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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod163

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod163 Module size 47 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 10555 AGPAT2 1-acylglycerol-3-phosphate O-acyltransferase 2 56894 AGPAT3 1-acylglycerol-3-phosphate O-acyltransferase 3 56895 AGPAT4 1-acylglycerol-3-phosphate O-acyltransferase 4 55326 AGPAT5 1-acylglycerol-3-phosphate O-acyltransferase 5 137964 AGPAT6 glycerol-3-phosphate acyltransferase 4 79888 AGPAT9 lysophosphatidylcholine acyltransferase 1 59344 ALOXE3 arachidonate lipoxygenase 3 11200 CDS1 checkpoint kinase 2 1056 CEL carboxyl ester lipase 747 DAGLA diacylglycerol lipase alpha 221955 DAGLB diacylglycerol lipase beta 84649 DGAT2 diacylglycerol O-acyltransferase 2 1606 DGKA diacylglycerol kinase alpha 1607 DGKB diacylglycerol kinase beta 8527 DGKD diacylglycerol kinase delta 8526 DGKE diacylglycerol kinase epsilon 1608 DGKG diacylglycerol kinase gamma 160851 DGKH diacylglycerol kinase eta 9162 DGKI diacylglycerol kinase iota 1609 DGKQ diacylglycerol kinase theta 8525 DGKZ diacylglycerol kinase zeta 1776 DNASE1L3 deoxyribonuclease 1 like 3 5168 ENPP2 ectonucleotide pyrophosphatase/phosphodiesterase 2 133121 ENPP6 ectonucleotide pyrophosphatase/phosphodiesterase 6 57678 GPAM glycerol-3-phosphate acyltransferase, mitochondrial 150763 GPAT2 glycerol-3-phosphate acyltransferase 2, mitochondrial 266722 HS6ST3 heparan sulfate 6-O-sulfotransferase 3 253558 LCLAT1 lysocardiolipin acyltransferase 1 3990 LIPC lipase C, hepatic type 8513 LIPF lipase F, gastric type 9388 LIPG lipase G, endothelial type 10162 LPCAT3 lysophosphatidylcholine acyltransferase 3 79143 MBOAT7 membrane bound O-acyltransferase domain containing 7 11343 MGLL monoglyceride lipase 346606 MOGAT3 monoacylglycerol O-acyltransferase 3 58475 MS4A7 membrane spanning 4-domains A7 26167 PCDHB5 protocadherin beta 5 23761 PISD phosphatidylserine decarboxylase 8398 PLA2G6 phospholipase A2 group VI 5337 PLD1 phospholipase D1 5338 PLD2 phospholipase D2 440503 PLIN5 perilipin 5 5406 PNLIP pancreatic lipase 119548 PNLIPRP3 pancreatic lipase related protein 3 57104 PNPLA2 patatin like phospholipase domain containing 2 80339 PNPLA3 patatin like phospholipase domain containing 3 50640 PNPLA8 patatin like phospholipase domain containing 8

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 4.49e-01 1.09e-22 GO diacylglycerol kinase activity molecular_function 3.26e-01 1.20e-18 GO CDP-diacylglycerol biosynthetic process biological_process 2.82e-01 1.30e-09 Reactome Digestion of dietary lipid Digestion and absorption 2.00e-01 1.56e-07 Reactome Arachidonate production from DAG Hemostasis#Signal Transduction 1.74e-01 2.60e-09 Reactome Acyl chain remodeling of DAG and TAG Metabolism 1.21e-01 5.45e-07 GO lipoprotein lipase activity molecular_function 1.05e-01 8.98e-18 GO phospholipid biosynthetic process biological_process 9.64e-02 4.64e-19 GO lipid phosphorylation biological_process 8.54e-02 2.61e-25 Reactome Effects of PIP2 hydrolysis Hemostasis#Signal Transduction 8.13e-02 7.27e-14 GO triglyceride lipase activity molecular_function 4.49e-02 3.98e-23 GO phosphatidic acid biosynthetic process biological_process 4.48e-02 3.58e-09 GO arachidonic acid metabolic process biological_process 4.22e-02 3.68e-08 Reactome Triglyceride biosynthesis Metabolism 3.72e-02 1.16e-16 GO 1-acylglycerol-3-phosphate O-acyltransferase activity molecular_function 1.49e-02 9.56e-05 Reactome Acyl chain remodeling of CL Metabolism 1.44e-02 8.16e-30 Reactome Glycerophospholipid biosynthesis Metabolism 9.42e-03 3.47e-05 GO cell motility 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 0e+00 0e+00 glycerolipid metabolic process 0e+00 0e+00 protein kinase C-activating G-protein coupled receptor signaling pathway 0e+00 0e+00 lipid biosynthetic process 0e+00 0e+00 phospholipid biosynthetic process 0e+00 0e+00 triglyceride metabolic process 0e+00 0e+00 glycerophospholipid metabolic process 0e+00 0e+00 phospholipid metabolic process 0e+00 0e+00 phosphatidic acid biosynthetic process 0e+00 0e+00 neutral lipid metabolic process 0e+00 0e+00 CDP-diacylglycerol metabolic process 0e+00 0e+00 phosphatidic acid metabolic process 0e+00 0e+00 glycerophospholipid biosynthetic process 0e+00 0e+00 triglyceride biosynthetic process 0e+00 0e+00 CDP-diacylglycerol biosynthetic process 0e+00 0e+00 lipid catabolic process 0e+00 0e+00 diacylglycerol kinase activity 0e+00 0e+00 1-acylglycerol-3-phosphate O-acyltransferase activity 0e+00 0e+00 lysophospholipid acyltransferase activity 0e+00 0e+00 transferase activity, transferring acyl groups 0e+00 0e+00 lysophosphatidic acid acyltransferase activity

