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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod53

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod53 Module size 50 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 16 AARS alanyl-tRNA synthetase 57505 AARS2 alanyl-tRNA synthetase 2, mitochondrial 9255 AIMP1 aminoacyl tRNA synthetase complex interacting multifunctional protein 1 7965 AIMP2 aminoacyl tRNA synthetase complex interacting multifunctional protein 2 833 CARS cysteinyl-tRNA synthetase 79587 CARS2 cysteinyl-tRNA synthetase 2, mitochondrial 55152 DALRD3 DALR anticodon binding domain containing 3 1615 DARS aspartyl-tRNA synthetase 55157 DARS2 aspartyl-tRNA synthetase 2, mitochondrial 124454 EARS2 glutamyl-tRNA synthetase 2, mitochondrial 2058 EPRS glutamyl-prolyl-tRNA synthetase 10667 FARS2 phenylalanyl-tRNA synthetase 2, mitochondrial 2193 FARSA phenylalanyl-tRNA synthetase subunit alpha 10056 FARSB phenylalanyl-tRNA synthetase subunit beta 2618 GARS phosphoribosylglycinamide formyltransferase, phosphoribosylglycinamide synthetase, phosphoribosylaminoimidazole synthetase 84705 GTPBP3 GTP binding protein 3, mitochondrial 3035 HARS histidyl-tRNA synthetase 23438 HARS2 histidyl-tRNA synthetase 2, mitochondrial 3376 IARS isoleucyl-tRNA synthetase 55699 IARS2 isoleucyl-tRNA synthetase 2, mitochondrial 3735 KARS lysyl-tRNA synthetase 51520 LARS leucyl-tRNA synthetase 23395 LARS2 leucyl-tRNA synthetase 2, mitochondrial 57470 LRRC47 leucine rich repeat containing 47 84174 MARS Src like adaptor 2 92935 MARS2 methionyl-tRNA synthetase 2, mitochondrial 79922 MRM1 mitochondrial rRNA methyltransferase 1 25821 MTO1 mitochondrial tRNA translation optimization 1 4677 NARS asparaginyl-tRNA synthetase 79731 NARS2 asparaginyl-tRNA synthetase 2, mitochondrial 25973 PARS2 prolyl-tRNA synthetase 2, mitochondrial 5188 PET112 glutamyl-tRNA amidotransferase subunit B 11232 POLG2 DNA polymerase gamma 2, accessory subunit 5859 QARS glutaminyl-tRNA synthetase 5917 RARS arginyl-tRNA synthetase 57038 RARS2 arginyl-tRNA synthetase 2, mitochondrial 55178 RNMTL1 mitochondrial rRNA methyltransferase 3 6301 SARS seryl-tRNA synthetase 54938 SARS2 seryl-tRNA synthetase 2, mitochondrial 51204 TACO1 translational activator of cytochrome c oxidase I 6894 TARBP1 TAR (HIV-1) RNA binding protein 1 6897 TARS threonyl-tRNA synthetase 80222 TARS2 threonyl-tRNA synthetase 2, mitochondrial 123283 TARSL2 threonyl-tRNA synthetase like 2 7407 VARS valyl-tRNA synthetase 57176 VARS2 valyl-tRNA synthetase 2, mitochondrial 7453 WARS tryptophanyl-tRNA synthetase 10352 WARS2 tryptophanyl tRNA synthetase 2, mitochondrial 8565 YARS tyrosyl-tRNA synthetase 51067 YARS2 tyrosyl-tRNA synthetase 2

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 6.06e-01 1.37e-108 Reactome tRNA Aminoacylation Metabolism of proteins 1.67e-01 3.27e-53 Reactome Mitochondrial tRNA aminoacylation Metabolism of proteins 1.14e-01 8.76e-58 Reactome Cytosolic tRNA aminoacylation Metabolism of proteins 8.40e-02 4.58e-80 GO tRNA aminoacylation for protein translation biological_process 4.44e-02 2.39e-04 Reactome tRNA modification in the mitochondrion Metabolism of RNA

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 cellular amide metabolic process 0.00e+00 0.00e+00 tRNA metabolic process 0.00e+00 0.00e+00 cellular amino acid metabolic process 0.00e+00 0.00e+00 tRNA aminoacylation 0.00e+00 0.00e+00 translation 0.00e+00 0.00e+00 tRNA aminoacylation for protein translation 0.00e+00 0.00e+00 peptide metabolic process 0.00e+00 0.00e+00 peptide biosynthetic process 0.00e+00 0.00e+00 regulation of translational fidelity 0.00e+00 0.00e+00 regulation of translational elongation 0.00e+00 0.00e+00 mitochondrial matrix 0.00e+00 0.00e+00 ligase activity, forming aminoacyl-tRNA and related compounds 0.00e+00 0.00e+00 tRNA binding 0.00e+00 0.00e+00 ligase activity 0.00e+00 0.00e+00 aminoacyl-tRNA editing activity 8.60e-13 4.95e-10 aminoacyl-tRNA synthetase multienzyme complex 2.89e-11 2.52e-08 tRNA aminoacylation for mitochondrial protein translation 1.14e-08 5.15e-06 phenylalanine-tRNA ligase activity 5.14e-08 3.04e-05 regulation of translation

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 0e+00 0e+00 TRNA AMINOACYLATION 0e+00 0e+00 CYTOSOLIC TRNA AMINOACYLATION 0e+00 0e+00 MITOCHONDRIAL TRNA AMINOACYLATION 0e+00 0e+00 TRNA AMINOACYLATION 0e+00 0e+00 CYTOSOLIC TRNA AMINOACYLATION 0e+00 0e+00 MITOCHONDRIAL TRNA AMINOACYLATION

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 1.92e-06 1.43e-02 preweaning lethality 1.58e-05 6.44e-02 embryonic lethality 2.50e-04 3.99e-01 decreased mitochondrial DNA content 1.78e-03 1.00e+00 abnormal mitochondrion morphology 3.09e-03 1.00e+00 increased grip strength 5.61e-03 1.00e+00 sinoatrial block 5.61e-03 1.00e+00 cardiac muscle necrosis 5.61e-03 1.00e+00 hair follicle outer rooth sheath hyperplasia 5.61e-03 1.00e+00 disorganized mitochondrial cristae 7.47e-03 1.00e+00 decreased QRS amplitude 7.48e-03 1.00e+00 ventricular premature beat 7.48e-03 1.00e+00 atrioventricular block 7.48e-03 1.00e+00 decreased cardiac output 7.48e-03 1.00e+00 decreased skeletal muscle fiber number 7.48e-03 1.00e+00 abnormal tibialis anterior morphology 9.33e-03 1.00e+00 dilated sarcoplasmic reticulum 9.36e-03 1.00e+00 decreased circulating sodium level 1.12e-02 1.00e+00 focal hair loss 1.12e-02 1.00e+00 abnormal PNS synaptic transmission 1.12e-02 1.00e+00 decreased muscle weight

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

²FDR corrected p-value (Benjamini-Hochberg)