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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod180

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod180 Module size 44 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 189 AGXT alanine--glyoxylate and serine--pyruvate aminotransferase 64902 AGXT2 alanine--glyoxylate aminotransferase 2 10840 ALDH1L1 aldehyde dehydrogenase 1 family member L1 160428 ALDH1L2 aldehyde dehydrogenase 1 family member L2 275 AMT aminomethyltransferase 471 ATIC 5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/IMP cyclohydrolase 23743 BHMT2 betaine--homocysteine S-methyltransferase 2 295586 CBS chloride voltage-gated channel 6 287305 DAO similar to L-amino acid oxidase 1 267012 DAOA D-amino acid oxidase activator 1719 DHFR dihydrofolate reductase 200895 DHFRL1 dihydrofolate reductase 2 29958 DMGDH dimethylglycine dehydrogenase 55572 FOXRED1 FAD dependent oxidoreductase domain containing 1 2356 FPGS folylpolyglutamate synthase 2628 GATM glycine amidinotransferase 2653 GCSH glycine cleavage system protein H 8836 GGH gamma-glutamyl hydrolase 2731 GLDC glycine decarboxylase 27232 GNMT glycine N-methyltransferase 9380 GRHPR glyoxylate and hydroxypyruvate reductase 54363 HAO1 hydroxyacid oxidase 1 51179 HAO2 hydroxyacid oxidase 2 112817 HOGA1 4-hydroxy-2-oxoglutarate aldolase 1 81888 HYI hydroxypyruvate isomerase (putative) 51601 LIPT1 lipoyltransferase 1 4522 MTHFD1 methylenetetrahydrofolate dehydrogenase, cyclohydrolase and formyltetrahydrofolate synthetase 1 25902 MTHFD1L methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 1 like 10797 MTHFD2 methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 2, methenyltetrahydrofolate cyclohydrolase 441024 MTHFD2L methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 2 like 362657 MTHFR methylenetetrahydrofolate reductase 4548 MTR 5-methyltetrahydrofolate-homocysteine methyltransferase 10606 PAICS phosphoribosylaminoimidazole carboxylase and phosphoribosylaminoimidazolesuccinocarboxamide synthase 55066 PDPR pyruvate dehydrogenase phosphatase regulatory subunit 54858 PGP pyroglutamyl-peptidase I 51268 PIPOX pipecolic acid and sarcosine oxidase 80347 PPAT Coenzyme A synthase 5723 PSPH phosphoserine phosphatase 1757 SARDH sarcosine dehydrogenase 51119 SDS SBDS, ribosome maturation factor 113675 SDSL serine dehydratase like 6470 SHMT1 serine hydroxymethyltransferase 1 6472 SHMT2 serine hydroxymethyltransferase 2 63826 SRR serine racemase

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 4.09e-01 5.84e-06 GO alanine-glyoxylate transaminase activity molecular_function 3.17e-01 3.09e-11 GO methenyltetrahydrofolate cyclohydrolase activity molecular_function 2.86e-01 5.43e-08 Reactome Glycine degradation Metabolism 2.57e-01 5.47e-26 Reactome Metabolism of folate and pterines Metabolism 1.71e-01 3.66e-22 Reactome Glyoxylate metabolism and glycine degradation Metabolism 1.60e-01 5.97e-20 GO one-carbon metabolic process biological_process 1.42e-01 5.81e-05 Reactome Threonine catabolism Metabolism 1.30e-01 4.73e-07 GO L-serine biosynthetic process biological_process 1.22e-01 4.11e-15 GO tetrahydrofolate metabolic process biological_process 1.08e-01 8.70e-05 Reactome Choline catabolism Metabolism 1.04e-01 4.88e-03 Reactome Cysteine formation from homocysteine Metabolism 8.50e-02 2.95e-06 Reactome Purine ribonucleoside monophosphate biosynthesis Metabolism 6.30e-02 4.88e-03 Reactome Defective MTR causes methylmalonic aciduria and homocystinuria type cblG Disease 5.48e-02 4.88e-03 Reactome Defective MTRR causes methylmalonic aciduria and homocystinuria type cblE Disease 2.81e-02 2.42e-16 GO tetrahydrofolate interconversion biological_process 1.49e-02 4.38e-13 GO pyridoxal phosphate binding molecular_function 1.46e-02 2.45e-09 GO peroxisomal matrix cellular_component 9.94e-03 7.39e-25 GO folic acid metabolic process biological_process 6.61e-03 3.17e-04 GO nucleoside metabolic process biological_process 5.55e-03 3.82e-06 GO purine ribonucleoside monophosphate biosynthetic process biological_process 4.18e-03 4.86e-06 GO glycine binding molecular_function 3.08e-03 5.59e-28 Reactome Metabolism of amino acids and derivatives 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 amino acid metabolic process 0e+00 0e+00 carboxylic acid catabolic process 0e+00 0e+00 cellular amino acid catabolic process 0e+00 0e+00 dicarboxylic acid metabolic process 0e+00 0e+00 pteridine-containing compound metabolic process 0e+00 0e+00 pteridine-containing compound biosynthetic process 0e+00 0e+00 folic acid-containing compound biosynthetic process 0e+00 0e+00 tetrahydrofolate metabolic process 0e+00 0e+00 folic acid-containing compound metabolic process 0e+00 0e+00 cofactor metabolic process 0e+00 0e+00 cellular modified amino acid metabolic process 0e+00 0e+00 folic acid metabolic process 0e+00 0e+00 vitamin metabolic process 0e+00 0e+00 one-carbon metabolic process 0e+00 0e+00 L-serine metabolic process 0e+00 0e+00 serine family amino acid catabolic process 0e+00 0e+00 serine family amino acid biosynthetic process 0e+00 0e+00 cellular amino acid biosynthetic process 0e+00 0e+00 serine family amino acid metabolic process 0e+00 0e+00 sulfur amino acid metabolic process

