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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod196

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod196 Module size 41 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 84696 ABHD1 abhydrolase domain containing 1 55347 ABHD10 abhydrolase domain containing 10 83451 ABHD11 abhydrolase domain containing 11 25864 ABHD14A abhydrolase domain containing 14A 84836 ABHD14B abhydrolase domain containing 14B 11057 ABHD2 abhydrolase domain containing 2 171586 ABHD3 abhydrolase domain containing 3 63874 ABHD4 abhydrolase domain containing 4 51099 ABHD5 abhydrolase domain containing 5 211 ALAS1 5'-aminolevulinate synthase 1 212 ALAS2 5'-aminolevulinate synthase 2 670 BPHL biphenyl hydrolase like 54980 C2orf42 chromosome 2 open reading frame 42 64834 ELOVL1 ELOVL fatty acid elongase 1 79993 ELOVL7 ELOVL fatty acid elongase 7 3995 FADS3 fatty acid desaturase 3 23464 GCAT glycine C-acetyltransferase 3988 LIPA lipase A, lysosomal acid type 142910 LIPJ lipase family member J 643414 LIPK lipase family member K 340654 LIPM lipase family member M 643418 LIPN lipase family member N 348938 NIPAL4 NIPA like domain containing 4 94101 ORMDL1 ORMDL sphingolipid biosynthesis regulator 1 29095 ORMDL2 ORMDL sphingolipid biosynthesis regulator 2 94103 ORMDL3 ORMDL sphingolipid biosynthesis regulator 3 57645 POGK pogo transposable element derived with KRAB domain 253190 SERHL2 serine hydrolase like 2 8034 SLC25A16 solute carrier family 25 member 16 11001 SLC27A2 solute carrier family 27 member 2 11000 SLC27A3 solute carrier family 27 member 3 10999 SLC27A4 solute carrier family 27 member 4 10998 SLC27A5 solute carrier family 27 member 5 28965 SLC27A6 solute carrier family 27 member 6 10558 SPTLC1 serine palmitoyltransferase long chain base subunit 1 9517 SPTLC2 serine palmitoyltransferase long chain base subunit 2 55304 SPTLC3 serine palmitoyltransferase long chain base subunit 3 171546 SPTSSA serine palmitoyltransferase small subunit A 165679 SPTSSB serine palmitoyltransferase small subunit B 81789 TIGD6 tigger transposable element derived 6 51114 ZDHHC9 zinc finger DHHC-type containing 9

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 7.04e-01 3.03e-14 GO serine C-palmitoyltransferase activity molecular_function 3.00e-01 4.80e-19 GO lipase activity molecular_function 2.08e-01 7.57e-12 GO very long-chain fatty acid-CoA ligase activity molecular_function 1.52e-01 6.96e-18 GO cellular lipid metabolic process biological_process 1.34e-01 2.37e-11 GO long-chain fatty acid transporter activity molecular_function 3.38e-02 2.94e-07 GO lipoprotein lipase activity molecular_function 3.02e-02 3.85e-11 GO long-chain fatty acid-CoA ligase activity molecular_function 2.97e-02 9.41e-06 GO ceramide metabolic process biological_process 2.56e-02 8.91e-05 GO fatty acid elongation, saturated fatty acid biological_process 2.41e-02 8.91e-05 GO fatty acid elongation, polyunsaturated fatty acid biological_process 2.16e-02 2.32e-04 Reactome Heme biosynthesis Metabolism 1.95e-02 8.91e-05 GO fatty acid elongase activity molecular_function 1.68e-02 8.91e-05 GO fatty acid elongation, monounsaturated fatty acid 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 serine C-palmitoyltransferase complex 0.00e+00 0.00e+00 palmitoyltransferase complex 0.00e+00 0.00e+00 carboxylic ester hydrolase activity 0.00e+00 0.00e+00 transferase activity, transferring acyl groups 5.21e-12 3.52e-09 serine C-palmitoyltransferase activity 1.07e-11 9.61e-09 sphingolipid metabolic process 1.31e-10 1.07e-07 very long-chain fatty acid metabolic process 1.84e-10 1.49e-07 lipid biosynthetic process 2.04e-10 1.64e-07 ceramide metabolic process 2.33e-10 1.86e-07 membrane lipid metabolic process 4.70e-10 2.63e-07 very long-chain fatty acid-CoA ligase activity 8.07e-10 3.68e-07 SPOTS complex 1.95e-09 1.40e-06 lipid catabolic process 2.44e-09 1.22e-06 palmitoyltransferase activity 3.11e-09 1.53e-06 lipase activity 3.40e-09 1.66e-06 long-chain fatty acid-CoA ligase activity 4.00e-09 2.74e-06 fatty acid metabolic process 1.25e-08 5.61e-06 fatty acid ligase activity 2.05e-08 8.90e-06 pyridoxal phosphate binding 2.15e-08 1.34e-05 sphingolipid biosynthetic process

