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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod247

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod247 Module size 53 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 64801 ARV1 ARV1 homolog, fatty acid homeostasis modulator 538 ATP7A ATPase copper transporting alpha 540 ATP7B ATPase copper transporting beta 158833 AWAT1 acyl-CoA wax alcohol acyltransferase 1 138199 C9orf41 carnosine N-methyltransferase 1 51596 CUTA cutA divalent cation tolerance homolog 8694 DGAT1 diacylglycerol O-acyltransferase 1 347516 DGAT2L6 diacylglycerol O-acyltransferase 2 like 6 646409 DGAT2L7P diacylglycerol O-acyltransferase 2 like 7, pseudogene 22875 ENPP4 ectonucleotide pyrophosphatase/phosphodiesterase 4 59084 ENPP5 ectonucleotide pyrophosphatase/phosphodiesterase 5 (putative) 339221 ENPP7 ectonucleotide pyrophosphatase/phosphodiesterase 7 9847 KIAA0528 C2 calcium dependent domain containing 5 113655 MFSD3 major facilitator superfamily domain containing 3 116255 MOGAT1 monoacylglycerol O-acyltransferase 1 288058 PTPLA 3-hydroxyacyl-CoA dehydratase 2 51495 PTPLAD1 3-hydroxyacyl-CoA dehydratase 3 401494 PTPLAD2 3-hydroxyacyl-CoA dehydratase 4 201562 PTPLB 3-hydroxyacyl-CoA dehydratase 2 51097 SCCPDH saccharopine dehydrogenase (putative) 6319 SCD stearoyl-CoA desaturase 79966 SCD5 stearoyl-CoA desaturase 5 7779 SLC30A1 solute carrier family 30 member 1 55532 SLC30A10 solute carrier family 30 member 10 7780 SLC30A2 solute carrier family 30 member 2 7781 SLC30A3 solute carrier family 30 member 3 7782 SLC30A4 solute carrier family 30 member 4 64924 SLC30A5 solute carrier family 30 member 5 55676 SLC30A6 solute carrier family 30 member 6 148867 SLC30A7 solute carrier family 30 member 7 169026 SLC30A8 solute carrier family 30 member 8 9197 SLC33A1 solute carrier family 33 member 1 55343 SLC35C1 solute carrier family 35 member C1 27173 SLC39A1 solute carrier family 39 member 1 57181 SLC39A10 solute carrier family 39 member 10 201266 SLC39A11 solute carrier family 39 member 11 221074 SLC39A12 solute carrier family 39 member 12 91252 SLC39A13 solute carrier family 39 member 13 23516 SLC39A14 solute carrier family 39 member 14 29986 SLC39A2 solute carrier family 39 member 2 29985 SLC39A3 solute carrier family 39 member 3 55630 SLC39A4 solute carrier family 39 member 4 283375 SLC39A5 solute carrier family 39 member 5 25800 SLC39A6 solute carrier family 39 member 6 64116 SLC39A8 solute carrier family 39 member 8 29015 SLC43A3 solute carrier family 43 member 3 6646 SOAT1 sterol O-acyltransferase 1 8435 SOAT2 sterol O-acyltransferase 2 9524 TECR trans-2,3-enoyl-CoA reductase 253017 TECRL trans-2,3-enoyl-CoA reductase like 7069 THRSP thyroid hormone responsive 84065 TMEM222 transmembrane protein 222 56063 TMEM234 transmembrane protein 234

