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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod147

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod147 Module size 64 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 47 ACLY ATP citrate lyase 48 ACO1 aconitase 1 50 ACO2 aconitase 2 125061 AFMID arylformamidase 84883 AIFM2 apoptosis inducing factor, mitochondria associated 2 7915 ALDH5A1 aldehyde dehydrogenase 5 family member A1 586 BCAT1 branched chain amino acid transaminase 1 587 BCAT2 branched chain amino acid transaminase 2 593 BCKDHA branched chain keto acid dehydrogenase E1, alpha polypeptide 594 BCKDHB branched chain keto acid dehydrogenase E1 subunit beta 171425 CLYBL citrate lyase beta like 290408 CS SGT1 homolog, MIS12 kinetochore complex assembly cochaperone 1629 DBT dihydrolipoamide branched chain transacylase E2 8528 DDO D-aspartate oxidase 55526 DHTKD1 dehydrogenase E1 and transketolase domain containing 1 1737 DLAT dihydrolipoamide S-acetyltransferase 197257 DLD lactate dehydrogenase D 1743 DLST dihydrolipoamide S-succinyltransferase 3075 FH complement factor H 137362 GOT1L1 glutamic-oxaloacetic transaminase 1 like 1 54511 HMGCLL1 3-hydroxymethyl-3-methylglutaryl-CoA lyase like 1 3417 IDH1 isocitrate dehydrogenase (NADP(+)) 1, cytosolic 3418 IDH2 isocitrate dehydrogenase (NADP(+)) 2, mitochondrial 3419 IDH3A isocitrate dehydrogenase 3 (NAD(+)) alpha 3420 IDH3B isocitrate dehydrogenase 3 (NAD(+)) beta 3421 IDH3G isocitrate dehydrogenase 3 (NAD(+)) gamma 10994 ILVBL ilvB acetolactate synthase like 3658 IREB2 iron responsive element binding protein 2 246269 LACE1 AFG1 like ATPase 3939 LDHA lactate dehydrogenase A 160287 LDHAL6A lactate dehydrogenase A like 6A 92483 LDHAL6B lactate dehydrogenase A like 6B 3945 LDHB lactate dehydrogenase B 3948 LDHC lactate dehydrogenase C 197257 LDHD lactate dehydrogenase D 11019 LIAS lipoic acid synthetase 387787 LIPT2 lipoyl(octanoyl) transferase 2 4190 MDH1 malate dehydrogenase 1 130752 MDH1B malate dehydrogenase 1B 4191 MDH2 malate dehydrogenase 2 57717 ME1 protocadherin beta 16 56125 ME2 protocadherin beta 11 56110 ME3 protocadherin gamma subfamily A, 5 51660 MPC1 mitochondrial pyruvate carrier 1 25874 MPC2 mitochondrial pyruvate carrier 2 56954 NIT2 nitrilase family member 2 158046 NXNL2 nucleoredoxin like 2 4967 OGDH oxoglutarate dehydrogenase 55753 OGDHL oxoglutarate dehydrogenase like 5091 PC pyruvate carboxylase 5160 PDHA1 pyruvate dehydrogenase E1 alpha 1 subunit 5161 PDHA2 pyruvate dehydrogenase E1 alpha 2 subunit 5162 PDHB pyruvate dehydrogenase E1 beta subunit 8050 PDHX pyruvate dehydrogenase complex component X 6389 SDHA succinate dehydrogenase complex flavoprotein subunit A 6576 SLC25A1 solute carrier family 25 member 1 89874 SLC25A21 solute carrier family 25 member 21 284723 SLC25A34 solute carrier family 25 member 34 399512 SLC25A35 solute carrier family 25 member 35 8803 SUCLA2 succinate-CoA ligase ADP-forming beta subunit 8802 SUCLG1 succinate-CoA ligase alpha subunit 8801 SUCLG2 succinate-CoA ligase GDP-forming beta subunit 10587 TXNRD2 thioredoxin reductase 2 114112 TXNRD3 thioredoxin reductase 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 4.61e-01 4.23e-63 GO tricarboxylic acid cycle biological_process 1.93e-01 8.02e-30 Reactome Glyoxylate metabolism and glycine degradation Metabolism 1.84e-01 3.98e-17 GO malate metabolic process biological_process 1.61e-01 3.40e-63 Reactome Pyruvate metabolism and Citric Acid (TCA) cycle Metabolism 1.54e-01 1.23e-04 GO thioredoxin-disulfide reductase activity molecular_function 1.22e-01 5.00e-09 GO citrate metabolic process biological_process 1.22e-01 7.09e-03 GO hydroxymethylglutaryl-CoA lyase activity molecular_function 1.22e-01 7.09e-03 Reactome Degradation of GABA Neuronal System 1.10e-01 7.57e-28 Reactome Pyruvate metabolism Metabolism 9.54e-02 1.50e-10 Reactome Branched-chain amino acid catabolism Metabolism 6.85e-02 1.24e-05 GO isocitrate dehydrogenase (NADP+) activity molecular_function 3.56e-02 2.17e-10 GO oxaloacetate metabolic process biological_process 3.00e-02 4.36e-18 GO pyruvate metabolic process biological_process 1.69e-02 5.48e-04 GO fatty-acyl-CoA biosynthetic process biological_process 1.51e-02 6.59e-21 GO NAD binding molecular_function 3.44e-03 2.54e-07 GO branched-chain amino acid catabolic process biological_process 1.36e-03 5.47e-08 GO flavin adenine dinucleotide binding 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 dicarboxylic acid metabolic process 0e+00 0e+00 generation of precursor metabolites and energy 0e+00 0e+00 energy derivation by oxidation of organic compounds 0e+00 0e+00 citrate metabolic process 0e+00 0e+00 cellular respiration 0e+00 0e+00 tricarboxylic acid cycle 0e+00 0e+00 acyl-CoA metabolic process 0e+00 0e+00 tricarboxylic acid metabolic process 0e+00 0e+00 cofactor metabolic process 0e+00 0e+00 aerobic respiration 0e+00 0e+00 cellular aldehyde metabolic process 0e+00 0e+00 glyoxylate metabolic process 0e+00 0e+00 monocarboxylic acid metabolic process 0e+00 0e+00 cellular amino acid catabolic process 0e+00 0e+00 acetyl-CoA metabolic process 0e+00 0e+00 pyruvate metabolic process 0e+00 0e+00 malate metabolic process 0e+00 0e+00 acetyl-CoA biosynthetic process from pyruvate 0e+00 0e+00 acetyl-CoA biosynthetic process 0e+00 0e+00 mitochondrial acetyl-CoA biosynthetic process from pyruvate

