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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod347

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod347 Module size 77 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 414149 ACBD7 acyl-CoA binding domain containing 7 120 ADD3 adducin 3 55256 ADI1 acireductone dioxygenase 1 83440 ADPGK ADP dependent glucokinase 9131 AIFM1 apoptosis inducing factor mitochondria associated 1 84964 ALKBH6 alkB homolog 6 51074 APIP APAF1 interacting protein 84326 C16orf13 methyltransferase like 26 116173 CMTM5 CKLF like MARVEL transmembrane domain containing 5 1428 CRYM crystallin mu 728294 D2HGDH D-2-hydroxyglutarate dehydrogenase 706 DBI translocator protein 23576 DDAH1 dimethylarginine dimethylaminohydrolase 1 23564 DDAH2 dimethylarginine dimethylaminohydrolase 2 53905 DUOX1 dual oxidase 1 58478 ENOPH1 enolase-phosphatase 1 23474 ETHE1 ETHE1, persulfide dioxygenase 2169 FABP2 fatty acid binding protein 2 51011 FAHD2A fumarylacetoacetate hydrolase domain containing 2A 151313 FAHD2B fumarylacetoacetate hydrolase domain containing 2B 81926 FAM108A1 abhydrolase domain containing 17A 84188 FAR1 fatty acyl-CoA reductase 1 55711 FAR2 fatty acyl-CoA reductase 2 55277 FGGY FGGY carbohydrate kinase domain containing 8790 FPGT fucose-1-phosphate guanylyltransferase 79068 FTO FTO, alpha-ketoglutarate dependent dioxygenase 197258 FUK fucokinase 282969 FUOM fucose mutarotase 2582 GALE UDP-galactose-4-epimerase 130589 GALM galactose mutarotase 79411 GLB1L galactosidase beta 1 like 89944 GLB1L2 galactosidase beta 1 like 2 112937 GLB1L3 galactosidase beta 1 like 3 8443 GNPAT glyceronephosphate O-acyltransferase 133558 HEATR7B2 maestro heat like repeat family member 2B 730249 IRG1 aconitate decarboxylase 1 112849 L3HYPDH trans-L-3-hydroxyproline dehydratase 51110 LACTB2 lactamase beta 2 54996 MARC2 mitochondrial amidoxime reducing component 2 153364 MBLAC2 metallo-beta-lactamase domain containing 2 388931 MFSD2B major facilitator superfamily domain containing 2B 29318 MIF D-dopachrome tautomerase 25974 MMACHC metabolism of cobalamin associated C 27249 MMADHC metabolism of cobalamin associated D 57380 MRS2 magnesium transporter MRS2 221294 NT5DC1 5'-nucleotidase domain containing 1 64359 NXN nucleoredoxin 339229 OXLD1 oxidoreductase like domain containing 1 5106 PCK2 phosphoenolpyruvate carboxykinase 2, mitochondrial 8566 PDXK pyridoxal kinase 29085 PHPT1 phosphohistidine phosphatase 1 55163 PNPO pyridoxamine 5'-phosphate oxidase 5860 QDPR quinoid dihydropteridine reductase 729659 S100A14 S100 calcium binding protein A11 pseudogene 1 388697 S100A16 hornerin 8991 SELENBP1 selenium binding protein 1 22929 SEPHS1 selenophosphate synthetase 1 22928 SEPHS2 selenophosphate synthetase 2 60386 SLC25A19 solute carrier family 25 member 19 81894 SLC25A28 solute carrier family 25 member 28 84275 SLC25A33 solute carrier family 25 member 33 55186 SLC25A36 solute carrier family 25 member 36 51312 SLC25A37 solute carrier family 25 member 37 284439 SLC25A42 solute carrier family 25 member 42 203427 SLC25A43 solute carrier family 25 member 43 10463 SLC30A9 solute carrier family 30 member 9 58472 SQRDL sulfide quinone oxidoreductase 56910 STARD7 StAR related lipid transfer domain containing 7 6821 SUOX sulfite oxidase 6999 TDO2 tryptophan 2,3-dioxygenase 56165 TDRD1 tudor domain containing 1 7054 TH tyrosine hydroxylase 9777 TM9SF4 transmembrane 9 superfamily member 4 25816 TNFAIP8 TNF alpha induced protein 8 7263 TST thiosulfate sulfurtransferase 143941 TTC36 tetratricopeptide repeat domain 36 55020 TTC38 tetratricopeptide repeat domain 38

