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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod220

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod220 Module size 84 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 51205 ACP6 acid phosphatase 6, lysophosphatidic 137872 ADHFE1 alcohol dehydrogenase, iron containing 1 220 ALDH1A3 aldehyde dehydrogenase 1 family member A3 218 ALDH3A1 aldehyde dehydrogenase 3 family member A1 222 ALDH3B2 aldehyde dehydrogenase 3 family member B2 241 ALOX5AP arachidonate 5-lipoxygenase activating protein 130540 ALS2CR12 amyotrophic lateral sclerosis 2 chromosome region 12 57412 AS3MT arsenite methyltransferase 570 BAAT bile acid-CoA:amino acid N-acyltransferase 55973 BCAP29 B cell receptor associated protein 29 10134 BCAP31 B cell receptor associated protein 31 388701 C1orf189 chromosome 1 open reading frame 189 84996 C21orf119 URB1 antisense RNA 1 (head to head) 60526 C2orf43 lipid droplet associated hydrolase 83446 CCDC70 coiled-coil domain containing 70 55602 CDKN2AIP CDKN2A interacting protein 4502 CES1 metallothionein 2A 23491 CES3 carboxylesterase 3 283848 CES4A carboxylesterase 4A 221223 CES5A carboxylesterase 5A 1381 CRABP1 cellular retinoic acid binding protein 1 286464 CXorf59 cilia and flagella associated protein 47 1528 CYB5A cytochrome b5 type A 80777 CYB5B cytochrome b5 type B 1548 CYP2A6 cytochrome P450 family 2 subfamily A member 6 1571 CYP2E1 cytochrome P450 family 2 subfamily E member 1 84650 EBPL EBP like 2053 EPHX2 epoxide hydrolase 2 79852 EPHX3 epoxide hydrolase 3 8288 EPX eosinophil peroxidase 2098 ESD esterase D 3992 FADS6 fatty acid desaturase 1 127281 FAM213B peroxiredoxin like 2B 171483 FAM9B family with sequence similarity 9 member B 2230 FDX1 ferredoxin 1 112812 FDX1L ferredoxin 2 728441 GGT2 gamma-glutamyltransferase 2 92086 GGTLC1 gamma-glutamyltransferase light chain 1 91227 GGTLC2 gamma-glutamyltransferase light chain 2 728226 GGTLC3 gamma-glutamyltransferase light chain family member 3 389207 GRXCR1 glutaredoxin and cysteine rich domain containing 1 2936 GSR glutathione-disulfide reductase 55733 HHAT hedgehog acyltransferase 57467 HHATL hedgehog acyltransferase like 3162 HMOX1 heme oxygenase 1 3163 HMOX2 heme oxygenase 2 27306 HPGDS hematopoietic prostaglandin D synthase 3972 LHB luteinizing hormone beta polypeptide 222662 LHFPL5 LHFPL tetraspan subfamily member 5 3990 LIPH lipase C, hepatic type 4025 LPO lactoperoxidase 11313 LYPLA2 lysophospholipase II 127018 LYPLAL1 lysophospholipase like 1 57226 LYRM2 LYR motif containing 2 4232 MEST mesoderm specific transcript 55586 MIOX myo-inositol oxygenase 9 NAT1 N-acetyltransferase 1 79612 NAT2 N(alpha)-acetyltransferase 16, NatA auxiliary subunit 29937 NENF neudesin neurotrophic factor 58157 NGB neuroglobin 4817 NIT1 nitrilase 1 284958 NT5DC4 5'-nucleotidase domain containing 4 5049 PAFAH1B2 platelet activating factor acetylhydrolase 1b catalytic subunit 2 10857 PGRMC1 progesterone receptor membrane component 1 493911 PHOSPHO2 phosphatase, orphan 2 254295 PHYHD1 phytanoyl-CoA dioxygenase domain containing 1 5355 PLP2 proteolipid protein 2 646625 PRHOXNB ureidoimidazoline (2-oxo-4-hydroxy-4-carboxy-5-) decarboxylase 5730 PTGDS prostaglandin D2 synthase 9536 PTGES prostaglandin E synthase 80142 PTGES2 prostaglandin E synthase 2 5742 PTGS1 prostaglandin-endoperoxide synthase 1 5948 RBP2 retinol binding protein 2 5995 RGR retinal G protein coupled receptor 84268 RPAIN RPA interacting protein 63027 SLC22A23 solute carrier family 22 member 23 23169 SLC35D1 solute carrier family 35 member D1 6820 SULT2B1 sulfotransferase family 2B member 1 55061 SUSD4 sushi domain containing 4 7104 TM4SF4 transmembrane 4 L six family member 4 140738 TMEM37 transmembrane protein 37 90407 TMEM41A transmembrane protein 41A 440026 TMEM41B transmembrane protein 41B 169200 TMEM64 transmembrane protein 64

