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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod376

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod376 Module size 32 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 27236 ARFIP1 ADP ribosylation factor interacting protein 1 23621 BACE1 beta-secretase 1 8678 BECN1 beclin 1 79839 CCDC102B coiled-coil domain containing 102B 80157 CWH43 cell wall biogenesis 43 C-terminal homolog 79901 CYBRD1 cytochrome b reductase 1 23259 DDHD2 DDHD domain containing 2 10059 DNM1L dynamin 1 like 79180 EFHD2 EF-hand domain family member D2 57795 FAM5B BMP/retinoic acid inducible neural specific 2 54874 FNBP1L formin binding protein 1 like 9648 GCC2 GRIP and coiled-coil domain containing 2 84514 GHDC GH3 domain containing 2764 GMFB glia maturation factor beta 64083 GOLPH3 golgi phosphoprotein 3 2822 GPLD1 glycosylphosphatidylinositol specific phospholipase D1 55196 KIAA1551 KIAA1551 3881 KRT31 keratin 31 3885 KRT34 keratin 34 3916 LAMP1 lysosomal associated membrane protein 1 83876 MRO maestro 4599 MX1 MX dynamin like GTPase 1 27315 PGAP2 post-GPI attachment to proteins 2 6271 S100A1 S100 calcium binding protein A1 80851 SH3BP5L SH3 binding domain protein 5 like 56907 SPIRE1 spire type actin nucleation factor 1 8987 STBD1 starch binding domain 1 11075 STMN2 stathmin 2 171024 SYNPO2 synaptopodin 2 25851 TECPR1 tectonin beta-propeller repeat containing 1 391123 VSIG8 V-set and immunoglobulin domain containing 8 124220 ZG16B zymogen granule protein 16B

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 2.10e-02 1.20e-04 GO Golgi ribbon formation biological_process 1.34e-02 1.44e-04 GO amyloid-beta metabolic 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 2.37e-05 8.34e-03 GPI anchor metabolic process 1.67e-04 4.51e-02 membrane invagination 1.89e-04 5.00e-02 dynamin family protein polymerization involved in mitochondrial fission 2.36e-04 6.02e-02 Golgi ribbon formation 3.08e-04 5.52e-02 phosphatidylinositol-4-phosphate binding 3.09e-04 5.30e-02 trans-Golgi network 4.74e-04 1.07e-01 membrane fission 5.28e-04 1.17e-01 post-Golgi vesicle-mediated transport 5.48e-04 1.21e-01 beta-amyloid metabolic process 6.06e-04 1.31e-01 positive regulation of mitochondrial fission 6.94e-04 1.46e-01 regulation of supramolecular fiber organization 8.87e-04 1.79e-01 regulation of Arp2/3 complex-mediated actin nucleation 8.97e-04 1.40e-01 phosphatidylinositol phosphate binding 9.80e-04 1.94e-01 mitochondrial fission 9.99e-04 1.97e-01 glycolipid metabolic process 1.07e-03 2.08e-01 Golgi to plasma membrane protein transport 1.22e-03 2.32e-01 protein lipidation 1.25e-03 2.37e-01 regulation of mitochondrial fission 1.25e-03 2.37e-01 GPI anchor biosynthetic process 1.44e-03 2.66e-01 protein localization to Golgi apparatus

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 4.89e-03 4.03e-01 ANTIVIRAL MECHANISM BY IFN STIMULATED GENES 7.53e-03 6.38e-01 IRON UPTAKE AND TRANSPORT 1.50e-02 1.00e+00 ANTIVIRAL MECHANISM BY IFN STIMULATED GENES 1.70e-02 1.00e+00 APOPTOTIC EXECUTION PHASE 1.85e-02 1.00e+00 IRON UPTAKE AND TRANSPORT 2.53e-02 1.00e+00 APOPTOTIC EXECUTION PHASE 2.77e-02 1.00e+00 APOPTOSIS 2.88e-02 1.00e+00 INTERFERON ALPHA BETA SIGNALING 3.09e-02 1.00e+00 APOPTOSIS 3.45e-02 1.00e+00 INTERFERON ALPHA BETA SIGNALING 3.89e-02 1.00e+00 INTERFERON SIGNALING 4.41e-02 1.00e+00 CYTOKINE SIGNALING IN IMMUNE SYSTEM

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 1.37e-03 1e+00 abnormal autophagy 3.74e-03 1e+00 increased plasmacytoma incidence 3.74e-03 1e+00 increased follicular lymphoma incidence 4.24e-03 1e+00 impaired balance 4.53e-03 1e+00 abnormal muscle physiology 5.61e-03 1e+00 visceral vascular congestion 5.61e-03 1e+00 absent fibroblast proliferation 5.61e-03 1e+00 abnormal heart ventricle pressure 5.61e-03 1e+00 delayed hepatic development 5.61e-03 1e+00 tachypnea 5.61e-03 1e+00 decreased muscle spindle number 6.11e-03 1e+00 decreased anxiety-related response 7.47e-03 1e+00 pleural effusion 7.47e-03 1e+00 ascites 7.48e-03 1e+00 abnormal pilomotor reflex 9.33e-03 1e+00 absent trophoblast giant cells 9.33e-03 1e+00 abnormal muscle spindle morphology 9.33e-03 1e+00 absent amniotic folds 9.34e-03 1e+00 increased left ventricle diastolic pressure 9.35e-03 1e+00 increased lung carcinoma incidence

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

²FDR corrected p-value (Benjamini-Hochberg)