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 4.25e-01 1.25e-49 GO zinc ion transmembrane transporter activity molecular_function 4.09e-01 5.60e-10 GO diacylglycerol O-acyltransferase activity molecular_function 2.14e-01 2.60e-42 Reactome Zinc transporters Transport of small molecules 1.60e-01 1.48e-40 GO zinc ion transmembrane transport biological_process 7.03e-02 2.55e-06 GO very-low-density lipoprotein particle assembly biological_process 5.49e-02 7.70e-40 Reactome Metal ion SLC transporters Transport of small molecules 1.75e-02 2.85e-04 GO fatty-acyl-CoA biosynthetic process biological_process 1.38e-02 2.08e-06 Reactome Fatty acyl-CoA biosynthesis Metabolism 1.29e-02 3.48e-04 GO unsaturated fatty acid biosynthetic process biological_process 6.07e-03 4.38e-19 Reactome Zinc efflux and compartmentalization by the SLC30 family Transport of small molecules 5.72e-03 1.29e-24 GO cellular zinc ion homeostasis 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 divalent metal ion transport 0e+00 0e+00 metal ion homeostasis 0e+00 0e+00 cellular zinc ion homeostasis 0e+00 0e+00 cellular metal ion homeostasis 0e+00 0e+00 cellular ion homeostasis 0e+00 0e+00 zinc II ion transport 0e+00 0e+00 cation transmembrane transport 0e+00 0e+00 zinc II ion transmembrane import 0e+00 0e+00 zinc ion homeostasis 0e+00 0e+00 ion homeostasis 0e+00 0e+00 metal ion transport 0e+00 0e+00 zinc II ion transmembrane transport 0e+00 0e+00 cellular cation homeostasis 0e+00 0e+00 response to zinc ion 0e+00 0e+00 regulation of sequestering of zinc ion 0e+00 0e+00 response to metal ion 0e+00 0e+00 response to inorganic substance 0e+00 0e+00 inorganic cation transmembrane transporter activity 0e+00 0e+00 divalent inorganic cation transmembrane transporter activity 0e+00 0e+00 transition metal ion transmembrane transporter 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 TRANSMEMBRANE TRANSPORT OF SMALL MOLECULES 0.00e+00 0.00e+00 SLC MEDIATED TRANSMEMBRANE TRANSPORT 0.00e+00 0.00e+00 ZINC TRANSPORTERS 0.00e+00 0.00e+00 METAL ION SLC TRANSPORTERS 0.00e+00 0.00e+00 TRANSPORT OF GLUCOSE AND OTHER SUGARS BILE SALTS AND ORGANIC ACIDS METAL IONS AND AMINE COMPOUNDS 0.00e+00 0.00e+00 SLC MEDIATED TRANSMEMBRANE TRANSPORT 0.00e+00 0.00e+00 ZINC TRANSPORTERS 0.00e+00 0.00e+00 METAL ION SLC TRANSPORTERS 0.00e+00 0.00e+00 TRANSPORT OF GLUCOSE AND OTHER SUGARS BILE SALTS AND ORGANIC ACIDS METAL IONS AND AMINE COMPOUNDS 6.42e-04 7.98e-02 INSULIN SYNTHESIS AND PROCESSING 1.35e-03 1.31e-01 INSULIN SYNTHESIS AND PROCESSING 3.30e-03 3.25e-01 ION TRANSPORT BY P TYPE ATPASES 3.93e-03 3.74e-01 TRANSPORT OF VITAMINS NUCLEOSIDES AND RELATED MOLECULES 5.94e-03 5.27e-01 ION CHANNEL TRANSPORT 6.89e-03 5.41e-01 TRANSPORT OF VITAMINS NUCLEOSIDES AND RELATED MOLECULES 1.03e-02 8.15e-01 TRIGLYCERIDE BIOSYNTHESIS 1.72e-02 1.00e+00 ION TRANSPORT BY P TYPE ATPASES 2.31e-02 1.00e+00 ION CHANNEL TRANSPORT 3.34e-02 1.00e+00 DIABETES PATHWAYS 4.60e-02 1.00e+00 DIABETES PATHWAYS

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 0.00e+00 0.00e+00 abnormal zinc homeostasis 2.06e-05 7.73e-02 abnormal milk composition 4.04e-05 1.24e-01 Meibomian gland atrophy 5.35e-05 1.50e-01 maternal effect 5.48e-05 1.52e-01 decreased circulating copper level 5.48e-05 1.52e-01 decreased liver copper level 6.16e-05 1.63e-01 abnormal copper level 7.14e-05 1.80e-01 abnormal liver copper level 2.28e-04 3.78e-01 other phenotype 2.46e-04 3.97e-01 scaly skin 2.68e-04 4.19e-01 abnormal cholesterol homeostasis 5.67e-04 6.55e-01 abnormal hair shaft morphology 6.68e-04 7.19e-01 abnormal skin condition 1.56e-03 1.00e+00 decreased susceptibility to hepatic steatosis 1.88e-03 1.00e+00 decreased skin tensile strength 2.35e-03 1.00e+00 abnormal cutaneous collagen fibril morphology 2.44e-03 1.00e+00 abnormal mammary gland growth during lactation 2.83e-03 1.00e+00 curly vibrissae 2.95e-03 1.00e+00 abnormal long bone epiphysis morphology 2.96e-03 1.00e+00 decreased percent body fat

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

²FDR corrected p-value (Benjamini-Hochberg)