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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod302

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod302 Module size 38 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 57143 ADCK1 aarF domain containing kinase 1 90956 ADCK2 aarF domain containing kinase 2 56997 ADCK3 coenzyme Q8A 79934 ADCK4 coenzyme Q8B 203054 ADCK5 aarF domain containing kinase 5 51094 ADIPOR1 adiponectin receptor 1 79602 ADIPOR2 adiponectin receptor 2 10554 AGPAT1 1-acylglycerol-3-phosphate O-acyltransferase 1 93058 COQ10A coenzyme Q10A 80219 COQ10B coenzyme Q10B 27235 COQ2 coenzyme Q2, polyprenyltransferase 51805 COQ3 coenzyme Q3, methyltransferase 51117 COQ4 coenzyme Q4 84274 COQ5 coenzyme Q5, methyltransferase 25249 COQ7 coenzyme Q7, hydroxylase 498909 COQ9 coenzyme Q9 79947 DHDDS dehydrodolichyl diphosphate synthase subunit 2224 FDPS farnesyl diphosphate synthase 9453 GGPS1 geranylgeranyl diphosphate synthase 1 3422 IDI1 isopentenyl-diphosphate delta isomerase 1 91734 IDI2 isopentenyl-diphosphate delta isomerase 2 9926 LPGAT1 lysophosphatidylglycerol acyltransferase 1 23531 MMD monocyte to macrophage differentiation associated 221938 MMD2 monocyte to macrophage differentiation associated 2 4597 MVD mevalonate diphosphate decarboxylase 4598 MVK mevalonate kinase 116150 NUS1 NUS1, dehydrodolichyl diphosphate synthase subunit 152559 PAQR3 progestin and adipoQ receptor family member 3 124222 PAQR4 progestin and adipoQ receptor family member 4 79957 PAQR6 progestin and adipoQ receptor family member 6 164091 PAQR7 progestin and adipoQ receptor family member 7 85315 PAQR8 progestin and adipoQ receptor family member 8 344838 PAQR9 progestin and adipoQ receptor family member 9 23590 PDSS1 decaprenyl diphosphate synthase subunit 1 57107 PDSS2 decaprenyl diphosphate synthase subunit 2 10654 PMVK phosphomevalonate kinase 23623 RUSC1 RUN and SH3 domain containing 1 28968 SLC6A16 solute carrier family 6 member 16

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 3.19e-01 3.14e-25 GO ubiquinone biosynthetic process biological_process 3.00e-01 3.08e-19 Reactome Ubiquinol biosynthesis Metabolism 2.24e-01 1.17e-07 Reactome Synthesis of Dolichyl-phosphate Metabolism of proteins 1.15e-01 1.17e-14 GO isoprenoid biosynthetic process biological_process 1.14e-01 1.81e-14 Reactome Cholesterol biosynthesis Metabolism 5.92e-02 9.35e-05 Reactome AMPK inhibits chREBP transcriptional activation activity Metabolism 2.32e-02 9.31e-12 Reactome Activation of gene expression by SREBF (SREBP) Metabolism 2.67e-03 2.72e-06 GO steroid hormone mediated signaling pathway 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 lipid biosynthetic process 0.00e+00 0.00e+00 phospholipid biosynthetic process 0.00e+00 0.00e+00 alcohol metabolic process 0.00e+00 0.00e+00 isoprenoid biosynthetic process 0.00e+00 0.00e+00 isoprenoid metabolic process 0.00e+00 0.00e+00 cellular ketone metabolic process 0.00e+00 0.00e+00 quinone metabolic process 0.00e+00 0.00e+00 cofactor metabolic process 0.00e+00 0.00e+00 ubiquinone metabolic process 0.00e+00 0.00e+00 ubiquinone biosynthetic process 0.00e+00 0.00e+00 coenzyme biosynthetic process 8.83e-12 7.96e-09 isopentenyl diphosphate biosynthetic process 8.83e-12 7.96e-09 isopentenyl diphosphate metabolic process 6.57e-11 5.56e-08 cholesterol biosynthetic process 1.48e-10 1.21e-07 sterol biosynthetic process 6.52e-10 4.97e-07 phospholipid metabolic process 1.42e-09 7.36e-07 prenyltransferase activity 7.53e-09 4.97e-06 cholesterol metabolic process 1.55e-08 9.85e-06 sterol metabolic process 3.11e-08 1.89e-05 steroid biosynthetic 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 CHOLESTEROL BIOSYNTHESIS 1.83e-10 4.88e-08 CHOLESTEROL BIOSYNTHESIS 1.60e-03 1.53e-01 GLYCEROPHOSPHOLIPID BIOSYNTHESIS 2.00e-03 2.13e-01 GLYCEROPHOSPHOLIPID BIOSYNTHESIS 3.49e-03 3.03e-01 ACYL CHAIN REMODELLING OF PG 4.14e-03 3.91e-01 ACYL CHAIN REMODELLING OF PG 7.80e-03 6.58e-01 PHOSPHOLIPID METABOLISM 1.03e-02 8.15e-01 SYNTHESIS OF PA 1.03e-02 7.50e-01 PHOSPHOLIPID METABOLISM 2.19e-02 1.00e+00 TRIGLYCERIDE BIOSYNTHESIS 2.32e-02 1.00e+00 SYNTHESIS OF PA 3.24e-02 1.00e+00 INTEGRATION OF ENERGY METABOLISM 3.57e-02 1.00e+00 TRIGLYCERIDE BIOSYNTHESIS

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 1.67e-04 3.15e-01 abnormal mitochondrial ATP synthesis coupled electron transport 9.13e-04 8.54e-01 myopathy 1.15e-03 9.76e-01 abnormal enzyme/coenzyme level 1.32e-03 1.00e+00 abnormal mitochondrion morphology 2.82e-03 1.00e+00 hyperglycemia 3.32e-03 1.00e+00 oxidative stress 4.40e-03 1.00e+00 insulin resistance 4.70e-03 1.00e+00 increased circulating glucose level 5.61e-03 1.00e+00 abnormal glomerular capsule parietal layer morphology 5.61e-03 1.00e+00 decreased renal fat pad weight 7.47e-03 1.00e+00 abnormal mitochondrial chromosome morphology 7.96e-03 1.00e+00 abnormal lipid homeostasis 8.64e-03 1.00e+00 increased circulating insulin level 9.33e-03 1.00e+00 colorless urine 9.33e-03 1.00e+00 granular kidney 1.12e-02 1.00e+00 premature hair loss 1.12e-02 1.00e+00 abnormal embryonic neuroepithelial layer differentiation 1.12e-02 1.00e+00 decreased epididymis weight 1.21e-02 1.00e+00 weight loss 1.29e-02 1.00e+00 abnormal glucose homeostasis

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

²FDR corrected p-value (Benjamini-Hochberg)