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 1.72e-04 2.07e-02 SYNTHESIS OF BILE ACIDS AND BILE SALTS VIA 24 HYDROXYCHOLESTEROL 1.76e-04 2.57e-02 SYNTHESIS OF BILE ACIDS AND BILE SALTS VIA 24 HYDROXYCHOLESTEROL 3.64e-04 4.86e-02 SYNTHESIS OF BILE ACIDS AND BILE SALTS VIA 7ALPHA HYDROXYCHOLESTEROL 3.74e-04 4.18e-02 METABOLISM OF PORPHYRINS 4.15e-04 5.47e-02 METABOLISM OF PORPHYRINS 6.72e-04 8.32e-02 SYNTHESIS OF BILE ACIDS AND BILE SALTS 7.06e-04 7.35e-02 SYNTHESIS OF BILE ACIDS AND BILE SALTS VIA 7ALPHA HYDROXYCHOLESTEROL 7.73e-04 7.97e-02 SYNTHESIS OF VERY LONG CHAIN FATTY ACYL COAS 8.90e-04 1.06e-01 SYNTHESIS OF VERY LONG CHAIN FATTY ACYL COAS 9.73e-04 1.15e-01 FATTY ACYL COA BIOSYNTHESIS 9.91e-04 1.00e-01 SYNTHESIS OF BILE ACIDS AND BILE SALTS 1.14e-03 1.32e-01 BILE ACID AND BILE SALT METABOLISM 1.35e-03 1.31e-01 FATTY ACYL COA BIOSYNTHESIS 2.25e-03 2.06e-01 BILE ACID AND BILE SALT METABOLISM 2.41e-03 2.50e-01 VITAMIN B5 PANTOTHENATE METABOLISM 2.48e-03 2.25e-01 SPHINGOLIPID DE NOVO BIOSYNTHESIS 2.50e-03 2.58e-01 TRANSPORT OF VITAMINS NUCLEOSIDES AND RELATED MOLECULES 3.78e-03 3.63e-01 TRIGLYCERIDE BIOSYNTHESIS 3.90e-03 3.32e-01 TRANSPORT OF VITAMINS NUCLEOSIDES AND RELATED MOLECULES 4.13e-03 3.91e-01 HORMONE SENSITIVE LIPASE HSL MEDIATED TRIACYLGLYCEROL HYDROLYSIS

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 1.14e-07 1.55e-03 abnormal lipid level 6.83e-05 1.76e-01 impaired skin barrier function 9.09e-05 2.12e-01 abnormal skin appearance 3.43e-04 4.86e-01 decreased fatty acid level 3.81e-04 5.19e-01 shiny skin 4.91e-04 6.00e-01 abnormal circulating lipid level 8.76e-04 8.35e-01 abnormal skin physiology 1.29e-03 1.00e+00 decreased epididymal fat pad weight 3.23e-03 1.00e+00 increased liver triglyceride level 3.48e-03 1.00e+00 hyperkeratosis 5.62e-03 1.00e+00 decreased triglyceride lipase activity 7.48e-03 1.00e+00 abnormal interscapular fat pad morphology 7.49e-03 1.00e+00 epidermis stratum spinosum hyperplasia 7.51e-03 1.00e+00 abnormal white fat cell size 7.51e-03 1.00e+00 increased brown fat cell lipid droplet size 9.19e-03 1.00e+00 decreased birth weight 9.35e-03 1.00e+00 abnormal sphingomyelin level 1.01e-02 1.00e+00 abnormal hepatocyte morphology 1.12e-02 1.00e+00 abnormal ceramide level 1.12e-02 1.00e+00 abnormal epidermal lamellar body morphology

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

²FDR corrected p-value (Benjamini-Hochberg)