Back to main page

DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod282

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod282 Module size 50 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 26090 ABHD12 abhydrolase domain containing 12 11215 AKAP11 A-kinase anchoring protein 11 9495 AKAP5 A-kinase anchoring protein 5 8996 ARC nucleolar protein 3 55971 BAIAP2L1 BAI1 associated protein 2 like 1 40 BNC1 acid sensing ion channel subunit 2 79098 C1orf116 chromosome 1 open reading frame 116 57685 CACHD1 cache domain containing 1 55799 CACNA2D3 calcium voltage-gated channel auxiliary subunit alpha2delta 3 816 CAMK2B calcium/calmodulin dependent protein kinase II beta 817 CAMK2D calcium/calmodulin dependent protein kinase II delta 94032 CAMK2N2 calcium/calmodulin dependent protein kinase II inhibitor 2 140706 CCM2L CCM2 like scaffold protein 9419 CRIPT CXXC repeat containing interactor of PDZ3 domain 10522 DEAF1 DEAF1 transcription factor 1739 DLG1 discs large MAGUK scaffold protein 1 4355 DLG2 membrane palmitoylated protein 2 4356 DLG3 membrane palmitoylated protein 3 3996 DLG4 LLGL1, scribble cell polarity complex component 9229 DLGAP1 DLG associated protein 1 58512 DLGAP3 DLG associated protein 3 2009 EML1 echinoderm microtubule associated protein like 1 2036 EPB41L1 erythrocyte membrane protein band 4.1 like 1 2059 EPS8 epidermal growth factor receptor pathway substrate 8 221061 FAM171A1 family with sequence similarity 171 member A1 284069 FAM171A2 family with sequence similarity 171 member A2 286151 FBXO43 F-box protein 43 10691 GMEB1 glucocorticoid modulatory element binding protein 1 26205 GMEB2 glucocorticoid modulatory element binding protein 2 221395 GPR116 adhesion G protein-coupled receptor F5 56850 GRIPAP1 GRIP1 associated protein 1 9456 HOMER1 homer scaffold protein 1 3779 KCNMB1 potassium calcium-activated channel subfamily M regulatory beta subunit 1 27094 KCNMB2 potassium calcium-activated channel subfamily M regulatory beta subunit 3 27345 KCNMB4 potassium calcium-activated channel subfamily M regulatory beta subunit 4 23506 KIAA0240 BRD4 interacting chromatin remodeling complex associated protein like 337974 KRTAP19-7 keratin associated protein 19-7 80059 LRRTM4 leucine rich repeat transmembrane neuronal 4 63974 NEUROD6 neuronal differentiation 6 9463 PICK1 protein interacting with PRKCA 1 55012 PPP2R3C protein phosphatase 2 regulatory subunit B''gamma 2185 PTK2B protein tyrosine kinase 2 beta 10235 RASGRP2 RAS guanyl releasing protein 2 11341 SCRG1 stimulator of chondrogenesis 1 6386 SDCBP syndecan binding protein 50944 SHANK1 SH3 and multiple ankyrin repeat domains 1 6531 SLC6A3 solute carrier family 6 member 3 6546 SLC8A1 solute carrier family 8 member A1 8831 SYNGAP1 synaptic Ras GTPase activating protein 1 10206 TRIM13 tripartite motif containing 13

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 1.31e-01 1.30e-06 Reactome Ca2+ activated K+ channels Neuronal System 9.34e-02 1.72e-10 GO ionotropic glutamate receptor complex cellular_component 8.81e-02 7.78e-09 GO GDP metabolic process biological_process 7.83e-02 5.45e-07 Reactome NrCAM interactions Developmental Biology 5.69e-02 1.63e-14 Reactome Neurexins and neuroligins Neuronal System 5.37e-02 8.55e-13 Reactome Glutamate binding, activation of AMPA receptors and synaptic plasticity Neuronal System 5.22e-02 8.55e-13 Reactome Trafficking of AMPA receptors Neuronal System 4.76e-02 4.39e-11 GO receptor clustering biological_process 3.75e-02 2.28e-04 GO actin crosslink formation biological_process 3.68e-02 4.41e-06 GO detection of calcium ion biological_process 4.74e-03 4.16e-04 GO relaxation of cardiac muscle biological_process 4.04e-03 1.85e-06 GO dendritic shaft cellular_component 1.23e-03 2.68e-05 GO calmodulin-dependent protein kinase activity molecular_function