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 PYRUVATE METABOLISM AND CITRIC ACID TCA CYCLE 0.00e+00 0.00e+00 CITRIC ACID CYCLE TCA CYCLE 0.00e+00 0.00e+00 TCA CYCLE AND RESPIRATORY ELECTRON TRANSPORT 0.00e+00 0.00e+00 PYRUVATE METABOLISM AND CITRIC ACID TCA CYCLE 0.00e+00 0.00e+00 CITRIC ACID CYCLE TCA CYCLE 0.00e+00 0.00e+00 TCA CYCLE AND RESPIRATORY ELECTRON TRANSPORT 2.77e-11 1.05e-08 PYRUVATE METABOLISM 5.28e-10 1.33e-07 BRANCHED CHAIN AMINO ACID CATABOLISM 7.78e-10 1.92e-07 PYRUVATE METABOLISM 1.13e-09 3.71e-07 BRANCHED CHAIN AMINO ACID CATABOLISM 1.35e-08 3.89e-06 REGULATION OF PYRUVATE DEHYDROGENASE PDH COMPLEX 3.23e-08 6.72e-06 METABOLISM OF AMINO ACIDS AND DERIVATIVES 4.51e-08 1.21e-05 METABOLISM OF AMINO ACIDS AND DERIVATIVES 6.30e-07 1.13e-04 REGULATION OF PYRUVATE DEHYDROGENASE PDH COMPLEX 1.18e-04 1.80e-02 GLUCONEOGENESIS 1.36e-04 2.04e-02 MITOCHONDRIAL PROTEIN IMPORT 2.29e-04 2.68e-02 MITOCHONDRIAL PROTEIN IMPORT 3.21e-04 3.65e-02 GLUCONEOGENESIS 1.43e-03 1.60e-01 GLUCOSE METABOLISM 2.20e-03 2.02e-01 GLUCOSE METABOLISM

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 3.04e-06 2.03e-02 abnormal amino acid level 5.20e-04 6.20e-01 bradykinesia 6.86e-04 7.28e-01 decreased circulating aspartate transaminase level 1.25e-03 1.00e+00 decreased circulating alanine transaminase level 2.49e-03 1.00e+00 abnormal iron homeostasis 3.64e-03 1.00e+00 abnormal enzyme/coenzyme activity 4.78e-03 1.00e+00 increased energy expenditure 5.61e-03 1.00e+00 abnormal prechordal plate morphology 5.61e-03 1.00e+00 failure of ejaculation 5.61e-03 1.00e+00 abnormal intestinal iron level 7.48e-03 1.00e+00 abnormal testis physiology 7.48e-03 1.00e+00 decreased fetal cardiomyocyte proliferation 7.48e-03 1.00e+00 abnormal pituitary gland physiology 7.48e-03 1.00e+00 altered tumor pathology 7.48e-03 1.00e+00 abnormal corpora quadrigemina morphology 7.84e-03 1.00e+00 decreased percent body fat 8.46e-03 1.00e+00 polyuria 9.34e-03 1.00e+00 thin hair shaft 9.37e-03 1.00e+00 decreased adiponectin level 1.03e-02 1.00e+00 abnormal erythrocyte morphology

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

²FDR corrected p-value (Benjamini-Hochberg)