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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod48

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod48 Module size 90 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 84680 ACCS 1-aminocyclopropane-1-carboxylate synthase homolog (inactive) 390110 ACCSL 1-aminocyclopropane-1-carboxylate synthase homolog (inactive) like 95 ACY1 aminoacylase 1 113451 ADC antizyme inhibitor 2 56985 ADPRM ADP-ribose/CDP-alcohol diphosphatase, manganese dependent 159 ADSS adenylosuccinate synthase 122622 ADSSL1 adenylosuccinate synthase like 1 191 AHCY adenosylhomocysteinase 10768 AHCYL1 adenosylhomocysteinase like 1 23382 AHCYL2 adenosylhomocysteinase like 2 262 AMD1 adenosylmethionine decarboxylase 1 290 ANPEP alanyl aminopeptidase, membrane 51582 AZIN1 antizyme inhibitor 1 84909 C9orf3 chromosome 9 open reading frame 3 790 CAD carbamoyl-phosphate synthetase 2, aspartate transcarbamylase, and dihydroorotase 56267 CCBL2 kynurenine aminotransferase 3 27440 CECR5 haloacid dehalogenase like hydrolase domain containing 5 8192 CLPP caseinolytic mitochondrial matrix peptidase proteolytic subunit 1589 CPS1 cytochrome P450 family 21 subfamily A member 2 23549 DNPEP aspartyl aminopeptidase 2028 ENPEP glutamyl aminopeptidase 51752 ERAP1 endoplasmic reticulum aminopeptidase 1 64167 ERAP2 endoplasmic reticulum aminopeptidase 2 2618 GART phosphoribosylglycinamide formyltransferase, phosphoribosylglycinamide synthetase, phosphoribosylaminoimidazole synthetase 2673 GFPT1 glutamine--fructose-6-phosphate transaminase 1 9945 GFPT2 glutamine-fructose-6-phosphate transaminase 2 1798 GPT dolichyl-phosphate N-acetylglucosaminephosphotransferase 1 51020 HDDC2 HD domain containing 2 84064 HDHD2 haloacid dehalogenase like hydrolase domain containing 2 10247 HRSP12 reactive intermediate imine deaminase A homolog 200205 IBA57 IBA57, iron-sulfur cluster assembly 196294 IMMP1L inner mitochondrial membrane peptidase subunit 1 51056 LAP3 leucine aminopeptidase 3 84316 LSMD1 N(alpha)-acetyltransferase 38, NatC auxiliary subunit 4048 LTA4H leukotriene A4 hydrolase 4143 MAT1A methionine adenosyltransferase 1A 4144 MAT2A methionine adenosyltransferase 2A 4285 MIPEP mitochondrial intermediate peptidase 84245 MRI1 methylthioribose-1-phosphate isomerase 1 10588 MTHFS methenyltetrahydrofolate synthetase 64779 MTHFSD methenyltetrahydrofolate synthetase domain containing 8260 NAA10 N(alpha)-acetyltransferase 10, NatA catalytic subunit 84779 NAA11 N(alpha)-acetyltransferase 11, NatA catalytic subunit 80155 NAA15 N(alpha)-acetyltransferase 15, NatA auxiliary subunit 79612 NAA16 N(alpha)-acetyltransferase 16, NatA auxiliary subunit 51126 NAA20 N(alpha)-acetyltransferase 20, NatB catalytic subunit 80018 NAA25 N(alpha)-acetyltransferase 25, NatB auxiliary subunit 122830 NAA30 N(alpha)-acetyltransferase 30, NatC catalytic subunit 60560 NAA35 N(alpha)-acetyltransferase 35, NatC auxiliary subunit 9027 NAT8 N-acetyltransferase 8 (putative) 9054 NFS1 NFS1, cysteine desulfurase 27247 NFU1 NFU1 iron-sulfur cluster scaffold 57486 NLN neurolysin 122945 NOXRED1 NADP dependent oxidoreductase domain containing 1 79716 NPEPL1 aminopeptidase like 1 11164 NUDT5 nudix hydrolase 5 53343 NUDT9 nudix hydrolase 9 54995 OXSM 3-oxoacyl-ACP synthase, mitochondrial 5184 PEPD peptidase D 5198 PFAS phosphoribosylformylglycinamidine synthase 26227 PHGDH phosphoglycerate dehydrogenase 148811 PM20D1 peptidase M20 domain containing 1 135293 PM20D2 peptidase M20 domain containing 2 5372 PMM1 phosphomannomutase 1 5373 PMM2 phosphomannomutase 2 5498 PPOX protoporphyrinogen oxidase 29968 PSAT1 phosphoserine aminotransferase 1 5831 PYCR1 pyrroline-5-carboxylate reductase 1 29920 PYCR2 pyrroline-5-carboxylate reductase 2 65263 PYCRL pyrroline-5-carboxylate reductase 3 64285 RHBDF1 rhomboid 5 homolog 1 79651 RHBDF2 rhomboid 5 homolog 2 6051 RNPEP arginyl aminopeptidase 57140 RNPEPL1 arginyl aminopeptidase like 1 51540 SCLY selenocysteine lyase 6611 SMS spermine synthase 79896 THNSL1 threonine synthase like 1 55258 THNSL2 threonine synthase like 2 7064 THOP1 thimet oligopeptidase 1 29087 THYN1 thymocyte nuclear protein 1 155006 TMEM213 transmembrane protein 213 29953 TRHDE thyrotropin releasing hormone degrading enzyme 100131187 TSTD1 thiosulfate sulfurtransferase like domain containing 1 6675 UAP1 UDP-N-acetylglucosamine pyrophosphorylase 1 91373 UAP1L1 UDP-N-acetylglucosamine pyrophosphorylase 1 like 1 7390 UROS uroporphyrinogen III synthase 7511 XPNPEP1 X-prolyl aminopeptidase 1 7512 XPNPEP2 X-prolyl aminopeptidase 2 63929 XPNPEP3 X-prolyl aminopeptidase 3 374887 YJEFN3 YjeF N-terminal domain containing 3

