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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod139

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod139 Module size 96 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 28971 AAMDC adipogenesis associated Mth938 domain containing 10157 AASS aminoadipate-semialdehyde synthase 18 ABAT 4-aminobutyrate aminotransferase 100526760 ABHD14A-ACY1 ABHD14A-ACY1 readthrough 26 ABP1 amine oxidase, copper containing 1 130013 ACMSD aminocarboxymuconate semialdehyde decarboxylase 91703 ACY3 aminoacylase 3 97 ACYP1 acylphosphatase 1 98 ACYP2 acylphosphatase 2 79814 AGMAT agmatinase 123688 AGPHD1 hydroxylysine kinase 85007 AGXT2L2 5-phosphohydroxy-L-lysine phospho-lyase 57016 AKR1B10 aldo-keto reductase family 1 member B10 5832 ALDH18A1 aldehyde dehydrogenase 18 family member A1 219 ALDH1B1 aldehyde dehydrogenase 1 family member B1 224 ALDH3A2 aldehyde dehydrogenase 3 family member A2 8659 ALDH4A1 aldehyde dehydrogenase 4 family member A1 501 ALDH7A1 aldehyde dehydrogenase 7 family member A1 223 ALDH9A1 aldehyde dehydrogenase 9 family member A1 144193 AMDHD1 amidohydrolase domain containing 1 314 AOC2 amine oxidase, copper containing 2 8639 AOC3 amine oxidase, copper containing 3 383 ARG1 arginase 1 384 ARG2 arginase 2 435 ASL argininosuccinate lyase 438 ASMT acetylserotonin O-methyltransferase 440 ASNS asparagine synthetase (glutamine-hydrolyzing) 443 ASPA aspartoacylase 445 ASS1 argininosuccinate synthase 1 8424 BBOX1 gamma-butyrobetaine hydroxylase 1 635 BHMT betaine--homocysteine S-methyltransferase 57571 CARNS1 carnosine synthase 1 1036 CDO1 cysteine dioxygenase type 1 84735 CNDP1 carnosine dipeptidase 1 55748 CNDP2 carnosine dipeptidase 2 51380 CSAD cysteine sulfinic acid decarboxylase 1621 DBH dopamine beta-hydroxylase 1644 DDC dopa decarboxylase 2346 FOLH1 folate hydrolase 1 89833 FTCD formimidoyltransferase cyclodeaminase 2571 GAD1 glutamate decarboxylase 1 2572 GAD2 glutamate decarboxylase 2 339896 GADL1 glutamate decarboxylase like 1 2729 GCLC glutamate-cysteine ligase catalytic subunit 2730 GCLM glutamate-cysteine ligase modifier subunit 79017 GGCT gamma-glutamylcyclotransferase 2739 GLO1 glyoxalase I 27165 GLS glutaminase 2 2746 GLUD1 glutamate dehydrogenase 1 2747 GLUD2 glutamate dehydrogenase 2 2752 GLUL glutamate-ammonia ligase 132158 GLYCTK glycerate kinase 84656 GLYR1 glyoxylate reductase 1 homolog 127845 GOT1 golgi transport 1A 2806 GOT2 glutamic-oxaloacetic transaminase 2 23498 HAAO 3-hydroxyanthranilate 3,4-dioxygenase 3034 HAL histidine ammonia-lyase 3067 HDC histidine decarboxylase 51409 HEMK1 HemK methyltransferase family member 1 3081 HGD homogentisate 1,2-dioxygenase 11112 HIBADH 3-hydroxyisobutyrate dehydrogenase 3176 HNMT histamine N-methyltransferase 3242 HPD 4-hydroxyphenylpyruvate dioxygenase 84842 HPDL 4-hydroxyphenylpyruvate dioxygenase like 3620 IDO1 indoleamine 2,3-dioxygenase 1 169355 IDO2 indoleamine 2,3-dioxygenase 2 259307 IL4I1 interleukin 4 induced 1 100526825 INMT-FAM188B INMT-MINDY4 readthrough (NMD candidate) 8942 KYNU kynureninase 79944 L2HGDH L-2-hydroxyglutarate dehydrogenase 4128 MAOA monoamine oxidase A 4129 MAOB monoamine oxidase B 55798 METTL2B methyltransferase like 2B 131965 METTL6 methyltransferase like 6 326625 MMAB metabolism of cobalamin associated B 162417 NAGS N-acetylglutamate synthase 339983 NAT8L N-acetyltransferase 8 like 80896 NPL N-acetylneuraminate pyruvate lyase 4942 OAT ornithine aminotransferase 5009 OTC ornithine carbamoyltransferase 683381 PAH SIN3 transcription regulator family member B 196743 PAOX polyamine oxidase 5409 PNMT phenylethanolamine N-methyltransferase 284716 RIMKLA ribosomal modification protein rimK like family member A 57494 RIMKLB ribosomal modification protein rimK like family member B 54407 SAT2 solute carrier family 38 member 2 10166 SLC25A15 solute carrier family 25 member 15 83884 SLC25A2 solute carrier family 25 member 2 54498 SMOX spermine oxidase 79969 TAT alpha tubulin acetyltransferase 1 7166 TPH1 tryptophan hydroxylase 1 6999 TPH2 tryptophan 2,3-dioxygenase 7299 TYR tyrosinase 51733 UPB1 beta-ureidopropionase 1 131669 UROC1 urocanate hydratase 1 253769 WDR27 WD repeat domain 27

