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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod218

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod218 Module size 40 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 7187 CAP1 TNF receptor associated factor 3 5271 CAP2 serpin family B member 8 140894 CNBD2 cyclic nucleotide binding domain containing 2 285527 FRYL FRY like transcription coactivator 2784 GNB3 G protein subunit beta 3 2811 GP1BA glycoprotein Ib platelet subunit alpha 2812 GP1BB glycoprotein Ib platelet subunit beta 2815 GP9 glycoprotein IX platelet 56261 GPCPD1 glycerophosphocholine phosphodiesterase 1 166647 GPR125 adhesion G protein-coupled receptor A3 57531 HACE1 HECT domain and ankyrin repeat containing E3 ubiquitin protein ligase 1 3483 IGFALS insulin like growth factor binding protein acid labile subunit 285313 IGSF10 immunoglobulin superfamily member 10 79932 KIAA0319L KIAA0319 like 55366 LGR4 leucine rich repeat containing G protein-coupled receptor 4 8549 LGR5 leucine rich repeat containing G protein-coupled receptor 5 59352 LGR6 leucine rich repeat containing G protein-coupled receptor 6 89782 LMLN leishmanolysin like peptidase 121227 LRIG3 leucine rich repeats and immunoglobulin like domains 3 26103 LRIT1 leucine rich repeat, Ig-like and transmembrane domains 1 345193 LRIT3 leucine rich repeat, Ig-like and transmembrane domains 3 122769 LRR1 leucine rich repeat protein 1 54674 LRRN3 leucine rich repeat neuronal 3 90678 LRSAM1 leucine rich repeat and sterile alpha motif containing 1 57721 METTL14 methyltransferase like 14 142678 MIB2 mindbomb E3 ubiquitin protein ligase 2 4603 MYBL1 MYB proto-oncogene like 1 54981 NMRK1 nicotinamide riboside kinase 1 27231 NMRK2 nicotinamide riboside kinase 2 728378 POTEF POTE ankyrin domain family member F 653269 POTEI POTE ankyrin domain family member I 653781 POTEJ POTE ankyrin domain family member J 5573 PRKAR1A protein kinase cAMP-dependent type I regulatory subunit alpha 5575 PRKAR1B protein kinase cAMP-dependent type I regulatory subunit beta 5576 PRKAR2A protein kinase cAMP-dependent type II regulatory subunit alpha 5593 PRKG2 protein kinase cGMP-dependent 2 25930 PTPN23 protein tyrosine phosphatase, non-receptor type 23 54101 RIPK4 receptor interacting serine/threonine kinase 4 7162 TPBG trophoblast glycoprotein 9213 XPR1 xenotropic and polytropic retrovirus receptor 1

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 1.19e-01 4.42e-03 Reactome Hydrolysis of LPE Metabolism 1.10e-01 5.55e-07 GO cAMP-dependent protein kinase complex cellular_component 9.92e-02 1.19e-06 Reactome GP1b-IX-V activation signalling Hemostasis 9.41e-02 5.55e-07 GO negative regulation of cAMP-dependent protein kinase activity biological_process 5.36e-02 1.32e-04 Reactome Role of ABL in ROBO-SLIT signaling Developmental Biology 4.00e-02 2.81e-06 Reactome Platelet Adhesion to exposed collagen Hemostasis 2.81e-02 6.62e-03 GO mRNA (2'-O-methyladenosine-N6-)-methyltransferase activity molecular_function 2.40e-02 8.32e-07 GO cAMP-dependent protein kinase inhibitor activity molecular_function 2.33e-02 1.29e-05 Reactome Regulation of FZD by ubiquitination Signal Transduction 2.20e-02 1.75e-07 GO cAMP binding molecular_function 2.12e-02 7.00e-07 GO activation of adenylate cyclase activity biological_process 1.32e-02 3.10e-04 GO NAD biosynthetic process biological_process 4.57e-03 6.65e-06 GO blood coagulation, intrinsic pathway biological_process 2.70e-03 6.65e-06 Reactome Intrinsic Pathway of Fibrin Clot Formation Hemostasis 1.73e-03 3.10e-04 GO actin polymerization or depolymerization 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 1.02e-08 4.64e-06 cyclic nucleotide binding 2.17e-07 6.96e-05 cAMP-dependent protein kinase complex 2.31e-07 8.30e-05 cAMP binding 6.81e-07 2.23e-04 cAMP-dependent protein kinase regulator activity 9.81e-07 4.66e-04 negative regulation of cAMP-dependent protein kinase activity 1.61e-06 7.36e-04 activation of protein kinase A activity 1.68e-06 7.66e-04 cellular response to glucagon stimulus 3.20e-06 1.38e-03 multicellular organismal homeostasis 3.55e-06 1.52e-03 response to glucagon 3.57e-06 1.02e-03 cAMP-dependent protein kinase inhibitor activity 5.17e-06 2.13e-03 regulation of cAMP-dependent protein kinase activity 6.10e-06 1.66e-03 protein kinase A catalytic subunit binding 8.43e-06 3.32e-03 blood coagulation 8.82e-06 3.46e-03 coagulation 8.97e-06 3.51e-03 wound healing 9.44e-06 3.67e-03 hemostasis 1.34e-05 3.40e-03 protein kinase inhibitor activity 1.57e-05 3.94e-03 kinase inhibitor activity 2.24e-05 7.94e-03 blood coagulation, intrinsic pathway 2.42e-05 8.49e-03 response to wounding

