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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod171

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod171 Module size 38 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 30 ACAA1 acetyl-CoA acyltransferase 1 10449 ACAA2 acetyl-CoA acyltransferase 2 27034 ACAD8 acyl-CoA dehydrogenase family member 8 28976 ACAD9 acyl-CoA dehydrogenase family member 9 33 ACADL acyl-CoA dehydrogenase long chain 34 ACADM acyl-CoA dehydrogenase medium chain 35 ACADS acyl-CoA dehydrogenase short chain 36 ACADSB acyl-CoA dehydrogenase short/branched chain 37 ACADVL acyl-CoA dehydrogenase very long chain 6646 ACAT1 sterol O-acyltransferase 1 39 ACAT2 acetyl-CoA acetyltransferase 2 8309 ACOX2 acyl-CoA oxidase 2 8310 ACOX3 acyl-CoA oxidase 3, pristanoyl 55289 ACOXL acyl-CoA oxidase like 23600 AMACR alpha-methylacyl-CoA racemase 549 AUH AU RNA binding methylglutaconyl-CoA hydratase 79783 C7orf10 succinyl-CoA:glutarate-CoA transferase 9085 CDY1 chromodomain Y-linked 1 253175 CDY1B chromodomain Y-linked 1B 9426 CDY2A chromodomain Y-linked 2A 203611 CDY2B chromodomain Y-linked 2B 124359 CDYL2 chromodomain Y like 2 51084 CRYL1 crystallin lambda 1 1891 ECH1 enoyl-CoA hydratase 1 55862 ECHDC1 ethylmalonyl-CoA decarboxylase 1 55268 ECHDC2 enoyl-CoA hydratase domain containing 2 79746 ECHDC3 enoyl-CoA hydratase domain containing 3 1892 ECHS1 enoyl-CoA hydratase, short chain 1 1632 ECI1 enoyl-CoA delta isomerase 1 10455 ECI2 enoyl-CoA delta isomerase 2 2639 GCDH glutaryl-CoA dehydrogenase 3033 HADH hydroxyacyl-CoA dehydrogenase 3030 HADHA hydroxyacyl-CoA dehydrogenase trifunctional multienzyme complex subunit alpha 3032 HADHB hydroxyacyl-CoA dehydrogenase trifunctional multienzyme complex subunit beta 26275 HIBCH 3-hydroxyisobutyryl-CoA hydrolase 3028 HSD17B10 hydroxysteroid 17-beta dehydrogenase 10 3712 IVD isovaleryl-CoA dehydrogenase 64064 OXCT2 3-oxoacid CoA-transferase 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 3.90e-01 1.13e-21 GO enoyl-CoA hydratase activity molecular_function 3.39e-01 3.10e-08 GO acyl-CoA oxidase activity molecular_function 2.20e-01 1.27e-15 GO acyl-CoA dehydrogenase activity molecular_function 1.82e-01 8.69e-16 GO branched-chain amino acid catabolic process biological_process 1.44e-01 2.41e-05 Reactome Utilization of Ketone Bodies Metabolism 1.41e-01 9.51e-15 GO fatty acid beta-oxidation using acyl-CoA dehydrogenase biological_process 1.18e-01 5.99e-40 GO fatty acid beta-oxidation biological_process 8.89e-02 3.81e-15 GO 3-hydroxyacyl-CoA dehydrogenase activity molecular_function 8.65e-02 2.06e-20 Reactome mitochondrial fatty acid beta-oxidation of saturated fatty acids Metabolism 7.50e-02 2.61e-14 Reactome Beta oxidation of hexanoyl-CoA to butanoyl-CoA Metabolism 7.44e-02 2.61e-14 Reactome Beta oxidation of octanoyl-CoA to hexanoyl-CoA Metabolism 5.44e-02 1.81e-09 Reactome Beta-oxidation of pristanoyl-CoA Metabolism 4.58e-02 2.25e-13 GO fatty acid beta-oxidation using acyl-CoA oxidase biological_process 4.48e-02 1.73e-12 GO fatty-acyl-CoA binding molecular_function 4.43e-02 2.61e-14 Reactome Beta oxidation of lauroyl-CoA to decanoyl-CoA-CoA Metabolism 3.35e-02 5.13e-22 GO flavin adenine dinucleotide binding molecular_function 2.60e-02 1.44e-11 GO acetyl-CoA C-acetyltransferase activity 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 fatty acid catabolic process 0e+00 0e+00 lipid oxidation 0e+00 0e+00 fatty acid metabolic process 0e+00 0e+00 carboxylic acid catabolic process 0e+00 0e+00 fatty acid beta-oxidation 0e+00 0e+00 fatty acid oxidation 0e+00 0e+00 lipid catabolic process 0e+00 0e+00 cellular lipid catabolic process 0e+00 0e+00 lipid modification 0e+00 0e+00 monocarboxylic acid metabolic process 0e+00 0e+00 branched-chain amino acid catabolic process 0e+00 0e+00 mitochondrial matrix 0e+00 0e+00 acyl-CoA dehydrogenase activity 0e+00 0e+00 coenzyme binding 0e+00 0e+00 oxidoreductase activity, acting on the CH-CH group of donors 0e+00 0e+00 flavin adenine dinucleotide binding 0e+00 0e+00 cofactor binding 0e+00 0e+00 oxidoreductase activity 0e+00 0e+00 acetyl-CoA C-acyltransferase activity 0e+00 0e+00 enoyl-CoA hydratase 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 BRANCHED CHAIN AMINO ACID CATABOLISM 0.00e+00 0.00e+00 MITOCHONDRIAL FATTY ACID BETA OXIDATION 0.00e+00 0.00e+00 MITOCHONDRIAL FATTY ACID BETA OXIDATION 4.80e-11 1.35e-08 BRANCHED CHAIN AMINO ACID CATABOLISM 1.10e-10 2.99e-08 FATTY ACID TRIACYLGLYCEROL AND KETONE BODY METABOLISM 1.10e-09 3.62e-07 FATTY ACID TRIACYLGLYCEROL AND KETONE BODY METABOLISM 2.05e-07 5.12e-05 METABOLISM OF AMINO ACIDS AND DERIVATIVES 8.94e-07 1.57e-04 PEROXISOMAL LIPID METABOLISM 2.60e-06 5.45e-04 PEROXISOMAL LIPID METABOLISM 2.62e-06 4.27e-04 METABOLISM OF AMINO ACIDS AND DERIVATIVES 1.12e-03 1.11e-01 SYNTHESIS OF BILE ACIDS AND BILE SALTS VIA 7ALPHA HYDROXYCHOLESTEROL 1.87e-03 1.75e-01 SYNTHESIS OF BILE ACIDS AND BILE SALTS 3.39e-03 3.32e-01 SYNTHESIS OF BILE ACIDS AND BILE SALTS VIA 7ALPHA HYDROXYCHOLESTEROL 5.07e-03 4.63e-01 SYNTHESIS OF BILE ACIDS AND BILE SALTS 5.34e-03 4.34e-01 BILE ACID AND BILE SALT METABOLISM 1.00e-02 7.99e-01 BILE ACID AND BILE SALT METABOLISM 2.51e-02 1.00e+00 SYNTHESIS OF BILE ACIDS AND BILE SALTS VIA 24 HYDROXYCHOLESTEROL 3.93e-02 1.00e+00 GLYCEROPHOSPHOLIPID BIOSYNTHESIS 4.31e-02 1.00e+00 ALPHA LINOLENIC ACID ALA METABOLISM

