Back to main page

DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod80

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod80 Module size 48 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 239 ALOX12 arachidonate 12-lipoxygenase, 12S type 242 ALOX12B arachidonate 12-lipoxygenase, 12R type 246 ALOX15 arachidonate 15-lipoxygenase 247 ALOX15B arachidonate 15-lipoxygenase, type B 10390 CEPT1 choline/ethanolamine phosphotransferase 1 55349 CHDH choline dehydrogenase 56994 CHPT1 choline phosphotransferase 1 85465 EPT1 selenoprotein I 9415 FADS2 fatty acid desaturase 2 8681 JMJD7-PLA2G4B JMJD7-PLA2G4B readthrough 79888 LPCAT1 lysophosphatidylcholine acyltransferase 1 54947 LPCAT2 lysophosphatidylcholine acyltransferase 2 129642 LPCAT4 membrane bound O-acyltransferase domain containing 2 10434 LYPLA1 lysophospholipase I 154141 MBOAT1 membrane bound O-acyltransferase domain containing 1 129642 MBOAT2 membrane bound O-acyltransferase domain containing 2 5050 PAFAH1B3 platelet activating factor acetylhydrolase 1b catalytic subunit 3 5051 PAFAH2 platelet activating factor acetylhydrolase 2 293688 PEMT transmembrane 7 superfamily member 2 8399 PLA2G10 phospholipase A2 group X 81579 PLA2G12A phospholipase A2 group XIIA 84647 PLA2G12B phospholipase A2 group XIIB 23659 PLA2G15 phospholipase A2 group XV 11145 PLA2G16 phospholipase A2 group XVI 5319 PLA2G1B phospholipase A2 group IB 5320 PLA2G2A phospholipase A2 group IIA 391013 PLA2G2C phospholipase A2 group IIC 30814 PLA2G2E phospholipase A2 group IIE 64600 PLA2G2F phospholipase A2 group IIF 50487 PLA2G3 phospholipase A2 group III 5321 PLA2G4A phospholipase A2 group IVA 100137049 PLA2G4B phospholipase A2 group IVB 8605 PLA2G4C phospholipase A2 group IVC 283748 PLA2G4D phospholipase A2 group IVD 123745 PLA2G4E phospholipase A2 group IVE 255189 PLA2G4F phospholipase A2 group IVF 5322 PLA2G5 phospholipase A2 group V 7941 PLA2G7 phospholipase A2 group VII 22925 PLA2R1 phospholipase A2 receptor 1 151056 PLB1 phospholipase B1 79887 PLBD1 phospholipase B domain containing 1 23646 PLD3 phospholipase D family member 3 122618 PLD4 phospholipase D family member 4 9791 PTDSS1 phosphatidylserine synthase 1 81490 PTDSS2 phosphatidylserine synthase 2 5743 PTGS2 prostaglandin-endoperoxide synthase 2 124925 SEZ6 seizure related 6 homolog 653067 XAGE1E X antigen family member 1B

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 5.58e-01 6.71e-06 Reactome Synthesis of PS Metabolism 4.74e-01 1.68e-08 GO arachidonate 15-lipoxygenase activity molecular_function 4.74e-01 1.68e-08 GO arachidonate 12-lipoxygenase activity molecular_function 2.45e-01 2.17e-39 GO calcium-dependent phospholipase A2 activity molecular_function 2.18e-01 1.49e-52 Reactome Acyl chain remodelling of PC Metabolism 1.42e-01 1.23e-11 GO 2-acylglycerol-3-phosphate O-acyltransferase activity molecular_function 1.39e-01 1.03e-20 Reactome Hydrolysis of LPC Metabolism 1.25e-01 6.68e-52 GO phosphatidylcholine acyl-chain remodeling biological_process 9.08e-02 8.79e-46 GO phospholipase A2 activity molecular_function 3.14e-02 5.64e-31 GO lipid catabolic process biological_process 2.93e-02 6.99e-55 Reactome Glycerophospholipid biosynthesis Metabolism 2.87e-02 6.76e-13 GO lipoxygenase pathway biological_process 1.48e-02 1.86e-04 Reactome Synthesis of PG Metabolism 1.38e-02 5.80e-21 GO lysophospholipase activity molecular_function 9.64e-03 7.30e-36 GO phosphatidylserine acyl-chain remodeling biological_process 8.89e-03 1.98e-38 GO phospholipid metabolic process biological_process 8.34e-03 7.30e-36 Reactome Acyl chain remodelling of PS Metabolism

