLEX AND SUBSEQUENTLY THE 43S COMPLEX 1.54e-02 1.00e+00 FORMATION OF THE TERNARY COMPLEX AND SUBSEQUENTLY THE 43S COMPLEX

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 1.87e-03 1e+00 increased ear pigmentation 1.87e-03 1e+00 abnormal cerebellar layer morphology 1.87e-03 1e+00 decreased cerebellar granule cell number 3.74e-03 1e+00 decreased hematopoietic cell number 3.74e-03 1e+00 hyperpigmentation 5.61e-03 1e+00 increased tail pigmentation 5.61e-03 1e+00 thin external granule cell layer 5.62e-03 1e+00 ectopic Purkinje cell 7.47e-03 1e+00 abnormal embryonic tissue physiology 7.93e-03 1e+00 embryonic lethality 9.33e-03 1e+00 increased foot pad pigmentation 1.12e-02 1e+00 pancytopenia 1.12e-02 1e+00 abnormal hematopoietic system morphology/development 1.40e-02 1e+00 preweaning lethality 1.49e-02 1e+00 increased mortality induced by gamma-irradiation 1.49e-02 1e+00 abnormal cerebellum external granule cell layer morphology 1.68e-02 1e+00 abnormal bone marrow cell physiology 1.68e-02 1e+00 decreased hematopoietic stem cell number 1.86e-02 1e+00 decreased sensitivity to induced cell death 1.87e-02 1e+00 small spleen

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

²FDR corrected p-value (Benjamini-Hochberg)