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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod37

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod37 Module size 61 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 226 ALDOA aldolase, fructose-bisphosphate A 229 ALDOB aldolase, fructose-bisphosphate B 230 ALDOC aldolase, fructose-bisphosphate C 51005 AMDHD2 amidohydrolase domain containing 2 669 BPGM bisphosphoglycerate mutase 57103 C12orf5 TP53 induced glycolysis regulatory phosphatase 51071 DERA deoxyribose-phosphate aldolase 2023 ENO1 enolase 1 2026 ENO2 enolase 2 2027 ENO3 enolase 3 387712 ENO4 enolase 4 646486 FABP12 fatty acid binding protein 12 2173 FABP7 fatty acid binding protein 7 646480 FABP9 fatty acid binding protein 9 2203 FBP1 fructose-bisphosphatase 1 8570 FBP2 KH-type splicing regulatory protein 2538 G6PC glucose-6-phosphatase catalytic subunit 92579 G6PC3 glucose-6-phosphatase catalytic subunit 3 8266 G6PD ubiquitin like 4A 100240709 GAPDH glyceraldehyde 3 phosphate dehydrogenase pseudogene 44 26330 GAPDHS glyceraldehyde-3-phosphate dehydrogenase, spermatogenic 10007 GNPDA1 glucosamine-6-phosphate deaminase 1 132789 GNPDA2 glucosamine-6-phosphate deaminase 2 10007 GPI glucosamine-6-phosphate deaminase 1 9563 H6PD hexose-6-phosphate dehydrogenase/glucose 1-dehydrogenase 3739 HK1 potassium voltage-gated channel subfamily A member 4 3741 HK2 potassium voltage-gated channel subfamily A member 5 3101 HK3 hexokinase 3 80201 HKDC1 hexokinase domain containing 1 414328 IDNK IDNK, gluconokinase 3795 KHK ketohexokinase 6590 MPI secretory leukocyte peptidase inhibitor 5207 PFKFB1 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 1 5208 PFKFB2 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 2 5209 PFKFB3 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 3 5210 PFKFB4 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 4 5211 PFKL phosphofructokinase, liver type 5213 PFKM phosphofructokinase, muscle 5214 PFKP phosphofructokinase, platelet 5223 PGAM1 phosphoglycerate mutase 1 5224 PGAM2 phosphoglycerate mutase 2 441531 PGAM4 phosphoglycerate mutase family member 4 5226 PGD phosphogluconate dehydrogenase 5230 PGK1 phosphoglycerate kinase 1 5232 PGK2 phosphoglycerate kinase 2 25796 PGLS 6-phosphogluconolactonase 5236 PGM1 phosphoglucomutase 1 55276 PGM2 phosphoglucomutase 2 283209 PGM2L1 phosphoglucomutase 2 like 1 5239 PGM5 phosphoglucomutase 5 5313 PKLR pyruvate kinase L/R 5315 PKM pyruvate kinase M1/2 57469 PNMAL2 PNMA family member 8B 5837 PYGM glycogen phosphorylase, muscle associated 64080 RBKS ribokinase 116362 RBP7 retinol binding protein 7 6888 TALDO1 transaldolase 1 7086 TKT transketolase 8277 TKTL1 transketolase like 1 84076 TKTL2 transketolase like 2 7167 TPI1 triosephosphate isomerase 1