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 glycerophospholipid metabolic process 0e+00 0e+00 phospholipid metabolic process 0e+00 0e+00 fatty acid metabolic process 0e+00 0e+00 phosphatidylcholine metabolic process 0e+00 0e+00 glycerolipid metabolic process 0e+00 0e+00 lipid catabolic process 0e+00 0e+00 monocarboxylic acid metabolic process 0e+00 0e+00 glycerophospholipid biosynthetic process 0e+00 0e+00 lipid biosynthetic process 0e+00 0e+00 phospholipid biosynthetic process 0e+00 0e+00 arachidonic acid metabolic process 0e+00 0e+00 icosanoid metabolic process 0e+00 0e+00 long-chain fatty acid metabolic process 0e+00 0e+00 cellular modified amino acid metabolic process 0e+00 0e+00 long-chain fatty acid transport 0e+00 0e+00 fatty acid transport 0e+00 0e+00 arachidonic acid secretion 0e+00 0e+00 monocarboxylic acid transport 0e+00 0e+00 acid secretion 0e+00 0e+00 phosphatidylcholine acyl-chain remodeling

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 GLYCEROPHOSPHOLIPID BIOSYNTHESIS 0.00e+00 0.00e+00 PHOSPHOLIPID METABOLISM 0.00e+00 0.00e+00 ACYL CHAIN REMODELLING OF PC 0.00e+00 0.00e+00 ACYL CHAIN REMODELLING OF PG 0.00e+00 0.00e+00 ACYL CHAIN REMODELLING OF PE 0.00e+00 0.00e+00 ACYL CHAIN REMODELLING OF PS 0.00e+00 0.00e+00 ACYL CHAIN REMODELLING OF PI 0.00e+00 0.00e+00 SYNTHESIS OF PA 0.00e+00 0.00e+00 GLYCEROPHOSPHOLIPID BIOSYNTHESIS 0.00e+00 0.00e+00 PHOSPHOLIPID METABOLISM 0.00e+00 0.00e+00 ACYL CHAIN REMODELLING OF PC 0.00e+00 0.00e+00 ACYL CHAIN REMODELLING OF PG 0.00e+00 0.00e+00 ACYL CHAIN REMODELLING OF PE 0.00e+00 0.00e+00 ACYL CHAIN REMODELLING OF PS 0.00e+00 0.00e+00 ACYL CHAIN REMODELLING OF PI 0.00e+00 0.00e+00 SYNTHESIS OF PA 8.09e-05 1.28e-02 SYNTHESIS OF PC 1.93e-04 2.29e-02 SYNTHESIS OF PC 1.27e-03 1.24e-01 SYNTHESIS OF PE 1.75e-03 1.89e-01 SYNTHESIS OF PE

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 7.08e-05 1.80e-01 abnormal phospholipid level 1.04e-04 2.32e-01 abnormal macrophage physiology 1.38e-04 2.81e-01 abnormal mast cell differentiation 3.91e-04 5.24e-01 decreased prostaglandin level 8.24e-04 8.06e-01 altered response of heart to induced stress 1.67e-03 1.00e+00 abnormal male reproductive system physiology 2.10e-03 1.00e+00 decreased myocardial infarction size 2.36e-03 1.00e+00 abnormal circulating cholesterol level 2.71e-03 1.00e+00 abnormal cardiac muscle contractility 2.87e-03 1.00e+00 decreased cerebral infarction size 3.00e-03 1.00e+00 increased circulating follicle stimulating hormone level 3.59e-03 1.00e+00 abnormal spleen white pulp morphology 4.10e-03 1.00e+00 abnormal response to injury 4.49e-03 1.00e+00 abnormal reproductive system physiology 5.62e-03 1.00e+00 abnormal memory B cell differentiation 5.64e-03 1.00e+00 kidney medulla hypoplasia 5.64e-03 1.00e+00 decreased urine prostaglandin level 5.84e-03 1.00e+00 decreased physiological sensitivity to xenobiotic 7.09e-03 1.00e+00 abnormal renal tubule morphology 7.51e-03 1.00e+00 renal tubule hypertrophy

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

²FDR corrected p-value (Benjamini-Hochberg)