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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod284

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod284 Module size 71 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 203102 ADAM32 ADAM metallopeptidase domain 32 64283 ARHGEF28 Rho guanine nucleotide exchange factor 28 55024 BANK1 B cell scaffold protein with ankyrin repeats 1 552900 BOLA2 bolA family member 2 654483 BOLA2B bolA family member 2B 220136 CCDC11 cilia and flagella associated protein 53 256309 CCDC110 coiled-coil domain containing 110 64798 DEPTOR DEP domain containing MTOR interacting protein 84766 EFCAB4B calcium release activated channel regulator 2A 1978 EIF4EBP1 eukaryotic translation initiation factor 4E binding protein 1 8637 EIF4EBP3 eukaryotic translation initiation factor 4E binding protein 3 203259 FAM219A family with sequence similarity 219 member A 2823 GPM6A glycoprotein M6A 165082 GPR113 adhesion G protein-coupled receptor F3 51696 HECA hdc homolog, cell cycle regulator 9454 HOMER3 homer scaffold protein 3 85450 ITPRIP inositol 1,4,5-trisphosphate receptor interacting protein 9711 KIAA0226 RUN and cysteine rich domain containing beclin 1 interacting protein 9764 KIAA0513 KIAA0513 55915 LANCL2 LanC like 2 29995 LMCD1 LIM and cysteine rich domains 1 4033 LRMP lymphoid restricted membrane protein 79109 MAPKAP1 mitogen-activated protein kinase associated protein 1 100911158 MARCKS - 4207 MEF2BNB-MEF2B BORCS8-MEF2B readthrough 64223 MLST8 MTOR associated protein, LST8 homolog 308899 MRVI1 murine retrovirus integration site 1 homolog 2475 MTOR mechanistic target of rapamycin kinase 266680 MYT1 ST18, C2H2C-type zinc finger 200030 NBPF11 NBPF member 11 4900 NRGN neurogranin 84876 ORAI1 ORAI calcium release-activated calcium modulator 1 80228 ORAI2 ORAI calcium release-activated calcium modulator 2 93129 ORAI3 ORAI calcium release-activated calcium modulator 3 5066 PAM peptidylglycine alpha-amidating monooxygenase 55011 PIH1D1 PIH1 domain containing 1 5289 PIK3C3 phosphatidylinositol 3-kinase catalytic subunit type 3 30849 PIK3R4 phosphoinositide-3-kinase regulatory subunit 4 23007 PLCH1 phospholipase C eta 1 9651 PLCH2 phospholipase C eta 2 23228 PLCL2 phospholipase C like 2 25865 PRKD2 protein kinase D2 23683 PRKD3 protein kinase D3 55615 PRR5 proline rich 5 79899 PRR5L proline rich 5 like 79657 RPAP3 RNA polymerase II associated protein 3 57521 RPTOR regulatory associated protein of MTOR complex 1 10670 RRAGA Ras related GTP binding A 10325 RRAGB Ras related GTP binding B 64121 RRAGC Ras related GTP binding C 58528 RRAGD Ras related GTP binding D 6305 SBF1 SET binding factor 1 6786 STIM1 stromal interaction molecule 1 57620 STIM2 stromal interaction molecule 2 81551 STMN4 stathmin 4 51256 TBC1D7 TBC1 domain family member 7 8115 TCL1A T cell leukemia/lymphoma 1A 9894 TELO2 telomere maintenance 2 117145 THEM4 thioesterase superfamily member 4 53373 TPCN1 two pore segment channel 1 219931 TPCN2 two pore segment channel 2 7220 TRPC1 transient receptor potential cation channel subfamily C member 1 7222 TRPC3 transient receptor potential cation channel subfamily C member 3 7223 TRPC4 transient receptor potential cation channel subfamily C member 4 7224 TRPC5 transient receptor potential cation channel subfamily C member 5 7225 TRPC6 transient receptor potential cation channel subfamily C member 6 57113 TRPC7 transient receptor potential cation channel subfamily C member 7 7226 TRPM2 transient receptor potential cation channel subfamily M member 2 7267 TTC3 tetratricopeptide repeat domain 3 9675 TTI1 TELO2 interacting protein 1 22911 WDR47 WD repeat domain 47

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 7.57e-01 8.50e-26 GO store-operated calcium channel activity molecular_function 2.54e-01 5.81e-15 GO TORC2 complex cellular_component 2.47e-01 7.69e-12 GO TORC1 complex cellular_component 2.07e-01 9.16e-11 GO positive regulation of TORC1 signaling biological_process 1.50e-01 2.01e-15 Reactome mTORC1-mediated signalling Signal Transduction 7.85e-02 1.67e-04 GO R2TP complex cellular_component 5.81e-02 1.30e-05 GO negative regulation of translational initiation biological_process 3.86e-02 5.81e-15 GO inositol 1,4,5 trisphosphate binding molecular_function 1.81e-02 1.14e-07 GO regulation of TOR signaling biological_process 1.72e-02 6.04e-04 Reactome Synthesis of PIPs at the late endosome membrane Metabolism 1.64e-02 1.68e-13 Reactome Macroautophagy Cellular responses to external stimuli 1.25e-02 7.24e-04 GO regulation of store-operated calcium entry biological_process 1.05e-02 7.24e-04 GO regulation of protein secretion biological_process 8.76e-03 1.11e-04 GO activation of store-operated calcium channel activity biological_process 7.28e-03 8.99e-05 GO phosphatidylinositol phospholipase C activity molecular_function 1.11e-03 8.53e-04 Reactome RHO GTPases Activate NADPH Oxidases Signal Transduction