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 5.97e-01 2.72e-05 Reactome GABA synthesis Neuronal System 5.30e-01 7.05e-10 Reactome Amine Oxidase reactions Metabolism 4.45e-01 3.51e-09 Reactome Serotonin and melatonin biosynthesis Metabolism 4.34e-01 1.84e-17 Reactome Urea cycle Metabolism 3.67e-01 5.66e-29 GO cellular amino acid biosynthetic process biological_process 3.29e-01 5.54e-07 Reactome Catecholamine biosynthesis Metabolism 2.61e-01 1.05e-08 GO primary amine oxidase activity molecular_function 2.32e-01 6.81e-16 GO histidine catabolic process biological_process 2.28e-01 6.81e-16 Reactome Histidine catabolism Metabolism 1.87e-01 1.27e-34 Reactome Histidine, lysine, phenylalanine, tyrosine, proline and tryptophan catabolism Metabolism 1.55e-01 1.62e-04 Reactome Carnitine synthesis Metabolism 1.53e-01 6.81e-09 GO aldehyde dehydrogenase (NAD) activity molecular_function 1.48e-01 2.01e-16 GO urea cycle biological_process 1.33e-01 1.73e-14 GO glutamate metabolic process biological_process 9.79e-02 4.37e-10 GO tryptophan catabolic process biological_process 9.49e-02 1.05e-02 Reactome Agmatine biosynthesis Metabolism 9.45e-02 4.86e-07 Reactome Glutathione synthesis and recycling Metabolism 6.67e-02 2.72e-05 Reactome PAOs oxidise polyamines to amines Metabolism 5.95e-02 1.05e-02 Reactome Degradation of GABA Neuronal System 4.26e-02 3.10e-26 Reactome Amino acid synthesis and interconversion (transamination) Metabolism 2.93e-02 1.43e-77 Reactome Metabolism of amino acids and derivatives Metabolism 2.88e-02 1.56e-02 Reactome Interconversion of 2-oxoglutarate and 2-hydroxyglutarate Metabolism 2.57e-02 6.78e-07 Reactome Degradation of cysteine and homocysteine Metabolism 2.41e-02 1.14e-05 GO cellular aldehyde metabolic process biological_process 2.39e-02 4.02e-04 Reactome Choline catabolism Metabolism 2.00e-02 4.74e-09 Reactome Sulfur amino acid metabolism Metabolism 1.04e-03 1.56e-02 Reactome Melanin biosynthesis 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 0.00e+00 0.00e+00 urea metabolic process 0.00e+00 0.00e+00 arginine metabolic process 0.00e+00 0.00e+00 urea cycle 0.00e+00 0.00e+00 dicarboxylic acid catabolic process 0.00e+00 0.00e+00 phenol-containing compound metabolic process 0.00e+00 0.00e+00 neurotransmitter metabolic process 0.00e+00 0.00e+00 amine biosynthetic process 0.00e+00 0.00e+00 histidine metabolic process 0.00e+00 0.00e+00 histidine catabolic process 0.00e+00 0.00e+00 glutamate catabolic process 0.00e+00 0.00e+00 carbon-carbon lyase activity 0.00e+00 0.00e+00 carboxy-lyase activity 9.53e-70 9.41e-67 cellular amino acid metabolic process 3.49e-52 3.44e-49 cellular amino acid catabolic process 5.66e-44 5.58e-41 carboxylic acid catabolic process 2.47e-33 2.43e-30 dicarboxylic acid metabolic process 3.23e-33 3.17e-30 cellular amino acid biosynthetic process 3.67e-33 3.60e-30 glutamate metabolic process 4.27e-33 4.19e-30 amine metabolic process 1.97e-30 1.93e-27 cellular biogenic amine 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 1.58e-58 6.35e-56 METABOLISM OF AMINO ACIDS AND DERIVATIVES 5.84e-12 1.72e-09 AMINO ACID SYNTHESIS AND INTERCONVERSION TRANSAMINATION 1.04e-10 3.77e-08 AMINO ACID SYNTHESIS AND INTERCONVERSION TRANSAMINATION 4.12e-09 9.38e-07 SULFUR AMINO ACID METABOLISM 9.88e-09 2.91e-06 SULFUR AMINO ACID METABOLISM 4.12e-07 7.56e-05 NEUROTRANSMITTER RELEASE CYCLE 4.99e-07 9.12e-05 TRYPTOPHAN CATABOLISM 7.97e-07 1.82e-04 AMINE DERIVED HORMONES 1.48e-06 2.51e-04 GLUTATHIONE CONJUGATION 2.56e-06 5.37e-04 TRYPTOPHAN CATABOLISM 2.77e-06 4.49e-04 AMINE DERIVED HORMONES 3.33e-06 5.35e-04 BIOLOGICAL OXIDATIONS 9.26e-06 1.38e-03 METABOLISM OF POLYAMINES 1.13e-05 2.14e-03 NEUROTRANSMITTER RELEASE CYCLE 2.93e-05 4.07e-03 GABA SYNTHESIS RELEASE REUPTAKE AND DEGRADATION 3.03e-05 5.31e-03 GLUTATHIONE CONJUGATION 5.92e-05 9.72e-03 METABOLISM OF POLYAMINES 1.13e-04 1.73e-02 BIOLOGICAL OXIDATIONS 1.35e-04 1.67e-02 TRANSMISSION ACROSS CHEMICAL SYNAPSES