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 EFFECTS OF PIP2 HYDROLYSIS 0.00e+00 0.00e+00 GLYCEROPHOSPHOLIPID BIOSYNTHESIS 0.00e+00 0.00e+00 TRIGLYCERIDE BIOSYNTHESIS 0.00e+00 0.00e+00 PHOSPHOLIPID METABOLISM 0.00e+00 0.00e+00 SYNTHESIS OF PA 0.00e+00 0.00e+00 EFFECTS OF PIP2 HYDROLYSIS 0.00e+00 0.00e+00 GLYCEROPHOSPHOLIPID BIOSYNTHESIS 0.00e+00 0.00e+00 PHOSPHOLIPID METABOLISM 0.00e+00 0.00e+00 SYNTHESIS OF PA 2.23e-10 5.87e-08 TRIGLYCERIDE BIOSYNTHESIS 1.24e-09 4.05e-07 PLATELET ACTIVATION SIGNALING AND AGGREGATION 1.10e-08 2.40e-06 PLATELET ACTIVATION SIGNALING AND AGGREGATION 5.00e-08 1.01e-05 G ALPHA Q SIGNALLING EVENTS 5.56e-08 1.12e-05 GASTRIN CREB SIGNALLING PATHWAY VIA PKC AND MAPK 8.64e-08 2.24e-05 G ALPHA Q SIGNALLING EVENTS 1.29e-07 3.29e-05 FATTY ACID TRIACYLGLYCEROL AND KETONE BODY METABOLISM 1.59e-07 4.03e-05 GASTRIN CREB SIGNALLING PATHWAY VIA PKC AND MAPK 4.72e-07 8.65e-05 FATTY ACID TRIACYLGLYCEROL AND KETONE BODY METABOLISM 1.85e-04 2.68e-02 ACYL CHAIN REMODELLING OF PC 2.02e-04 2.89e-02 ACYL CHAIN REMODELLING OF PE

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 1.64e-08 3.60e-04 abnormal lipid level 2.02e-06 1.48e-02 decreased fatty acid level 5.69e-06 3.17e-02 abnormal lipid homeostasis 4.80e-04 5.94e-01 increased oxygen consumption 5.50e-04 6.43e-01 abnormal fatty acid level 6.40e-04 6.98e-01 decreased circulating insulin level 6.71e-04 7.20e-01 abnormal gas homeostasis 6.75e-04 7.21e-01 decreased circulating VLDL triglyceride level 8.51e-04 8.22e-01 impaired lipolysis 9.60e-04 8.83e-01 decreased liver triglyceride level 9.91e-04 8.98e-01 decreased circulating triglyceride level 1.14e-03 9.71e-01 abnormal mitochondrion morphology 1.60e-03 1.00e+00 abnormal intestinal lipid absorption 1.85e-03 1.00e+00 increased liver triglyceride level 1.87e-03 1.00e+00 abnormal fatty acid oxidation 1.93e-03 1.00e+00 decreased circulating free fatty acid level 2.59e-03 1.00e+00 abnormal nervous system morphology 2.95e-03 1.00e+00 abnormal neuron proliferation 3.53e-03 1.00e+00 hyperactivity 3.87e-03 1.00e+00 decreased percent body fat

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

²FDR corrected p-value (Benjamini-Hochberg)