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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod178

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod178 Module size 34 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 54 ACP5 acid phosphatase 5, tartrate resistant 55750 AGK acylglycerol kinase 144233 BCDIN3D BCDIN3 domain containing RNA methyltransferase 375298 CERKL ceramide kinase like 54898 ELOVL2 ELOVL fatty acid elongase 2 6785 ELOVL4 ELOVL fatty acid elongase 4 60481 ELOVL5 ELOVL fatty acid elongase 5 9514 GAL3ST1 galactose-3-O-sulfotransferase 1 2629 GBA glucosylceramidase beta 2531 KDSR 3-ketodihydrosphingosine reductase 51162 NEU1 EGF like domain multiple 7 4759 NEU2 neuraminidase 2 10825 NEU3 neuraminidase 3 129807 NEU4 neuraminidase 4 196051 PPAPDC1A phospholipid phosphatase 4 84513 PPAPDC1B phospholipid phosphatase 5 5973 RENBP renin binding protein 8879 SGPL1 sphingosine-1-phosphate lyase 1 54414 SIAE sialic acid acetylesterase 6568 SLC17A1 solute carrier family 17 member 1 6569 SLC17A2 solute carrier family 34 member 1 10050 SLC17A4 solute carrier family 17 member 4 26503 SLC17A5 solute carrier family 17 member 5 57084 SLC17A6 solute carrier family 17 member 6 246213 SLC17A8 solute carrier family 17 member 8 63910 SLC17A9 solute carrier family 17 member 9 219855 SLC37A2 solute carrier family 37 member 2 84255 SLC37A3 solute carrier family 37 member 3 6609 SMPD1 sphingomyelin phosphodiesterase 1 80309 SPHKAP SPHK1 interactor, AKAP domain containing 55314 TMEM144 transmembrane protein 144 25963 TMEM87A transmembrane protein 87A 84910 TMEM87B transmembrane protein 87B 7357 UGCG UDP-glucose ceramide glucosyltransferase