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 4.53e-01 2.11e-20 GO pentose-phosphate shunt biological_process 4.40e-01 8.50e-26 GO fructose metabolic process biological_process 4.11e-01 2.73e-57 GO canonical glycolysis biological_process 2.58e-01 4.83e-56 GO glycolytic process biological_process 2.53e-01 7.26e-07 GO N-acetylneuraminate catabolic process biological_process 2.50e-01 5.84e-10 GO phosphoglucomutase activity molecular_function 1.27e-01 4.57e-19 GO glucose 6-phosphate metabolic process biological_process 1.17e-01 1.12e-05 Reactome Insulin effects increased synthesis of Xylulose-5-Phosphate Metabolism 1.16e-01 3.35e-05 GO glucose-6-phosphatase activity molecular_function 1.13e-01 1.17e-10 GO 6-phosphofructo-2-kinase activity molecular_function 1.06e-01 3.16e-14 GO fructose 6-phosphate metabolic process biological_process 9.99e-02 5.18e-13 GO glycogen catabolic process biological_process 6.35e-02 3.65e-37 Reactome Gluconeogenesis Metabolism 3.65e-02 6.36e-59 Reactome Glycolysis Metabolism 1.37e-02 5.38e-05 Reactome Triglyceride catabolism Metabolism 1.06e-02 4.21e-65 Reactome Glucose metabolism Metabolism 5.71e-03 2.74e-39 GO gluconeogenesis biological_process 5.21e-03 8.11e-09 GO galactose catabolic process biological_process 5.10e-03 8.99e-05 GO triglyceride catabolic process biological_process 4.31e-03 1.12e-05 GO fructose 1,6-bisphosphate 1-phosphatase 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 0e+00 0e+00 hexose biosynthetic process 0e+00 0e+00 hexose metabolic process 0e+00 0e+00 nucleotide phosphorylation 0e+00 0e+00 purine nucleotide metabolic process 0e+00 0e+00 nucleoside diphosphate phosphorylation 0e+00 0e+00 fructose metabolic process 0e+00 0e+00 glucose metabolic process 0e+00 0e+00 glucose catabolic process 0e+00 0e+00 monosaccharide metabolic process 0e+00 0e+00 nucleotide metabolic process 0e+00 0e+00 ATP generation from ADP 0e+00 0e+00 carbohydrate biosynthetic process 0e+00 0e+00 carbohydrate catabolic process 0e+00 0e+00 fructose 1,6-bisphosphate metabolic process 0e+00 0e+00 gluconeogenesis 0e+00 0e+00 generation of precursor metabolites and energy 0e+00 0e+00 glycolytic process 0e+00 0e+00 ADP metabolic process 0e+00 0e+00 ATP metabolic process 0e+00 0e+00 NAD 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 GLUCOSE METABOLISM 0.00e+00 0.00e+00 GLUCONEOGENESIS 0.00e+00 0.00e+00 METABOLISM OF CARBOHYDRATES 0.00e+00 0.00e+00 GLYCOLYSIS 0.00e+00 0.00e+00 GLUCOSE METABOLISM 0.00e+00 0.00e+00 GLUCONEOGENESIS 0.00e+00 0.00e+00 METABOLISM OF CARBOHYDRATES 0.00e+00 0.00e+00 GLYCOLYSIS 5.16e-08 1.38e-05 GLUCOSE TRANSPORT 1.02e-07 1.99e-05 GLUCOSE TRANSPORT 1.01e-04 1.57e-02 GLYCOGEN BREAKDOWN GLYCOGENOLYSIS 1.82e-04 2.18e-02 INTEGRATION OF ENERGY METABOLISM 5.95e-04 6.33e-02 GLYCOGEN BREAKDOWN GLYCOGENOLYSIS 3.48e-03 3.38e-01 INTEGRATION OF ENERGY METABOLISM 1.30e-02 9.80e-01 SLC MEDIATED TRANSMEMBRANE TRANSPORT 3.66e-02 1.00e+00 SLC MEDIATED TRANSMEMBRANE TRANSPORT

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 5.72e-06 3.17e-02 increased circulating bilirubin level 2.18e-05 8.13e-02 increased skeletal muscle glycogen level 2.52e-05 9.14e-02 decreased hematocrit 2.74e-05 9.75e-02 reticulocytosis 8.56e-05 2.05e-01 abnormal erythrocyte morphology 9.08e-05 2.12e-01 hemolytic anemia 9.35e-05 2.16e-01 increased mean corpuscular volume 9.65e-05 2.21e-01 abnormal erythrocyte osmotic lysis 1.22e-04 2.57e-01 increased spleen weight 4.44e-04 5.66e-01 decreased mean corpuscular hemoglobin 5.32e-04 6.31e-01 decreased erythrocyte cell number 5.57e-04 6.47e-01 abnormal enzyme/coenzyme activity 1.05e-03 9.25e-01 asthenozoospermia 1.81e-03 1.00e+00 abnormal erythrocyte physiology 3.03e-03 1.00e+00 abnormal spongiotrophoblast layer morphology 3.65e-03 1.00e+00 other aberrant phenotype 3.75e-03 1.00e+00 abnormal hair cycle catagen phase 3.75e-03 1.00e+00 absent vagina 3.89e-03 1.00e+00 decreased mean corpuscular hemoglobin concentration 3.96e-03 1.00e+00 decreased hemoglobin content

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

²FDR corrected p-value (Benjamini-Hochberg)