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 5.98e-01 6.90e-18 GO peptide alpha-N-acetyltransferase activity molecular_function 4.31e-01 2.14e-05 GO adenylosuccinate synthase activity molecular_function 2.97e-01 6.29e-27 GO aminopeptidase activity molecular_function 2.49e-01 8.02e-22 GO metalloaminopeptidase activity molecular_function 2.16e-01 3.36e-06 Reactome Phosphate bond hydrolysis by NUDT proteins Metabolism 1.80e-01 1.11e-12 GO glutamine metabolic process biological_process 1.62e-01 1.40e-07 GO UDP-N-acetylglucosamine biosynthetic process biological_process 1.55e-01 2.12e-04 Reactome Synthesis of GDP-mannose Metabolism of proteins 1.27e-01 5.36e-06 Reactome Metabolism of ingested SeMet, Sec, MeSec into H2Se Metabolism 1.20e-01 1.58e-08 GO one-carbon metabolic process biological_process 9.91e-02 4.22e-07 GO peptide metabolic process biological_process 8.24e-02 5.59e-09 Reactome Nucleobase biosynthesis Metabolism 6.38e-02 1.02e-08 Reactome Amino acid synthesis and interconversion (transamination) Metabolism 5.83e-02 5.89e-04 GO regulation of epidermal growth factor receptor signaling pathway biological_process 2.92e-02 1.05e-04 GO heme biosynthetic process biological_process 1.58e-02 3.17e-04 GO 'de novo' pyrimidine nucleobase biosynthetic process biological_process 1.08e-02 1.42e-05 GO cellular amino acid metabolic process biological_process 8.87e-03 7.06e-06 Reactome Sulfur amino acid metabolism Metabolism 7.88e-03 3.41e-05 Reactome Methylation Metabolism 4.82e-03 4.43e-04 GO glycine metabolic process biological_process 3.03e-03 1.37e-03 GO regulation of protein secretion biological_process 3.03e-03 1.37e-03 GO negative regulation of protein secretion 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 sulfur amino acid metabolic process 0.00e+00 0.00e+00 cellular amino acid metabolic process 0.00e+00 0.00e+00 N-terminal protein amino acid modification 0.00e+00 0.00e+00 N-terminal protein amino acid acetylation 0.00e+00 0.00e+00 glutamine metabolic process 0.00e+00 0.00e+00 cellular amino acid biosynthetic process 0.00e+00 0.00e+00 peptide catabolic process 0.00e+00 0.00e+00 peptide alpha-N-acetyltransferase activity 0.00e+00 0.00e+00 aminopeptidase activity 0.00e+00 0.00e+00 metalloaminopeptidase activity 2.42e-18 1.73e-15 metallopeptidase activity 2.64e-17 1.87e-14 metalloexopeptidase activity 1.90e-16 1.33e-13 exopeptidase activity 1.10e-15 7.69e-13 peptidase activity 2.43e-11 2.14e-08 S-adenosylmethionine metabolic process 4.69e-11 4.02e-08 cellular amide metabolic process 