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 1.48e-09 3.54e-07 METABOLISM OF AMINO ACIDS AND DERIVATIVES 3.72e-09 1.14e-06 METABOLISM OF AMINO ACIDS AND DERIVATIVES 2.16e-06 3.57e-04 PURINE RIBONUCLEOSIDE MONOPHOSPHATE BIOSYNTHESIS 6.35e-06 1.25e-03 METABOLISM OF VITAMINS AND COFACTORS 2.60e-05 3.65e-03 METABOLISM OF NUCLEOTIDES 3.59e-05 6.20e-03 PURINE RIBONUCLEOSIDE MONOPHOSPHATE BIOSYNTHESIS 5.79e-05 7.71e-03 METABOLISM OF VITAMINS AND COFACTORS 7.38e-05 9.62e-03 PURINE METABOLISM 1.77e-04 2.58e-02 METABOLISM OF NUCLEOTIDES 2.68e-04 3.72e-02 PURINE METABOLISM 1.87e-03 1.75e-01 SULFUR AMINO ACID METABOLISM 5.27e-03 4.77e-01 SULFUR AMINO ACID METABOLISM 5.44e-03 4.40e-01 G1 S SPECIFIC TRANSCRIPTION 7.26e-03 5.63e-01 E2F MEDIATED REGULATION OF DNA REPLICATION 8.59e-03 7.10e-01 G1 S SPECIFIC TRANSCRIPTION 8.60e-03 7.10e-01 E2F MEDIATED REGULATION OF DNA REPLICATION 1.29e-02 9.02e-01 TETRAHYDROBIOPTERIN BH4 SYNTHESIS RECYCLING SALVAGE AND REGULATION 2.07e-02 1.00e+00 G1 S TRANSITION 2.47e-02 1.00e+00 PYRIMIDINE CATABOLISM 2.50e-02 1.00e+00 G1 S TRANSITION

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 2.98e-09 8.75e-05 abnormal circulating amino acid level 1.41e-04 2.85e-01 abnormal amino acid level 1.47e-04 2.92e-01 urolithiasis 1.50e-04 2.95e-01 craniorachischisis 2.44e-04 3.96e-01 abnormal circulating homocysteine level 6.74e-04 7.21e-01 nephrocalcinosis 1.40e-03 1.00e+00 wavy neural tube 1.88e-03 1.00e+00 retinal gliosis 2.50e-03 1.00e+00 kidney failure 3.74e-03 1.00e+00 decreased creatine level 4.53e-03 1.00e+00 pale liver 5.54e-03 1.00e+00 exencephaly 5.63e-03 1.00e+00 short estrus 5.63e-03 1.00e+00 retinal ischemia 7.47e-03 1.00e+00 nephrolithiasis 7.48e-03 1.00e+00 increased hepatic hemangioma incidence 7.50e-03 1.00e+00 short estrous cycle 7.50e-03 1.00e+00 abnormal placenta junctional zone morphology 7.50e-03 1.00e+00 abnormal mandibular prominence morphology 7.52e-03 1.00e+00 thin hypodermis

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

²FDR corrected p-value (Benjamini-Hochberg)