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 3.69e-01 1.30e-10 GO exo-alpha-sialidase activity molecular_function 2.05e-01 1.09e-09 GO sialic acid transmembrane transporter activity molecular_function 1.75e-01 1.81e-09 Reactome Organic anion transporters Transport of small molecules 5.71e-02 1.85e-07 GO fatty acid elongation, polyunsaturated fatty acid biological_process 5.58e-02 1.85e-07 GO fatty acid elongase activity molecular_function 5.54e-02 1.85e-07 GO fatty acid elongation, saturated fatty acid biological_process 5.45e-02 1.85e-07 GO fatty acid elongation, monounsaturated fatty acid biological_process 4.88e-02 6.58e-05 GO glucose-6-phosphate transport biological_process 4.48e-02 4.25e-09 GO oligosaccharide catabolic process biological_process 1.21e-02 2.37e-14 Reactome Sphingolipid metabolism Metabolism 8.32e-03 2.93e-06 GO phosphate ion transmembrane transport biological_process 7.48e-03 1.54e-12 Reactome Glycosphingolipid metabolism Metabolism 2.36e-03 3.97e-10 GO sphingolipid biosynthetic process biological_process 6.06e-04 1.35e-05 GO ceramide biosynthetic process 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 membrane lipid metabolic process 0.00e+00 0.00e+00 sphingolipid metabolic process 0.00e+00 0.00e+00 sphingolipid biosynthetic process 0.00e+00 0.00e+00 glycosphingolipid metabolic process 0.00e+00 0.00e+00 ceramide metabolic process 0.00e+00 0.00e+00 sphingolipid catabolic process 0.00e+00 0.00e+00 membrane lipid catabolic process 5.12e-11 4.38e-08 glycosphingolipid catabolic process 7.92e-11 6.63e-08 glycolipid catabolic process 1.38e-10 1.13e-07 ceramide catabolic process 6.13e-10 4.69e-07 glycolipid metabolic process 6.69e-10 5.09e-07 phosphate ion transmembrane transport 1.07e-09 5.66e-07 phosphate ion transmembrane transporter activity 1.08e-09 8.02e-07 phosphate ion transport 1.35e-09 9.88e-07 ganglioside catabolic process 4.25e-09 2.05e-06 exo-alpha-(2->6)-sialidase activity 4.25e-09 2.05e-06 exo-alpha-(2->8)-sialidase activity 4.25e-09 2.05e-06 exo-alpha-(2->3)-sialidase activity 1.09e-08 7.06e-06 lipid biosynthetic process 1.81e-08 1.14e-05 oligosaccharide catabolic 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 SPHINGOLIPID METABOLISM 0.00e+00 0.00e+00 GLYCOSPHINGOLIPID METABOLISM 1.60e-11 4.64e-09 SPHINGOLIPID METABOLISM 3.63e-11 1.03e-08 GLYCOSPHINGOLIPID METABOLISM 2.01e-09 6.37e-07 PHOSPHOLIPID METABOLISM 2.25e-08 4.74e-06 PHOSPHOLIPID METABOLISM 2.17e-06 3.58e-04 SYNTHESIS OF VERY LONG CHAIN FATTY ACYL COAS 6.08e-06 9.42e-04 FATTY ACYL COA BIOSYNTHESIS 1.93e-05 2.76e-03 AMINO ACID AND OLIGOPEPTIDE SLC TRANSPORTERS 2.54e-05 3.57e-03 TRANSPORT OF INORGANIC CATIONS ANIONS AND AMINO ACIDS OLIGOPEPTIDES 3.61e-05 6.23e-03 SYNTHESIS OF VERY LONG CHAIN FATTY ACYL COAS 6.41e-05 1.04e-02 AMINO ACID AND OLIGOPEPTIDE SLC TRANSPORTERS 7.22e-05 1.16e-02 FATTY ACYL COA BIOSYNTHESIS 1.05e-04 1.33e-02 TRIGLYCERIDE BIOSYNTHESIS 2.26e-04 3.20e-02 TRANSPORT OF INORGANIC CATIONS ANIONS AND AMINO ACIDS OLIGOPEPTIDES 5.08e-04 5.51e-02 ALPHA LINOLENIC ACID ALA METABOLISM 5.98e-04 7.54e-02 TRIGLYCERIDE BIOSYNTHESIS 7.47e-04 9.11e-02 ALPHA LINOLENIC ACID ALA METABOLISM 6.56e-03 5.19e-01 SLC MEDIATED TRANSMEMBRANE TRANSPORT 7.69e-03 6.50e-01 SPHINGOLIPID DE NOVO BIOSYNTHESIS

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 2.70e-03 1e+00 tremors 2.94e-03 1e+00 reddish skin 3.89e-03 1e+00 abnormal choroid plexus morphology 5.61e-03 1e+00 increased unsaturated fatty acid level 5.96e-03 1e+00 perinatal lethality 7.38e-03 1e+00 decreased fetal weight 7.48e-03 1e+00 abnormal urothelium morphology 7.49e-03 1e+00 decreased secondary ovarian follicle number 7.75e-03 1e+00 abnormal skin condition 9.85e-03 1e+00 teratozoospermia 1.12e-02 1e+00 absent cochlear nerve compound action potential 1.12e-02 1e+00 increased ectoderm apoptosis 1.12e-02 1e+00 limp posture 1.26e-02 1e+00 hyperkeratosis 1.31e-02 1e+00 abnormal synaptic acetylcholine release 1.31e-02 1e+00 alpha-synuclein inclusion body 1.31e-02 1e+00 abnormal paranode morphology 1.49e-02 1e+00 decreased synaptic glutamate release 1.49e-02 1e+00 increased macrophage derived foam cell number 1.49e-02 1e+00 decreased skin turgor

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

²FDR corrected p-value (Benjamini-Hochberg)