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 regulation of TOR signaling 0.00e+00 0.00e+00 calcium ion transport 0.00e+00 0.00e+00 calcium ion transmembrane transport 0.00e+00 0.00e+00 divalent metal ion transport 0.00e+00 0.00e+00 TORC2 complex 0.00e+00 0.00e+00 divalent inorganic cation transmembrane transporter activity 0.00e+00 0.00e+00 calcium channel activity 0.00e+00 0.00e+00 calcium ion transmembrane transporter activity 0.00e+00 0.00e+00 store-operated calcium channel activity 4.15e-12 3.79e-09 TOR signaling 5.12e-12 4.66e-09 manganese ion transport 5.27e-12 4.79e-09 store-operated calcium entry 6.54e-11 3.46e-08 TORC1 complex 9.90e-11 8.22e-08 positive regulation of TOR signaling 3.98e-09 2.73e-06 metal ion transport 4.33e-09 2.08e-06 inositol 1,4,5 trisphosphate binding 6.43e-09 4.28e-06 macroautophagy 2.24e-08 1.39e-05 cation transmembrane transport 1.16e-07 4.41e-05 cation channel activity 2.86e-07 1.50e-04 autophagy

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 2.41e-10 8.44e-08 ELEVATION OF CYTOSOLIC CA2 LEVELS 6.20e-10 2.08e-07 ROLE OF SECOND MESSENGERS IN NETRIN1 SIGNALING 8.98e-10 2.20e-07 ELEVATION OF CYTOSOLIC CA2 LEVELS 2.10e-09 4.92e-07 ROLE OF SECOND MESSENGERS IN NETRIN1 SIGNALING 3.21e-09 9.86e-07 PLATELET CALCIUM HOMEOSTASIS 2.25e-08 4.74e-06 PLATELET CALCIUM HOMEOSTASIS 2.25e-07 5.57e-05 PI3K CASCADE 2.41e-07 4.51e-05 NETRIN1 SIGNALING 5.10e-07 1.20e-04 MTORC1 MEDIATED SIGNALLING 6.15e-07 1.11e-04 PI3K CASCADE 7.19e-07 1.65e-04 NETRIN1 SIGNALING 9.24e-07 1.61e-04 MTORC1 MEDIATED SIGNALLING 9.36e-07 2.13e-04 INSULIN RECEPTOR SIGNALLING CASCADE 1.14e-06 2.56e-04 PLATELET HOMEOSTASIS 1.79e-06 3.00e-04 PLATELET HOMEOSTASIS 2.18e-06 3.60e-04 INSULIN RECEPTOR SIGNALLING CASCADE 2.48e-06 5.21e-04 SIGNALING BY INSULIN RECEPTOR 5.17e-06 8.11e-04 SIGNALING BY INSULIN RECEPTOR 7.29e-06 1.12e-03 CD28 DEPENDENT PI3K AKT SIGNALING 8.62e-06 1.67e-03 CD28 DEPENDENT PI3K AKT SIGNALING

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 1.64e-03 1e+00 abnormal eye physiology 1.78e-03 1e+00 abnormal cell physiology 2.03e-03 1e+00 abnormal platelet activation 3.24e-03 1e+00 abnormal neuron physiology 3.63e-03 1e+00 abnormal B cell physiology 4.01e-03 1e+00 abnormal single cell response 4.38e-03 1e+00 abnormal calcium ion homeostasis 5.78e-03 1e+00 abnormal vascular smooth muscle physiology 6.68e-03 1e+00 abnormal trophoblast giant cells 7.11e-03 1e+00 decreased interferon-gamma secretion 8.50e-03 1e+00 decreased monocyte cell number 9.37e-03 1e+00 pyloric stenosis 1.12e-02 1e+00 thick placenta labyrinth 1.12e-02 1e+00 absent embryonic telencephalon 1.12e-02 1e+00 decreased excitatory postsynaptic current amplitude 1.12e-02 1e+00 liver abscess 1.12e-02 1e+00 decreased platelet calcium level 1.21e-02 1e+00 decreased susceptibility to type I hypersensitivity reaction 1.29e-02 1e+00 increased B cell proliferation 1.31e-02 1e+00 decreased splenocyte apoptosis

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

²FDR corrected p-value (Benjamini-Hochberg)