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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod207

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod207 Module size 47 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 25374 ALAD aminolevulinate dehydratase 388962 BOLA3 bolA family member 3 9973 CCS copper chaperone for superoxide dismutase 307649 CIAPIN1 cytokine induced apoptosis inhibitor 1 121506 ERP27 endoplasmic reticulum protein 27 23071 ERP44 endoplasmic reticulum protein 44 53940 FTHL17 ferritin heavy chain like 17 94033 FTMT ferritin mitochondrial 2745 GLRX glutaredoxin 51022 GLRX2 glutaredoxin 2 10539 GLRX3 glutaredoxin 3 51218 GLRX5 glutaredoxin 5 2880 GPX5 glutathione peroxidase 5 3029 HAGH hydroxyacylglutathione hydrolase 84264 HAGHL hydroxyacylglutathione hydrolase like 51557 LGSN lengsin, lens protein with glutamine synthetase domain 4357 MPST mercaptopyruvate sulfurtransferase 4482 MSRA methionine sulfoxide reductase A 51734 MSRB1 methionine sulfoxide reductase B1 22921 MSRB2 methionine sulfoxide reductase B2 253827 MSRB3 methionine sulfoxide reductase B3 51314 NME8 NME/NM23 family member 8 11315 PARK7 Parkinsonism associated deglycase 64714 PDIA2 protein disulfide isomerase family A member 2 10954 PDIA5 protein disulfide isomerase family A member 5 204474 PDILT protein disulfide isomerase like, testis expressed 25953 PNKD PNKD, MBL domain containing 5052 PRDX1 peroxiredoxin 1 7001 PRDX2 peroxiredoxin 2 10935 PRDX3 peroxiredoxin 3 10549 PRDX4 peroxiredoxin 4 25824 PRDX5 peroxiredoxin 5 9588 PRDX6 peroxiredoxin 6 6647 SOD1 superoxide dismutase 1 6649 SOD3 superoxide dismutase 3 83595 SOX7 SRY-box 7 54495 TMX3 thioredoxin related transmembrane protein 3 158427 TSTD2 thiosulfate sulfurtransferase like domain containing 2 25828 TXN thioredoxin 2 25828 TXN2 thioredoxin 2 51061 TXNDC11 thioredoxin domain containing 11 57544 TXNDC16 thioredoxin domain containing 16 84203 TXNDC2 thioredoxin domain containing 2 81567 TXNDC5 thioredoxin domain containing 5 255220 TXNDC8 thioredoxin domain containing 8 10190 TXNDC9 thioredoxin domain containing 9 7296 TXNRD1 thioredoxin reductase 1

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 4.88e-01 8.72e-14 GO thioredoxin peroxidase activity molecular_function 4.13e-01 5.22e-13 Reactome Protein repair Metabolism of proteins 3.31e-01 3.74e-11 GO peptide-methionine (R)-S-oxide reductase activity molecular_function 2.95e-01 1.56e-07 GO superoxide dismutase activity molecular_function 1.99e-01 2.92e-46 GO cell redox homeostasis biological_process 1.78e-01 2.56e-03 Reactome Metabolism of ingested MeSeO2H into MeSeH Metabolism 7.01e-02 5.45e-07 GO peptidyl-proline 4-dioxygenase activity molecular_function 5.89e-02 1.56e-12 GO protein disulfide isomerase activity molecular_function 5.05e-02 2.73e-23 Reactome Detoxification of Reactive Oxygen Species Cellular responses to external stimuli 3.73e-02 2.28e-04 GO ferroxidase activity molecular_function 3.60e-02 4.97e-14 GO protein disulfide oxidoreductase activity molecular_function 1.09e-02 2.85e-04 GO ferric iron 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 cellular homeostasis 0e+00 0e+00 cell redox homeostasis 0e+00 0e+00 protein repair 0e+00 0e+00 response to oxidative stress 0e+00 0e+00 response to toxic substance 0e+00 0e+00 cellular oxidant detoxification 0e+00 0e+00 response to reactive oxygen species 0e+00 0e+00 cellular response to oxidative stress 0e+00 0e+00 cellular response to reactive oxygen species 0e+00 0e+00 response to oxygen radical 0e+00 0e+00 oxidoreductase activity, acting on a sulfur group of donors 0e+00 0e+00 disulfide oxidoreductase activity 0e+00 0e+00 protein disulfide oxidoreductase activity 0e+00 0e+00 oxidoreductase activity 0e+00 0e+00 oxidoreductase activity, acting on a sulfur group of donors, disulfide as acceptor 0e+00 0e+00 antioxidant activity 0e+00 0e+00 oxidoreductase activity, acting on peroxide as acceptor 0e+00 0e+00 peroxiredoxin activity 0e+00 0e+00 protein disulfide isomerase activity 0e+00 0e+00 intramolecular oxidoreductase activity