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 5.91e-01 1.50e-05 Reactome Defective MMADHC causes methylmalonic aciduria and homocystinuria type cblD Disease 4.24e-01 3.15e-09 Reactome Sulfide oxidation to sulfate Metabolism 3.41e-01 4.49e-05 Reactome Vitamins B6 activation to pyridoxal phosphate Metabolism 2.66e-01 1.13e-06 GO beta-galactosidase activity molecular_function 2.64e-01 1.13e-06 Reactome GDP-fucose biosynthesis Metabolism of proteins 2.09e-01 8.95e-05 Reactome Wax biosynthesis Metabolism 1.50e-01 1.13e-06 GO L-methionine salvage from methylthioadenosine biological_process 1.50e-01 1.13e-06 Reactome Methionine salvage pathway Metabolism 1.10e-01 2.23e-04 GO NAD(P)H oxidase activity molecular_function 8.45e-02 6.21e-07 GO amino acid binding molecular_function 6.73e-02 7.79e-03 Reactome Plasmalogen biosynthesis Metabolism 5.78e-02 3.11e-04 GO arginine catabolic process biological_process 5.66e-02 2.23e-04 GO ether lipid biosynthetic process biological_process 3.02e-02 6.61e-04 GO mitochondrial genome maintenance biological_process 2.75e-02 1.17e-02 Reactome Interconversion of 2-oxoglutarate and 2-hydroxyglutarate Metabolism 1.23e-02 9.65e-04 Reactome Mitochondrial iron-sulfur cluster biogenesis Metabolism 9.56e-03 3.11e-04 GO fucose metabolic process biological_process 1.11e-03 1.58e-05 GO vacuole cellular_component

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 cofactor binding 2.12e-10 1.24e-07 coenzyme binding 1.21e-09 6.34e-07 oxidoreductase activity 1.23e-08 7.93e-06 sulfur compound metabolic process 1.47e-08 5.70e-06 mitochondrial inner membrane 2.45e-08 9.24e-06 mitochondrial envelope 4.64e-08 1.68e-05 organelle inner membrane 1.13e-07 3.83e-05 mitochondrial membrane 1.46e-07 8.01e-05 mitochondrial transport 2.84e-07 1.00e-04 beta-galactosidase activity 2.92e-07 1.53e-04 cellular amino acid metabolic process 6.66e-07 3.28e-04 cofactor metabolic process 1.25e-06 3.89e-04 racemase and epimerase activity 1.53e-06 7.03e-04 L-methionine salvage from methylthioadenosine 2.14e-06 9.54e-04 sulfide oxidation, using sulfide:quinone oxidoreductase 2.28e-06 1.01e-03 carbohydrate metabolic process 4.85e-06 2.01e-03 L-methionine salvage 1.23e-05 3.16e-03 nucleobase-containing compound transmembrane transporter activity 1.38e-05 5.16e-03 hexose metabolic process 1.72e-05 6.29e-03 methionine biosynthetic process

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 SULFUR AMINO ACID METABOLISM 0.00e+00 0.00e+00 SULFUR AMINO ACID METABOLISM 1.77e-10 6.31e-08 METABOLISM OF AMINO ACIDS AND DERIVATIVES 3.06e-09 7.07e-07 METABOLISM OF AMINO ACIDS AND DERIVATIVES 1.52e-05 2.82e-03 METABOLISM OF POLYAMINES 2.63e-05 3.68e-03 METABOLISM OF POLYAMINES 6.01e-05 9.85e-03 PEROXISOMAL LIPID METABOLISM 1.36e-04 1.68e-02 PEROXISOMAL LIPID METABOLISM 8.32e-03 6.31e-01 SYNTHESIS OF PA 2.05e-02 1.00e+00 SYNTHESIS OF PA 2.49e-02 1.00e+00 METABOLISM OF VITAMINS AND COFACTORS 4.20e-02 1.00e+00 GLUCONEOGENESIS 4.34e-02 1.00e+00 TRYPTOPHAN CATABOLISM 4.72e-02 1.00e+00 METABOLISM OF CARBOHYDRATES

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 1.19e-04 2.53e-01 increased lean body mass 8.14e-04 7.99e-01 increased circulating serum albumin level 4.52e-03 1.00e+00 increased susceptibility to diet-induced obesity 6.19e-03 1.00e+00 increased circulating cholesterol level 7.48e-03 1.00e+00 abnormal amino acid level 7.48e-03 1.00e+00 abnormal paranode morphology 7.48e-03 1.00e+00 abnormal paranodal axoglial junction morphology 8.54e-03 1.00e+00 abnormal enzyme/coenzyme activity 9.34e-03 1.00e+00 decreased uterine fat pad weight 9.51e-03 1.00e+00 abnormal spine curvature 9.57e-03 1.00e+00 small cerebellum 1.07e-02 1.00e+00 increased circulating HDL cholesterol level 1.31e-02 1.00e+00 small sebaceous gland 1.31e-02 1.00e+00 abnormal seminal vesicle development 1.31e-02 1.00e+00 abnormal triiodothyronine level 1.49e-02 1.00e+00 abnormal seizure response to pharmacological agent 1.49e-02 1.00e+00 abnormal neopterin level 1.55e-02 1.00e+00 abnormal circulating amino acid level 1.65e-02 1.00e+00 decreased heart rate 1.65e-02 1.00e+00 abnormal metabolism

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

²FDR corrected p-value (Benjamini-Hochberg)