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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod201

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod201 Module size 84 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 132949 AASDH aminoadipate-semialdehyde dehydrogenase 641372 ACOT6 acyl-CoA thioesterase 6 55 ACPP acid phosphatase, prostate 93650 ACPT acid phosphatase 4 54936 ADPRHL2 ADP-ribosylhydrolase like 2 309 ANXA6 annexin A6 8623 ASMTL acetylserotonin O-methyltransferase like 683 BST1 bone marrow stromal cell antigen 1 297767 BTD recombination signal binding protein for immunoglobulin kappa J region-like 2 84520 C14orf142 GON7, KEOPS complex subunit 79078 C1orf50 chromosome 1 open reading frame 50 813 CALU calumenin 952 CD38 CD38 molecule 25927 CNRIP1 cannabinoid receptor interacting protein 1 80347 COASY Coenzyme A synthase 118881 COMTD1 catechol-O-methyltransferase domain containing 1 25927 CRIP1 cannabinoid receptor interacting protein 1 79877 DCAKD dephospho-CoA kinase domain containing 1635 DCTD dCMP deaminase 112487 DTD2 D-tyrosyl-tRNA deacylase 2 (putative) 285605 DTWD2 DTW domain containing 2 1841 DTYMK deoxythymidylate kinase 84332 DYDC2 DPY30 domain containing 2 80820 EEPD1 endonuclease/exonuclease/phosphatase family domain containing 1 55531 ELMOD1 ELMO domain containing 1 5167 ENPP1 ectonucleotide pyrophosphatase/phosphodiesterase 1 5169 ENPP3 ectonucleotide pyrophosphatase/phosphodiesterase 3 57089 ENTPD7 ectonucleoside triphosphate diphosphohydrolase 7 80308 FLAD1 flavin adenine dinucleotide synthetase 1 2643 GCH1 GTP cyclohydrolase 1 9615 GDA guanine deaminase 2987 GUK1 guanylate kinase 1 374659 HDDC3 HD domain containing 3 727833 IMPDH1 inosine monophosphate dehydrogenase 1 pseudogene 11 3615 IMPDH2 inosine monophosphate dehydrogenase 2 65987 KCTD14 potassium channel tetramerization domain containing 14 26128 KIAA1279 KIF1 binding protein 220074 LRTOMT leucine rich transmembrane and O-methyltransferase domain containing 57149 LYRM1 LYR motif containing 1 4507 MTAP methylthioadenosine phosphorylase 65220 NADK NAD kinase 55191 NADSYN1 NAD synthetase 1 10135 NAMPT nicotinamide phosphoribosyltransferase NA NAMPTL 93100 NAPRT1 nicotinate phosphoribosyltransferase 60491 NIF3L1 NGG1 interacting factor 3 like 1 64802 NMNAT1 nicotinamide nucleotide adenylyltransferase 1 23057 NMNAT2 nicotinamide nucleotide adenylyltransferase 2 349565 NMNAT3 nicotinamide nucleotide adenylyltransferase 3 4837 NNMT nicotinamide N-methyltransferase 23530 NNT nicotinamide nucleotide transhydrogenase 51559 NT5DC3 5'-nucleotidase domain containing 3 4521 NUDT1 nudix hydrolase 1 83594 NUDT12 nudix hydrolase 12 256281 NUDT14 nudix hydrolase 14 55270 NUDT15 nudix hydrolase 15 79873 NUDT18 nudix hydrolase 18 114299 PALM2 paralemmin 2 79646 PANK3 pantothenate kinase 3 55229 PANK4 pantothenate kinase 4 5099 PCDH7 protocadherin 7 57026 PDXP pyridoxal phosphatase 56952 PRTFDC1 phosphoribosyl transferase domain containing 1 58497 PRUNE prune exopolyphosphatase 1 23475 QPRT quinolinate phosphoribosyltransferase 115286 SLC25A26 solute carrier family 25 member 26 54974 THG1L tRNA-histidine guanylyltransferase 1 like 643853 TMPPE transmembrane protein with metallophosphoesterase domain 112858 TP53RK TP53 regulating kinase 293894 TPD52 tumor protein D52-like 3 7165 TPD52L2 TPD52 like 2 89882 TPD52L3 TPD52 like 3 289159 TPMT methyltransferase like 13 51002 TPRKB TP53RK binding protein 83707 TRPT1 tRNA phosphotransferase 1 83549 UCK1 uridine-cytidine kinase 1 54963 UCKL1 uridine-cytidine kinase 1 like 1 139596 UPRT uracil phosphoribosyltransferase homolog 8876 VNN1 vanin 1 8875 VNN2 vanin 2 55350 VNN3 vanin 3 55093 WDYHV1 WDYHV motif containing 1 7498 XDH xanthine dehydrogenase 57002 YAE1D1 YAE1, ABCE1 maturation factor