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 3.20e-06 5.15e-04 SYNTHESIS AND INTERCONVERSION OF NUCLEOTIDE DI AND TRIPHOSPHATES 3.56e-06 7.30e-04 SYNTHESIS AND INTERCONVERSION OF NUCLEOTIDE DI AND TRIPHOSPHATES 1.05e-04 1.33e-02 METABOLISM OF NUCLEOTIDES 1.80e-04 2.62e-02 METABOLISM OF NUCLEOTIDES 1.24e-02 9.44e-01 THE NLRP3 INFLAMMASOME 1.80e-02 1.00e+00 INFLAMMASOMES 1.85e-02 1.00e+00 LYSOSOME VESICLE BIOGENESIS 2.21e-02 1.00e+00 NUCLEOTIDE BINDING DOMAIN LEUCINE RICH REPEAT CONTAINING RECEPTOR NLR SIGNALING PATHWAYS 2.27e-02 1.00e+00 THE NLRP3 INFLAMMASOME 2.42e-02 1.00e+00 METABOLISM OF PORPHYRINS 2.52e-02 1.00e+00 METABOLISM OF PORPHYRINS 2.87e-02 1.00e+00 INFLAMMASOMES 3.30e-02 1.00e+00 LYSOSOME VESICLE BIOGENESIS 3.77e-02 1.00e+00 ACTIVATION OF CHAPERONE GENES BY XBP1S 3.83e-02 1.00e+00 NUCLEOTIDE BINDING DOMAIN LEUCINE RICH REPEAT CONTAINING RECEPTOR NLR SIGNALING PATHWAYS 4.54e-02 1.00e+00 GOLGI ASSOCIATED VESICLE BIOGENESIS

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 2.21e-07 2.70e-03 increased cellular sensitivity to oxidative stress 2.87e-06 1.97e-02 oxidative stress 1.47e-04 2.92e-01 decreased hemoglobin content 6.24e-04 6.88e-01 abnormal erythrocyte morphology 9.88e-04 8.96e-01 decreased corpora lutea number 1.17e-03 9.85e-01 abnormal dopamine level 1.42e-03 1.00e+00 hemolytic anemia 1.43e-03 1.00e+00 increased cellular sensitivity to hydrogen peroxide 1.62e-03 1.00e+00 decreased mature ovarian follicle number 3.02e-03 1.00e+00 abnormal cellular respiration 3.68e-03 1.00e+00 decreased hematocrit 6.55e-03 1.00e+00 cochlear inner hair cell degeneration 7.50e-03 1.00e+00 abnormal Meibomian gland acinus morphology 7.82e-03 1.00e+00 reticulocytosis 9.37e-03 1.00e+00 pulmonary alveolar edema 1.10e-02 1.00e+00 abnormal enzyme/coenzyme level 1.12e-02 1.00e+00 increased hemoglobin concentration distribution width 1.12e-02 1.00e+00 abnormal copper homeostasis 1.12e-02 1.00e+00 suppressed circulating follicle stimulating hormone level 1.12e-02 1.00e+00 abnormal pulmonary alveolar duct morphology

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

²FDR corrected p-value (Benjamini-Hochberg)