Back to main page

DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod61

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod61 Module size 41 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 124 ADH1A alcohol dehydrogenase 1A (class I), alpha polypeptide 125 ADH1B alcohol dehydrogenase 1B (class I), beta polypeptide 131 ADH4 alcohol dehydrogenase 7 (class IV), mu or sigma polypeptide 128 ADH5 alcohol dehydrogenase 5 (class III), chi polypeptide 130 ADH6 alcohol dehydrogenase 6 (class V) 131 ADH7 alcohol dehydrogenase 7 (class IV), mu or sigma polypeptide 130813 C2orf50 chromosome 2 open reading frame 50 2052 EPHX1 epoxide hydrolase 1 2678 GGT1 gamma-glutamyltransferase 1 2687 GGT5 gamma-glutamyltransferase 5 124975 GGT6 gamma-glutamyltransferase 6 2686 GGT7 gamma-glutamyltransferase 7 2876 GPX1 glutathione peroxidase 1 2877 GPX2 glutathione peroxidase 2 2878 GPX3 glutathione peroxidase 3 2879 GPX4 glutathione peroxidase 4 257202 GPX6 glutathione peroxidase 6 2882 GPX7 glutathione peroxidase 7 493869 GPX8 glutathione peroxidase 8 (putative) 2937 GSS glutathione synthetase 2938 GSTA1 glutathione S-transferase alpha 1 2939 GSTA2 glutathione S-transferase alpha 2 2940 GSTA3 glutathione S-transferase alpha 3 2941 GSTA4 glutathione S-transferase alpha 4 221357 GSTA5 glutathione S-transferase alpha 5 373156 GSTK1 glutathione S-transferase kappa 1 2944 GSTM1 glutathione S-transferase mu 1 2946 GSTM2 glutathione S-transferase mu 2 2947 GSTM3 glutathione S-transferase mu 3 2948 GSTM4 glutathione S-transferase mu 4 2949 GSTM5 glutathione S-transferase mu 5 9446 GSTO1 glutathione S-transferase omega 1 119391 GSTO2 glutathione S-transferase omega 2 2950 GSTP1 glutathione S-transferase pi 1 2952 GSTT1 glutathione S-transferase theta 1 653689 GSTT2B glutathione S-transferase theta 2B (gene/pseudogene) 4056 LTC4S leukotriene C4 synthase 4257 MGST1 microsomal glutathione S-transferase 1 4258 MGST2 microsomal glutathione S-transferase 2 4259 MGST3 microsomal glutathione S-transferase 3 51060 TXNDC12 thioredoxin domain containing 12

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 4.73e-01 3.17e-13 GO alcohol dehydrogenase activity, zinc-dependent molecular_function 3.34e-01 4.67e-40 GO glutathione peroxidase activity molecular_function 2.40e-01 3.21e-58 Reactome Glutathione conjugation Metabolism 1.57e-01 3.15e-46 GO glutathione derivative biosynthetic process biological_process 1.04e-01 5.98e-50 GO glutathione transferase activity molecular_function 8.40e-02 2.23e-45 GO glutathione metabolic process biological_process 8.28e-02 3.15e-09 GO glutathione hydrolase activity molecular_function 7.15e-02 2.33e-07 Reactome Synthesis of 15-eicosatetraenoic acid derivatives Metabolism 6.12e-02 5.29e-06 Reactome Biosynthesis of DHA-derived sulfido conjugates Metabolism 5.43e-02 9.85e-14 GO ethanol oxidation biological_process 5.38e-02 9.85e-14 Reactome Ethanol oxidation Metabolism 4.86e-02 5.29e-06 Reactome Biosynthesis of maresin conjugates in tissue regeneration (MCTR) Metabolism 2.11e-02 4.07e-07 Reactome Synthesis of 12-eicosatetraenoic acid derivatives Metabolism 1.10e-02 6.99e-17 GO glutathione binding molecular_function 1.19e-03 1.62e-14 Reactome Aflatoxin activation and detoxification Metabolism

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 modified amino acid metabolic process 0e+00 0e+00 cellular oxidant detoxification 0e+00 0e+00 response to xenobiotic stimulus 0e+00 0e+00 sulfur compound metabolic process 0e+00 0e+00 response to toxic substance 0e+00 0e+00 peptide metabolic process 0e+00 0e+00 cellular amide metabolic process 0e+00 0e+00 glutathione metabolic process 0e+00 0e+00 glutathione derivative biosynthetic process 0e+00 0e+00 xenobiotic metabolic process 0e+00 0e+00 cellular response to xenobiotic stimulus 0e+00 0e+00 glutathione biosynthetic process 0e+00 0e+00 peroxidase activity 0e+00 0e+00 glutathione peroxidase activity 0e+00 0e+00 antioxidant activity 0e+00 0e+00 oxidoreductase activity 0e+00 0e+00 oxidoreductase activity, acting on peroxide as acceptor 0e+00 0e+00 glutathione transferase activity 0e+00 0e+00 glutathione binding 0e+00 0e+00 alcohol dehydrogenase (NAD) activity

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 BIOLOGICAL OXIDATIONS 0.00e+00 0.00e+00 PHASE II CONJUGATION 0.00e+00 0.00e+00 GLUTATHIONE CONJUGATION 0.00e+00 0.00e+00 BIOLOGICAL OXIDATIONS 0.00e+00 0.00e+00 PHASE II CONJUGATION 0.00e+00 0.00e+00 GLUTATHIONE CONJUGATION 3.92e-09 1.19e-06 ETHANOL OXIDATION 4.33e-08 8.84e-06 ETHANOL OXIDATION 7.49e-05 9.76e-03 PHASE1 FUNCTIONALIZATION OF COMPOUNDS 1.24e-04 1.88e-02 PHASE1 FUNCTIONALIZATION OF COMPOUNDS 4.83e-04 5.26e-02 METABOLISM OF VITAMINS AND COFACTORS 1.33e-02 9.97e-01 METABOLISM OF VITAMINS AND COFACTORS 4.10e-02 1.00e+00 ABACAVIR TRANSPORT AND METABOLISM

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 1.34e-05 5.71e-02 decreased spleen red pulp amount 1.74e-05 6.94e-02 decreased glutathione peroxidase activity 2.20e-04 3.69e-01 increased cellular sensitivity to oxidative stress 3.51e-04 4.91e-01 oxidative stress 1.05e-03 9.25e-01 increased cellular sensitivity to hydrogen peroxide 1.57e-03 1.00e+00 increased dopamine level 1.87e-03 1.00e+00 CNS ischemia 3.24e-03 1.00e+00 abnormal mitochondrial physiology 3.74e-03 1.00e+00 increased salivary gland tumor incidence 3.74e-03 1.00e+00 nervous 6.43e-03 1.00e+00 glomerulonephritis 7.16e-03 1.00e+00 abnormal lens morphology 7.47e-03 1.00e+00 cellular necrosis 7.47e-03 1.00e+00 abnormal selenium level 7.47e-03 1.00e+00 urinary bladder obstruction 7.47e-03 1.00e+00 stomach mucosa hyperplasia 7.48e-03 1.00e+00 vasculitis 7.48e-03 1.00e+00 priapism 7.79e-03 1.00e+00 increased neuron apoptosis 9.33e-03 1.00e+00 increased urine microalbumin level

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

²FDR corrected p-value (Benjamini-Hochberg)