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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod335

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod335 Module size 39 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 55331 ACER3 alkaline ceramidase 3 26060 APPL1 adaptor protein, phosphotyrosine interacting with PH domain and leucine zipper 1 22899 ARHGEF15 Rho guanine nucleotide exchange factor 15 128272 ARHGEF19 Rho guanine nucleotide exchange factor 19 26084 ARHGEF26 Rho guanine nucleotide exchange factor 26 445328 ARHGEF35 Rho guanine nucleotide exchange factor 35 10423 CDIPT CDP-diacylglycerol--inositol 3-phosphatidyltransferase 10087 COL4A3BP collagen type IV alpha 3 binding protein 11117 EMILIN1 elastin microfibril interfacer 1 84034 EMILIN2 elastin microfibril interfacer 2 51059 FAM135B family with sequence similarity 135 member B 79567 FAM65A RHO family interacting cell polarization regulator 1 151393 FAM82A1 regulator of microtubule dynamics 2 51477 ISYNA1 inositol-3-phosphate synthase 1 56947 MFF mitochondrial fission factor 64598 MOSPD3 motile sperm domain containing 3 54545 MTMR12 myotubularin related protein 12 5007 OSBP oxysterol binding protein 23762 OSBP2 oxysterol binding protein 2 9885 OSBPL2 oxysterol binding protein like 2 26031 OSBPL3 oxysterol binding protein like 3 114880 OSBPL6 oxysterol binding protein like 6 114881 OSBPL7 oxysterol binding protein like 7 9489 PGS1 phosphatidylglycerophosphate synthase 1 5298 PI4KB phosphatidylinositol 4-kinase beta 200576 PIKFYVE phosphoinositide kinase, FYVE-type zinc finger containing 201164 PLD6 phospholipase D family member 6 65977 PLEKHA3 pleckstrin homology domain containing A3 84725 PLEKHA8 pleckstrin homology domain containing A8 647286 RD3L retinal degeneration 3 like 22908 SACM1L SAC1 like phosphatidylinositide phosphatase 300147 SBF2 SET binding factor 1 126669 SHE Src homology 2 domain containing E 10948 STARD3 StAR related lipid transfer domain containing 3 83930 STARD3NL STARD3 N-terminal like 9238 TBRG4 transforming growth factor beta regulator 4 23731 TMEM245 transmembrane protein 245 9218 VAPA VAMP associated protein A 9217 VAPB VAMP associated protein B and C