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 5.92e-01 1.73e-05 Reactome Acetylation Metabolism 2.30e-01 3.52e-08 GO glutathione hydrolase activity molecular_function 2.07e-01 4.19e-03 Reactome COX reactions Metabolism 2.06e-01 1.96e-08 GO sterol esterase activity molecular_function 1.85e-01 2.44e-06 GO retinoid binding molecular_function 1.51e-01 4.46e-15 GO carboxylic ester hydrolase activity molecular_function 1.51e-01 1.72e-04 GO epoxide hydrolase activity molecular_function 1.46e-01 2.13e-11 Reactome Synthesis of Prostaglandins (PG) and Thromboxanes (TX) Metabolism 1.11e-01 2.57e-04 GO 3-chloroallyl aldehyde dehydrogenase activity molecular_function 1.01e-01 2.57e-04 Reactome Heme degradation Metabolism 7.88e-02 5.09e-10 GO cyclooxygenase pathway biological_process 5.68e-02 1.03e-04 GO prostaglandin-E synthase activity molecular_function 3.09e-02 1.87e-14 GO heme binding molecular_function 2.77e-02 1.25e-02 Reactome Electron transport from NADPH to Ferredoxin Metabolism 2.77e-02 1.25e-02 Reactome Formation of the active cofactor, UDP-glucuronate Metabolism 2.77e-02 1.25e-02 Reactome Interconversion of 2-oxoglutarate and 2-hydroxyglutarate Metabolism 2.41e-02 5.85e-08 GO leukotriene D4 biosynthetic process biological_process 1.96e-02 4.77e-04 Reactome Biosynthesis of maresins Metabolism 1.94e-04 6.49e-07 GO cellular oxidant detoxification biological_process

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 icosanoid metabolic process 0.00e+00 0.00e+00 icosanoid biosynthetic process 0.00e+00 0.00e+00 fatty acid metabolic process 0.00e+00 0.00e+00 xenobiotic metabolic process 0.00e+00 0.00e+00 cellular response to xenobiotic stimulus 0.00e+00 0.00e+00 response to xenobiotic stimulus 0.00e+00 0.00e+00 heme binding 1.57e-11 1.40e-08 monocarboxylic acid metabolic process 1.96e-11 1.74e-08 arachidonic acid metabolic process 2.17e-10 1.74e-07 prostaglandin biosynthetic process 5.42e-10 3.00e-07 oxidoreductase activity 2.16e-09 1.54e-06 prostaglandin metabolic process 4.10e-09 2.81e-06 cyclooxygenase pathway 5.60e-09 2.64e-06 carboxylic ester hydrolase activity 5.88e-09 3.94e-06 long-chain fatty acid metabolic process 1.92e-08 1.20e-05 unsaturated fatty acid biosynthetic process 2.57e-08 1.59e-05 leukotriene biosynthetic process 6.75e-08 3.92e-05 lipid biosynthetic process 1.28e-07 7.11e-05 leukotriene metabolic process 1.59e-07 5.92e-05 glutathione hydrolase activity

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 4.18e-08 8.55e-06 BIOLOGICAL OXIDATIONS 9.92e-07 2.25e-04 BIOLOGICAL OXIDATIONS 2.70e-05 3.77e-03 PHASE II CONJUGATION 3.23e-04 4.38e-02 PHASE II CONJUGATION 6.32e-04 7.88e-02 XENOBIOTICS 9.64e-04 9.76e-02 PHASE1 FUNCTIONALIZATION OF COMPOUNDS 1.27e-03 1.24e-01 METABOLISM OF PORPHYRINS 1.33e-03 1.50e-01 PHASE1 FUNCTIONALIZATION OF COMPOUNDS 1.87e-03 1.75e-01 XENOBIOTICS 2.07e-03 2.20e-01 METABOLISM OF PORPHYRINS 4.67e-03 4.32e-01 IRON UPTAKE AND TRANSPORT 6.16e-03 4.89e-01 IRON UPTAKE AND TRANSPORT 6.83e-03 5.37e-01 METABOLISM OF STEROID HORMONES AND VITAMINS A AND D 6.97e-03 5.46e-01 CYTOCHROME P450 ARRANGED BY SUBSTRATE TYPE 8.80e-03 7.23e-01 METABOLISM OF STEROID HORMONES AND VITAMINS A AND D 1.12e-02 8.71e-01 CYTOCHROME P450 ARRANGED BY SUBSTRATE TYPE 1.37e-02 9.46e-01 ANDROGEN BIOSYNTHESIS 2.05e-02 1.00e+00 GLYCOPROTEIN HORMONES 2.22e-02 1.00e+00 PEPTIDE HORMONE BIOSYNTHESIS 2.36e-02 1.00e+00 CYTOSOLIC SULFONATION OF SMALL MOLECULES

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 1.27e-04 2.64e-01 decreased leukotriene level 1.77e-04 3.24e-01 edema 2.51e-04 4.00e-01 abnormal xenobiotic pharmacokinetics 2.65e-04 4.15e-01 increased susceptibility to type I hypersensitivity reaction 2.76e-04 4.29e-01 abnormal thromboxane level 4.66e-04 5.83e-01 abnormal prostaglandin level 1.04e-03 9.21e-01 increased prostaglandin level 1.20e-03 1.00e+00 decreased prostaglandin level 1.40e-03 1.00e+00 chondrodystrophy 1.69e-03 1.00e+00 abnormal cochlear inner hair cell morphology 1.80e-03 1.00e+00 abnormal nasal cavity morphology 2.37e-03 1.00e+00 bidirectional circling 3.00e-03 1.00e+00 decreased inflammatory response 3.89e-03 1.00e+00 abnormal outer hair cell stereociliary bundle morphology 4.05e-03 1.00e+00 chronic inflammation 4.06e-03 1.00e+00 head tossing 6.28e-03 1.00e+00 abnormal pain threshold 7.52e-03 1.00e+00 abnormal nociception after inflammation 7.55e-03 1.00e+00 decreased susceptibility to type I hypersensitivity reaction 8.43e-03 1.00e+00 cochlear hair cell degeneration

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

²FDR corrected p-value (Benjamini-Hochberg)