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 2.58e-01 9.29e-09 GO nucleoside-triphosphate diphosphatase activity molecular_function 2.12e-01 2.70e-07 GO nicotinate-nucleotide adenylyltransferase activity molecular_function 2.06e-01 6.73e-07 GO pantothenate metabolic process biological_process 1.97e-01 7.11e-16 GO NAD metabolic process biological_process 1.45e-01 2.86e-13 Reactome Vitamin B5 (pantothenate) metabolism Metabolism 1.34e-01 2.12e-19 Reactome Nicotinate metabolism Metabolism 1.28e-01 2.34e-06 Reactome Phosphate bond hydrolysis by NUDT proteins Metabolism 1.21e-01 8.25e-03 Reactome Synthesis of dolichyl-phosphate-glucose Metabolism of proteins 1.11e-01 2.50e-04 GO EKC/KEOPS complex cellular_component 7.68e-02 8.65e-08 GO coenzyme A biosynthetic process biological_process 4.89e-02 1.74e-16 Reactome Metabolism of nucleotides Metabolism 2.66e-02 4.64e-04 GO O-methyltransferase activity molecular_function 2.38e-02 1.86e-07 GO purine nucleotide catabolic process biological_process 1.95e-02 1.24e-02 Reactome Enzymatic degradation of dopamine by COMT Neuronal System 1.74e-02 4.18e-27 Reactome Metabolism of water-soluble vitamins and cofactors Metabolism 1.04e-02 3.49e-04 Reactome Vitamin B2 (riboflavin) metabolism Metabolism 2.81e-04 3.53e-07 GO nucleobase-containing small molecule catabolic process 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 nucleobase-containing small molecule metabolic process 0.00e+00 0.00e+00 nucleotide biosynthetic process 0.00e+00 0.00e+00 nucleoside metabolic process 0.00e+00 0.00e+00 nucleotide metabolic process 0.00e+00 0.00e+00 cofactor metabolic process 0.00e+00 0.00e+00 NAD biosynthetic process 0.00e+00 0.00e+00 NAD metabolic process 0.00e+00 0.00e+00 nucleoside phosphate catabolic process 0.00e+00 0.00e+00 organophosphate catabolic process 3.07e-17 2.91e-14 coenzyme biosynthetic process 9.90e-13 9.17e-10 purine nucleotide metabolic process 1.71e-11 1.52e-08 ribonucleotide metabolic process 6.24e-11 5.29e-08 glycosyl compound metabolic process 2.29e-09 1.15e-06 nucleoside-triphosphate diphosphatase activity 2.53e-09 1.79e-06 ribose phosphate biosynthetic process 7.42e-09 4.90e-06 nucleotide catabolic process 1.06e-08 4.81e-06 NADH pyrophosphatase activity 2.88e-08 1.76e-05 purine nucleoside metabolic process 3.03e-08 1.85e-05 purine-containing compound biosynthetic process 3.42e-08 1.42e-05 hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds

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 VITAMINS AND COFACTORS 0.00e+00 0.00e+00 METABOLISM OF VITAMINS AND COFACTORS 1.67e-09 5.37e-07 METABOLISM OF NUCLEOTIDES 1.03e-08 2.26e-06 METABOLISM OF NUCLEOTIDES 1.82e-05 3.31e-03 PURINE METABOLISM 3.54e-05 4.86e-03 PURINE METABOLISM 6.11e-05 8.08e-03 VITAMIN B5 PANTOTHENATE METABOLISM 8.21e-05 1.30e-02 VITAMIN B5 PANTOTHENATE METABOLISM 1.83e-04 2.65e-02 PURINE CATABOLISM 6.03e-04 6.40e-02 PURINE CATABOLISM 1.62e-03 1.78e-01 PURINE RIBONUCLEOSIDE MONOPHOSPHATE BIOSYNTHESIS 2.86e-03 2.54e-01 PURINE RIBONUCLEOSIDE MONOPHOSPHATE BIOSYNTHESIS 3.77e-03 3.62e-01 PYRIMIDINE METABOLISM 5.19e-03 4.71e-01 SYNTHESIS AND INTERCONVERSION OF NUCLEOTIDE DI AND TRIPHOSPHATES 7.89e-03 6.04e-01 SYNTHESIS AND INTERCONVERSION OF NUCLEOTIDE DI AND TRIPHOSPHATES 8.74e-03 6.58e-01 PYRIMIDINE METABOLISM 1.87e-02 1.00e+00 PHASE II CONJUGATION 2.58e-02 1.00e+00 ABACAVIR TRANSPORT AND METABOLISM 3.16e-02 1.00e+00 ABACAVIR TRANSPORT AND METABOLISM 3.65e-02 1.00e+00 TETRAHYDROBIOPTERIN BH4 SYNTHESIS RECYCLING SALVAGE AND REGULATION

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 6.17e-04 6.83e-01 hunched posture 1.14e-03 9.71e-01 absent startle reflex 3.17e-03 1.00e+00 decreased bone mass 3.76e-03 1.00e+00 calcified retina 3.77e-03 1.00e+00 organ of Corti degeneration 3.85e-03 1.00e+00 abnormal behavior 5.61e-03 1.00e+00 cochlear ganglion degeneration 5.63e-03 1.00e+00 calcified skin 6.58e-03 1.00e+00 abnormal kidney development 7.48e-03 1.00e+00 absent optic tract 7.49e-03 1.00e+00 decreased corticospinal tract size 7.49e-03 1.00e+00 abnormal skin adnexa morphology 7.51e-03 1.00e+00 calcified aorta 7.52e-03 1.00e+00 calcified intervertebral disk 7.52e-03 1.00e+00 calcified joint 9.33e-03 1.00e+00 decreased circulating glucose level 9.37e-03 1.00e+00 abnormal ligament morphology 9.38e-03 1.00e+00 abnormal urethra morphology 9.38e-03 1.00e+00 exostosis 1.12e-02 1.00e+00 calcinosis

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

²FDR corrected p-value (Benjamini-Hochberg)