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 2.46e-01 3.46e-14 GO sterol binding molecular_function 1.65e-01 3.94e-07 GO intermembrane lipid transfer biological_process 9.31e-02 6.62e-11 GO perinuclear endoplasmic reticulum cellular_component 8.02e-02 7.94e-05 GO extracellular matrix constituent conferring elasticity molecular_function 5.91e-02 1.06e-04 Reactome Synthesis of PG Metabolism 5.20e-02 1.06e-04 GO phosphatase regulator activity molecular_function 3.30e-02 1.12e-13 GO sterol transporter activity molecular_function 3.08e-02 3.15e-11 GO phosphatidylinositol biosynthetic process biological_process 1.70e-02 5.67e-06 Reactome Synthesis of PIPs at the Golgi membrane Metabolism 1.12e-02 1.11e-06 Reactome Sphingolipid de novo biosynthesis Metabolism 1.08e-02 2.24e-12 GO cholesterol binding molecular_function 7.75e-03 2.48e-04 GO C21-steroid hormone biosynthetic process biological_process 3.57e-03 2.48e-04 Reactome Pregnenolone biosynthesis 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 0.00e+00 0.00e+00 lipid biosynthetic process 1.87e-11 1.21e-08 sterol binding 7.26e-11 4.49e-08 sterol transporter activity 4.15e-10 2.35e-07 alcohol binding 4.67e-10 2.62e-07 lipid transporter activity 5.65e-10 3.12e-07 steroid binding 7.32e-10 5.54e-07 lipid transport 9.00e-10 4.82e-07 cholesterol binding 1.25e-09 6.53e-07 lipid binding 1.33e-09 9.74e-07 lipid localization 1.99e-09 1.43e-06 sterol transport 6.46e-09 4.30e-06 bile acid biosynthetic process 7.36e-09 4.86e-06 steroid biosynthetic process 2.19e-08 1.36e-05 bile acid metabolic process 4.85e-08 2.88e-05 phospholipid biosynthetic process 1.72e-07 9.32e-05 phosphatidylinositol biosynthetic process 2.38e-07 1.26e-04 glycerophospholipid biosynthetic process 2.72e-07 1.43e-04 steroid metabolic process 7.49e-07 3.65e-04 phospholipid metabolic process 1.69e-06 7.69e-04 phosphatidylinositol metabolic 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 PHOSPHOLIPID METABOLISM 0.00e+00 0.00e+00 PHOSPHOLIPID METABOLISM 3.42e-08 9.36e-06 SPHINGOLIPID DE NOVO BIOSYNTHESIS 5.62e-07 1.02e-04 SPHINGOLIPID DE NOVO BIOSYNTHESIS 7.58e-07 1.74e-04 SPHINGOLIPID METABOLISM 6.25e-06 1.24e-03 SYNTHESIS OF PIPS AT THE GOLGI MEMBRANE 1.07e-05 1.59e-03 SPHINGOLIPID METABOLISM 1.22e-05 1.79e-03 SYNTHESIS OF PIPS AT THE GOLGI MEMBRANE 7.99e-05 1.27e-02 PI METABOLISM 3.42e-04 3.85e-02 PI METABOLISM 7.10e-04 8.70e-02 GLYCEROPHOSPHOLIPID BIOSYNTHESIS 7.29e-04 7.56e-02 GLYCEROPHOSPHOLIPID BIOSYNTHESIS 8.43e-03 7.00e-01 ROLE OF DCC IN REGULATING APOPTOSIS 1.08e-02 7.78e-01 SYNTHESIS OF PIPS AT THE EARLY ENDOSOME MEMBRANE 1.38e-02 1.00e+00 REGULATION OF APOPTOSIS 1.39e-02 9.57e-01 SYNTHESIS OF PIPS AT THE LATE ENDOSOME MEMBRANE 1.68e-02 1.00e+00 SYNTHESIS OF PIPS AT THE LATE ENDOSOME MEMBRANE 2.35e-02 1.00e+00 SYNTHESIS OF PIPS AT THE EARLY ENDOSOME MEMBRANE 2.99e-02 1.00e+00 ROLE OF DCC IN REGULATING APOPTOSIS 3.67e-02 1.00e+00 REGULATION OF APOPTOSIS

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 7.47e-04 7.62e-01 dilated heart right ventricle 1.50e-03 1.00e+00 thin ventricular wall 1.87e-03 1.00e+00 abnormal ventricle myocardium morphology 3.74e-03 1.00e+00 abnormal atrium myocardium morphology 3.74e-03 1.00e+00 abnormal pulmonary trunk morphology 3.74e-03 1.00e+00 neuronal cytoplasmic inclusions 5.61e-03 1.00e+00 abnormal pulmonary alveolar system morphology 5.61e-03 1.00e+00 abnormal heart right ventricle outflow tract morphology 7.47e-03 1.00e+00 absent sperm mitochondrial sheath 7.48e-03 1.00e+00 enlarged heart right atrium 9.34e-03 1.00e+00 increased heart ventricle size 9.34e-03 1.00e+00 hypotonia 9.35e-03 1.00e+00 skeletal muscle fiber atrophy 1.03e-02 1.00e+00 abnormal heart morphology 1.12e-02 1.00e+00 abnormal cerebellum deep nucleus morphology 1.12e-02 1.00e+00 abnormal blastocoele morphology 1.12e-02 1.00e+00 abnormal pons morphology 1.28e-02 1.00e+00 increased liver cholesterol level 1.30e-02 1.00e+00 abnormal aorta elastic tissue morphology 1.31e-02 1.00e+00 abnormal trophectoderm morphology

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

²FDR corrected p-value (Benjamini-Hochberg)