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 5.32e-10 2.18e-05 increased circulating carnitine level 1.75e-09 5.61e-05 hepatic steatosis 2.04e-07 2.53e-03 aciduria 1.01e-06 8.85e-03 decreased circulating carnitine level 5.54e-06 3.17e-02 hypoglycemia 7.68e-06 3.87e-02 abnormal urine homeostasis 9.16e-06 4.43e-02 impaired adaptive thermogenesis 2.62e-05 9.39e-02 increased fatty acid level 2.76e-05 9.76e-02 abnormal lipid homeostasis 2.93e-05 1.01e-01 cardiomyopathy 5.22e-05 1.47e-01 increased unsaturated fatty acid level 1.01e-04 2.28e-01 increased circulating free fatty acid level 1.08e-04 2.39e-01 cardiac fibrosis 2.03e-04 3.52e-01 abnormal adaptive thermogenesis 2.28e-04 3.78e-01 abnormal myocardial fiber morphology 3.42e-04 4.86e-01 myocardial fiber degeneration 6.11e-04 6.81e-01 abnormal brown adipose tissue morphology 1.06e-03 9.29e-01 abnormal fatty acid oxidation 1.16e-03 9.82e-01 abnormal heart morphology 1.40e-03 1.00e+00 abnormal bile composition

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

²FDR corrected p-value (Benjamini-Hochberg)