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 0.00e+00 0.00e+00 abnormal circulating amino acid level 3.88e-11 2.38e-06 increased circulating ammonia level 1.75e-06 1.33e-02 abnormal amino acid level 1.93e-06 1.43e-02 abnormal neurotransmitter level 1.63e-05 6.60e-02 abnormal serotonin level 5.30e-05 1.49e-01 abnormal urine homeostasis 1.37e-04 2.80e-01 oroticaciduria 7.40e-04 7.60e-01 decreased serotonin level 7.66e-04 7.70e-01 increased dopamine level 7.97e-04 7.90e-01 abnormal noradrenaline level 1.02e-03 9.10e-01 abnormal protein level 1.29e-03 1.00e+00 abnormal nervous system electrophysiology 1.69e-03 1.00e+00 delayed hair appearance 2.69e-03 1.00e+00 increased aggression towards males 3.62e-03 1.00e+00 abnormal retinal ganglion layer morphology 4.44e-03 1.00e+00 jerky movement 4.53e-03 1.00e+00 hypopigmentation 4.95e-03 1.00e+00 abnormal enzyme/coenzyme activity 4.99e-03 1.00e+00 abnormal hair follicle morphology 5.08e-03 1.00e+00 abnormal coat/hair pigmentation

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

²FDR corrected p-value (Benjamini-Hochberg)