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 4.67e-10 2.19e-07 postsynaptic density 6.57e-10 3.02e-07 asymmetric synapse 2.14e-09 9.25e-07 postsynapse 4.69e-09 1.94e-06 ionotropic glutamate receptor complex 1.53e-08 9.73e-06 chemical synaptic transmission 3.19e-08 1.18e-05 postsynaptic membrane 4.95e-08 2.93e-05 receptor clustering 5.17e-08 1.87e-05 cation channel complex 7.05e-08 2.47e-05 ion channel complex 1.08e-07 4.13e-05 guanylate kinase activity 1.31e-07 4.37e-05 synapse 1.55e-07 8.47e-05 receptor localization to synapse 1.68e-07 6.20e-05 ionotropic glutamate receptor binding 2.07e-07 6.70e-05 transmembrane transporter complex 2.30e-07 1.22e-04 GDP metabolic process 3.73e-07 1.92e-04 localization within membrane 6.85e-07 2.06e-04 synaptic membrane 7.75e-07 3.76e-04 response to calcium ion 8.40e-07 2.71e-04 glutamate receptor binding 1.05e-06 4.97e-04 regulation of cation channel activity

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 NEURONAL SYSTEM 4.18e-11 1.18e-08 NEURONAL SYSTEM 1.25e-09 3.01e-07 TRAFFICKING OF AMPA RECEPTORS 1.48e-09 4.79e-07 TRAFFICKING OF AMPA RECEPTORS 6.34e-08 1.68e-05 TRANSMISSION ACROSS CHEMICAL SYNAPSES 1.81e-07 3.43e-05 TRANSMISSION ACROSS CHEMICAL SYNAPSES 2.61e-06 5.47e-04 NEUROTRANSMITTER RECEPTOR BINDING AND DOWNSTREAM TRANSMISSION IN THE POSTSYNAPTIC CELL 4.74e-06 7.48e-04 NEUROTRANSMITTER RECEPTOR BINDING AND DOWNSTREAM TRANSMISSION IN THE POSTSYNAPTIC CELL 6.74e-05 8.84e-03 CGMP EFFECTS 1.18e-04 1.48e-02 NITRIC OXIDE STIMULATES GUANYLATE CYCLASE 1.81e-04 2.63e-02 CGMP EFFECTS 2.58e-04 2.99e-02 PLATELET HOMEOSTASIS 4.79e-04 6.19e-02 NITRIC OXIDE STIMULATES GUANYLATE CYCLASE 6.08e-04 7.64e-02 PLATELET HOMEOSTASIS 1.37e-03 1.54e-01 UNBLOCKING OF NMDA RECEPTOR GLUTAMATE BINDING AND ACTIVATION 1.60e-03 1.77e-01 POTASSIUM CHANNELS 1.63e-03 1.79e-01 CREB PHOSPHORYLATION THROUGH THE ACTIVATION OF CAMKII 1.98e-03 1.85e-01 CREB PHOSPHORYLATION THROUGH THE ACTIVATION OF CAMKII 2.02e-03 2.15e-01 RAS ACTIVATION UOPN CA2 INFUX THROUGH NMDA RECEPTOR 2.35e-03 2.45e-01 IONOTROPIC ACTIVITY OF KAINATE RECEPTORS

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 6.41e-06 3.41e-02 abnormal spatial learning 6.47e-06 3.43e-02 abnormal AMPA-mediated synaptic currents 1.86e-05 7.20e-02 abnormal excitatory postsynaptic potential 3.56e-05 1.14e-01 abnormal CNS synaptic transmission 6.27e-05 1.65e-01 abnormal synaptic plasticity 7.20e-05 1.81e-01 enhanced long term potentiation 1.93e-04 3.41e-01 enhanced NMDA-mediated synaptic currents 2.08e-04 3.57e-01 abnormal miniature excitatory postsynaptic currents 3.19e-04 4.68e-01 abnormal hippocampus pyramidal cell morphology 5.53e-04 6.45e-01 abnormal nociception after inflammation 8.00e-04 7.91e-01 impaired smooth muscle contractility 8.72e-04 8.34e-01 decreased anxiety-related response 9.51e-04 8.78e-01 reduced long term potentiation 1.15e-03 9.76e-01 abnormal spatial working memory 1.18e-03 9.89e-01 abnormal discrimination learning 1.55e-03 1.00e+00 decreased neurotransmitter release 1.59e-03 1.00e+00 impaired coordination 2.22e-03 1.00e+00 abnormal action potential 2.55e-03 1.00e+00 abnormal maternal nurturing 2.81e-03 1.00e+00 enhanced behavioral response to cocaine

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

²FDR corrected p-value (Benjamini-Hochberg)