9.35e-11 5.72e-08 N-acetyltransferase activity 1.59e-10 1.29e-07 N-terminal peptidyl-methionine acetylation 2.94e-10 2.33e-07 sulfur compound metabolic process 2.95e-10 2.34e-07 serine family amino acid metabolic 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 METABOLISM OF AMINO ACIDS AND DERIVATIVES 0.00e+00 0.00e+00 METABOLISM OF AMINO ACIDS AND DERIVATIVES 7.76e-08 1.53e-05 PURINE RIBONUCLEOSIDE MONOPHOSPHATE BIOSYNTHESIS 1.65e-07 4.17e-05 PURINE RIBONUCLEOSIDE MONOPHOSPHATE BIOSYNTHESIS 6.82e-07 1.58e-04 AMINO ACID SYNTHESIS AND INTERCONVERSION TRANSAMINATION 2.48e-06 4.05e-04 METABOLISM OF POLYAMINES 2.55e-06 4.17e-04 AMINO ACID SYNTHESIS AND INTERCONVERSION TRANSAMINATION 3.03e-06 6.29e-04 METABOLISM OF POLYAMINES 1.17e-05 1.72e-03 PURINE METABOLISM 1.53e-05 2.22e-03 SULFUR AMINO ACID METABOLISM 1.54e-05 2.85e-03 PURINE METABOLISM 2.36e-05 4.20e-03 SULFUR AMINO ACID METABOLISM 3.75e-05 6.46e-03 METABOLISM OF NUCLEOTIDES 5.82e-05 7.72e-03 METABOLISM OF NUCLEOTIDES 1.33e-04 1.65e-02 SYNTHESIS OF SUBSTRATES IN N GLYCAN BIOSYTHESIS 2.20e-04 3.12e-02 SYNTHESIS OF SUBSTRATES IN N GLYCAN BIOSYTHESIS 5.37e-04 5.79e-02 BIOSYNTHESIS OF THE N GLYCAN PRECURSOR DOLICHOL LIPID LINKED OLIGOSACCHARIDE LLO AND TRANSFER TO A NASCENT PROTEIN 8.74e-04 1.05e-01 BIOSYNTHESIS OF THE N GLYCAN PRECURSOR DOLICHOL LIPID LINKED OLIGOSACCHARIDE LLO AND TRANSFER TO A NASCENT PROTEIN 3.77e-03 3.62e-01 METABOLISM OF PORPHYRINS 4.27e-03 3.59e-01 PHASE II CONJUGATION

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 1.23e-03 1e+00 decreased circulating HDL cholesterol level 1.39e-03 1e+00 decreased body length 1.59e-03 1e+00 forebrain hypoplasia 2.72e-03 1e+00 decreased bone mineral content 2.76e-03 1e+00 abnormal dermal layer morphology 2.87e-03 1e+00 abnormal cellular respiration 3.46e-03 1e+00 decreased total body fat amount 3.96e-03 1e+00 increased NK cell number 4.36e-03 1e+00 decreased lean body mass 5.61e-03 1e+00 abnormal exocrine pancreas physiology 7.18e-03 1e+00 decreased mean corpuscular volume 7.48e-03 1e+00 myocardial hypertrophy 7.48e-03 1e+00 abnormal antigen presentation via MHC class I 9.34e-03 1e+00 abnormal interfrontal bone morphology 9.34e-03 1e+00 abnormal dermis papillary layer morphology 9.73e-03 1e+00 thick epidermis 1.12e-02 1e+00 pancreatic acinar hypoplasia 1.12e-02 1e+00 porphyria 1.30e-02 1e+00 abnormal transitional stage B cell morphology 1.30e-02 1e+00 decreased collagen level

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

²FDR corrected p-value (Benjamini-Hochberg)