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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod205

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod205 Module size 72 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 178 AGL amylo-alpha-1, 6-glucosidase, 4-alpha-glucanotransferase 10327 AKR1A1 aldo-keto reductase family 1 member A1 231 AKR1B1 aldo-keto reductase family 1 member B 441282 AKR1B15 aldo-keto reductase family 1 member B15 1645 AKR1C1 aldo-keto reductase family 1 member C1 1646 AKR1C2 aldo-keto reductase family 1 member C2 8644 AKR1C3 aldo-keto reductase family 1 member C3 1109 AKR1C4 aldo-keto reductase family 1 member C4 340811 AKR1CL1 aldo-keto reductase family 1 member C8, pseudogene 83592 AKR1E2 aldo-keto reductase family 1 member E2 8574 AKR7A2 aldo-keto reductase family 7 member A2 22977 AKR7A3 aldo-keto reductase family 7 member A3 307526 AMMECR1 AMMECR1 like 83607 AMMECR1L AMMECR1 like 276 AMY1A amylase, alpha 1A (salivary) 277 AMY1B amylase, alpha 1B (salivary) 278 AMY1C amylase, alpha 1C (salivary) 279 AMY2A amylase, alpha 2A (pancreatic) 280 AMY2B amylase, alpha 2B (pancreatic) 57136 APMAP adipocyte plasma membrane associated protein 128240 APOA1BP NAD(P)HX epimerase 80162 ATHL1 protein-glucosylgalactosylhydroxylysine glucosidase 55739 CARKD NAD(P)HX dehydratase 873 CBR1 carbonyl reductase 1 134147 CMBL carboxymethylenebutenolidase homolog 1429 CRYZ crystallin zeta 9946 CRYZL1 crystallin zeta like 1 26007 DAK triokinase and FMN cyclase 28960 DCPS decapping enzyme, scavenger 2584 GALK1 galactokinase 1 2585 GALK2 galactokinase 2 2592 GALT galactose-1-phosphate uridylyltransferase 2632 GBE1 1,4-alpha-glucan branching enzyme 1 54438 GFOD1 glucose-fructose oxidoreductase domain containing 1 81577 GFOD2 glucose-fructose oxidoreductase domain containing 2 10020 GNE glucosamine (UDP-N-acetyl)-2-epimerase/N-acetylmannosamine kinase 2819 GPD1 glycerol-3-phosphate dehydrogenase 1 23171 GPD1L glycerol-3-phosphate dehydrogenase 1 like 2992 GYG1 glycogenin 1 8908 GYG2 glycogenin 2 2997 GYS1 glycogen synthase 1 2998 GYS2 glycogen synthase 2 8226 HDHD1 pseudouridine 5'-phosphatase 4123 MAN2C1 mannosidase alpha class 2C member 1 51102 MECR mitochondrial trans-2-enoyl-CoA reductase 51072 MEMO1 mediator of cell motility 1 255027 MPV17L MPV17 mitochondrial inner membrane protein like 54187 NANS N-acetylneuraminate synthase 378884 NHLRC1 NHL repeat containing E3 ubiquitin protein ligase 1 22949 PTGR1 prostaglandin reductase 1 145482 PTGR2 prostaglandin reductase 2 5827 PXMP2 peroxisomal membrane protein 2 5834 PYGB glycogen phosphorylase B 5836 PYGL glycogen phosphorylase L 112724 RDH13 retinol dehydrogenase 13 57665 RDH14 retinol dehydrogenase 14 9104 RGN regucalcin 8635 RNASET2 ribonuclease T2 6252 RTN1 reticulon 1 6253 RTN2 reticulon 2 10313 RTN3 reticulon 3 57142 RTN4 reticulon 4 84816 RTN4IP1 reticulon 4 interacting protein 1 51091 SEPSECS Sep (O-phosphoserine) tRNA:Sec (selenocysteine) tRNA synthase 55217 TMLHE trimethyllysine hydroxylase, epsilon 11181 TREH trehalase 706 TSPO translocator protein 7360 UGP2 UDP-glucose pyrophosphorylase 2 10493 VAT1 vesicle amine transport 1 57687 VAT1L vesicle amine transport 1 like 9942 XYLB xylulokinase 284273 ZADH2 zinc binding alcohol dehydrogenase domain containing 2

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 3.27e-01 4.68e-20 GO alditol:NADP+ 1-oxidoreductase activity molecular_function 3.12e-01 1.40e-10 Reactome Digestion of dietary carbohydrate Digestion and absorption 1.84e-01 1.32e-05 Reactome Glycogen storage disease type 0 (liver GYS2) Disease 1.84e-01 1.32e-05 Reactome Glycogen storage disease type 0 (muscle GYS1) Disease 1.77e-01 1.32e-05 Reactome Glycogen storage disease type IV (GBE1) Disease 1.77e-01 1.32e-05 Reactome Glycogen storage disease type XV (GYG1) Disease 1.53e-01 1.67e-18 Reactome Glycogen metabolism Metabolism 1.43e-01 5.60e-12 GO prostaglandin metabolic process biological_process 1.05e-01 3.13e-11 GO oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor molecular_function 9.24e-02 2.51e-15 GO glycogen biosynthetic process biological_process 6.79e-02 1.01e-17 GO alcohol dehydrogenase (NADP+) activity molecular_function 5.95e-02 3.66e-04 GO endoplasmic reticulum tubular network organization biological_process 5.81e-02 3.89e-06 GO NADP-retinol dehydrogenase activity molecular_function 5.31e-02 5.31e-14 GO daunorubicin metabolic process biological_process 5.25e-02 1.38e-06 GO carbohydrate phosphorylation biological_process 4.66e-02 5.31e-14 GO doxorubicin metabolic process biological_process 4.58e-02 1.31e-04 Reactome Formation of xylulose-5-phosphate Metabolism 2.30e-02 7.96e-08 GO glucose binding molecular_function 1.46e-02 3.89e-06 GO cellular aldehyde metabolic process biological_process 1.30e-02 8.53e-04 GO negative regulation of nitric oxide biosynthetic process biological_process 1.05e-02 1.91e-16 GO oxidoreductase activity molecular_function 1.02e-03 5.60e-12 GO aldo-keto reductase (NADP) activity molecular_function