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 7.63e-06 1.49e-03 INTRINSIC PATHWAY 1.86e-05 3.38e-03 PLATELET ADHESION TO EXPOSED COLLAGEN 3.16e-05 4.37e-03 PLATELET ADHESION TO EXPOSED COLLAGEN 4.30e-05 7.31e-03 GLUCAGON SIGNALING IN METABOLIC REGULATION 4.35e-05 5.88e-03 INTRINSIC PATHWAY 5.47e-05 7.31e-03 GLUCAGON SIGNALING IN METABOLIC REGULATION 6.19e-05 1.01e-02 FORMATION OF FIBRIN CLOT CLOTTING CASCADE 7.32e-05 1.17e-02 REGULATION OF INSULIN SECRETION BY GLUCAGON LIKE PEPTIDE1 7.34e-05 1.18e-02 REGULATION OF WATER BALANCE BY RENAL AQUAPORINS 9.16e-05 1.43e-02 AQUAPORIN MEDIATED TRANSPORT 1.06e-04 1.34e-02 REGULATION OF WATER BALANCE BY RENAL AQUAPORINS 1.10e-04 1.39e-02 REGULATION OF INSULIN SECRETION BY GLUCAGON LIKE PEPTIDE1 1.52e-04 1.85e-02 FORMATION OF FIBRIN CLOT CLOTTING CASCADE 1.66e-04 2.01e-02 AQUAPORIN MEDIATED TRANSPORT 1.69e-04 2.48e-02 PKA MEDIATED PHOSPHORYLATION OF CREB 1.92e-04 2.28e-02 PKA MEDIATED PHOSPHORYLATION OF CREB 2.81e-04 3.87e-02 DARPP 32 EVENTS 2.93e-04 3.36e-02 DARPP 32 EVENTS 4.10e-04 4.54e-02 PLATELET AGGREGATION PLUG FORMATION 4.77e-04 6.17e-02 REGULATION OF INSULIN SECRETION

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 2.06e-04 3.55e-01 increased mean platelet volume 4.31e-04 5.55e-01 abnormal testis morphology 1.71e-03 1.00e+00 thin retinal inner nuclear layer 2.22e-03 1.00e+00 thrombocytopenia 3.77e-03 1.00e+00 abnormal rete testis morphology 5.61e-03 1.00e+00 decreased axial mesoderm size 5.64e-03 1.00e+00 epididymis hypoplasia 5.64e-03 1.00e+00 abnormal nephron morphology 7.49e-03 1.00e+00 abnormal testis weight 7.50e-03 1.00e+00 dilated rete testis 7.50e-03 1.00e+00 small caput epididymis 7.52e-03 1.00e+00 abnormal metanephric ureteric bud development 7.52e-03 1.00e+00 iris stroma hypoplasia 9.06e-03 1.00e+00 small seminiferous tubules 9.36e-03 1.00e+00 abnormal efferent ductules of testis morphology 9.37e-03 1.00e+00 increased thyroid tumor incidence 9.37e-03 1.00e+00 small metanephros 9.38e-03 1.00e+00 decreased posterior semicircular canal size 1.12e-02 1.00e+00 corneal deposits 1.12e-02 1.00e+00 hypoplastic trabecular meshwork

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

²FDR corrected p-value (Benjamini-Hochberg)