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 cellular ketone metabolic process 0.00e+00 0.00e+00 carbohydrate metabolic process 0.00e+00 0.00e+00 quinone metabolic process 0.00e+00 0.00e+00 daunorubicin metabolic process 0.00e+00 0.00e+00 doxorubicin metabolic process 0.00e+00 0.00e+00 generation of precursor metabolites and energy 0.00e+00 0.00e+00 cellular carbohydrate metabolic process 0.00e+00 0.00e+00 carbohydrate catabolic process 0.00e+00 0.00e+00 cellular polysaccharide biosynthetic process 0.00e+00 0.00e+00 energy reserve metabolic process 0.00e+00 0.00e+00 polysaccharide metabolic process 0.00e+00 0.00e+00 glycogen biosynthetic process 0.00e+00 0.00e+00 glycogen metabolic process 0.00e+00 0.00e+00 carbohydrate biosynthetic process 0.00e+00 0.00e+00 polysaccharide biosynthetic process 0.00e+00 0.00e+00 oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor 0.00e+00 0.00e+00 alditol:NADP+ 1-oxidoreductase activity 0.00e+00 0.00e+00 aldo-keto reductase (NADP) activity 0.00e+00 0.00e+00 alcohol dehydrogenase (NADP+) activity 7.27e-22 5.27e-19 oxidoreductase activity, acting on CH-OH group of donors

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 CARBOHYDRATES 0.00e+00 0.00e+00 GLUCOSE METABOLISM 0.00e+00 0.00e+00 METABOLISM OF CARBOHYDRATES 0.00e+00 0.00e+00 GLUCOSE METABOLISM 5.94e-11 2.19e-08 DIGESTION OF DIETARY CARBOHYDRATE 7.74e-11 2.14e-08 DIGESTION OF DIETARY CARBOHYDRATE 1.26e-09 3.03e-07 GLYCOGEN BREAKDOWN GLYCOGENOLYSIS 6.97e-09 2.08e-06 GLYCOGEN BREAKDOWN GLYCOGENOLYSIS 1.73e-03 1.88e-01 SYNTHESIS OF PA 2.62e-03 2.36e-01 SYNTHESIS OF PA 3.23e-03 2.83e-01 MRNA DECAY BY 3 TO 5 EXORIBONUCLEASE 4.95e-03 4.53e-01 MRNA DECAY BY 3 TO 5 EXORIBONUCLEASE 1.03e-02 8.15e-01 GLUCURONIDATION 1.16e-02 8.29e-01 TRIGLYCERIDE BIOSYNTHESIS 1.21e-02 9.26e-01 TRIGLYCERIDE BIOSYNTHESIS 2.57e-02 1.00e+00 SYNTHESIS OF BILE ACIDS AND BILE SALTS VIA 24 HYDROXYCHOLESTEROL 3.03e-02 1.00e+00 SYNTHESIS OF BILE ACIDS AND BILE SALTS VIA 24 HYDROXYCHOLESTEROL

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 2.31e-07 2.78e-03 abnormal vitamin C level 4.11e-07 4.49e-03 increased liver glycogen level 1.26e-06 1.04e-02 decreased glycogen catabolism rate 1.33e-05 5.71e-02 increased skeletal muscle glycogen level 1.65e-05 6.67e-02 increased glycogen level 3.37e-04 4.81e-01 decreased skeletal muscle glycogen level 5.56e-04 6.46e-01 vasculature congestion 1.11e-03 9.56e-01 decreased liver glycogen level 1.48e-03 1.00e+00 abnormal hepatocyte morphology 1.69e-03 1.00e+00 fragile skeleton 1.87e-03 1.00e+00 anterior subcapsular cataracts 2.10e-03 1.00e+00 pulmonary vascular congestion 2.71e-03 1.00e+00 abnormal fetal cardiomyocyte proliferation 3.51e-03 1.00e+00 abnormal brain morphology 3.56e-03 1.00e+00 decreased glycogen level 3.75e-03 1.00e+00 abnormal turbinate morphology 3.75e-03 1.00e+00 abnormal liver vasculature morphology 4.82e-03 1.00e+00 abnormal muscle cell glucose uptake 5.12e-03 1.00e+00 abnormal enzyme/coenzyme activity 6.61e-03 1.00e+00 neuron degeneration

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

²FDR corrected p-value (Benjamini-Hochberg)