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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod57

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod57 Module size 61 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 93953 ACRC germ cell nuclear acidic peptidase 55860 ACTR10 actin related protein 10 homolog 10120 ACTR1B ARP1 actin related protein 1 homolog B 9590 AKAP12 A-kinase anchoring protein 12 127829 ARL8A ADP ribosylation factor like GTPase 8A 55207 ARL8B ADP ribosylation factor like GTPase 8B 10776 ARPP19 cAMP regulated phosphoprotein 19 127247 ASB17 ankyrin repeat and SOCS box containing 17 6795 AURKC aurora kinase C 160140 C11orf65 chromosome 11 open reading frame 65 404550 C16orf74 chromosome 16 open reading frame 74 801 CALM1 calmodulin 1 805 CALM2 calmodulin 2 808 CALM3 calmodulin 3 23125 CAMTA2 calmodulin binding transcription activator 2 283234 CCDC88B coiled-coil domain containing 88B 57126 CD177 CD177 molecule 201161 CENPV centromere protein V 79947 CIT dehydrodolichyl diphosphate synthase subunit 9635 CLCA2 chloride channel accessory 2 22802 CLCA4 chloride channel accessory 4 1262 CNGA4 cyclic nucleotide gated channel alpha 4 55118 CRTAC1 cartilage acidic protein 1 667 DST dystonin 79733 E2F8 E2F transcription factor 8 2029 ENSA endosulfine alpha 348487 FAM131C family with sequence similarity 131 member C 2850 GPR27 G protein-coupled receptor 27 2978 GUCA1A guanylate cyclase activator 1A 2979 GUCA1B guanylate cyclase activator 1B 9626 GUCA1C guanylate cyclase activator 1C 9001 HAP1 huntingtin associated protein 1 84223 IQCG IQ motif containing G 23254 KAZN kazrin, periplakin interacting protein 80726 KIAA1683 IQ motif containing N 26153 KIF26A kinesin family member 26A 3799 KIF5B kinesin family member 5B 22920 KIFAP3 kinesin associated protein 3 64569 LST1 leukocyte specific transcript 1 10988 MAP2 methionyl aminopeptidase 2 79929 MAP6D1 MAP6 domain containing 1 84930 MASTL microtubule associated serine/threonine kinase like 55329 MNS1 meiosis specific nuclear structural 1 441161 OOEP oocyte expressed protein 90102 PHLDB2 pleckstrin homology like domain family B member 2 10769 PLK2 polo like kinase 2 126520 PLK5 polo like kinase 5 134359 POC5 POC5 centriolar protein 5510 PPP1R7 protein phosphatase 1 regulatory subunit 7 27303 RBMS3 RNA binding motif single stranded interacting protein 3 5957 RCVRN recoverin 9481 SLC25A27 solute carrier family 25 member 27 6620 SNCB synuclein beta 25876 SPEF1 sperm flagellar 1 55638 SYBU syntabulin 643382 TMEM253 transmembrane protein 253 11076 TPPP tubulin polymerization promoting protein 51673 TPPP3 tubulin polymerization promoting protein family member 3 10612 TRIM3 tripartite motif containing 3 23376 UFL1 UFM1 specific ligase 1 9094 UNC119 unc-119 lipid binding chaperone

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 1.79e-01 2.83e-08 GO positive regulation of guanylate cyclase activity biological_process 1.24e-01 3.47e-06 Reactome MASTL Facilitates Mitotic Progression Cell Cycle 1.16e-01 6.11e-08 GO adenylate cyclase binding molecular_function 8.61e-02 1.29e-08 GO spindle midzone cellular_component 4.39e-02 4.76e-06 GO protein phosphatase activator activity molecular_function 4.29e-02 3.44e-04 GO dynactin complex cellular_component 4.26e-02 3.44e-04 GO retrograde axonal transport biological_process 3.00e-02 6.33e-06 GO negative regulation of ryanodine-sensitive calcium-release channel activity biological_process 2.79e-02 9.40e-03 Reactome MTF1 activates gene expression Cellular responses to external stimuli 2.47e-02 5.64e-08 Reactome Inactivation, recovery and regulation of the phototransduction cascade Signal Transduction 2.27e-02 1.44e-04 GO regulation of high voltage-gated calcium channel activity biological_process 2.16e-02 8.22e-06 GO detection of calcium ion biological_process 1.76e-02 1.05e-06 GO positive regulation of protein dephosphorylation biological_process 1.60e-02 1.04e-05 GO titin binding molecular_function 1.20e-02 1.95e-06 GO phototransduction biological_process 5.06e-03 2.02e-04 GO nitric-oxide synthase regulator activity molecular_function 4.03e-03 7.40e-04 GO microtubule polymerization biological_process 3.69e-03 8.15e-05 GO microtubule bundle formation biological_process 3.17e-03 7.40e-04 GO positive regulation of synaptic transmission, GABAergic biological_process 2.79e-03 2.51e-07 GO spindle microtubule cellular_component 1.76e-03 1.01e-04 GO positive regulation of insulin secretion involved in cellular response to glucose stimulus biological_process 2.88e-04 6.60e-08 Reactome The phototransduction cascade 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 1.09e-09 8.09e-07 microtubule-based process 1.12e-09 5.89e-07 calcium sensitive guanylate cyclase activator activity 1.55e-09 7.96e-07 tubulin binding 7.22e-09 3.36e-06 guanylate cyclase activator activity 1.66e-08 7.31e-06 guanylate cyclase regulator activity 2.94e-07 1.54e-04 positive regulation of guanylate cyclase activity 4.98e-07 1.67e-04 microtubule binding 6.16e-07 1.86e-04 spindle midzone 8.32e-07 4.02e-04 positive regulation of cGMP biosynthetic process 9.57e-07 4.56e-04 positive regulation of cGMP metabolic process 1.39e-06 6.43e-04 positive regulation of cyclic nucleotide metabolic process 1.41e-06 6.52e-04 regulation of cGMP biosynthetic process 1.98e-06 8.89e-04 positive regulation of cyclase activity 2.01e-06 5.59e-04 microtubule 2.07e-06 9.27e-04 positive regulation of lyase activity 2.19e-06 9.74e-04 regulation of cytokinesis 2.33e-06 1.03e-03 regulation of cGMP metabolic process 3.47e-06 1.48e-03 regulation of protein dephosphorylation 6.84e-06 1.73e-03 microtubule associated complex 7.77e-06 3.09e-03 regulation of rhodopsin mediated signaling pathway

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 1.45e-06 3.19e-04 IONOTROPIC ACTIVITY OF KAINATE RECEPTORS 1.60e-06 2.69e-04 IONOTROPIC ACTIVITY OF KAINATE RECEPTORS 3.35e-06 5.38e-04 TETRAHYDROBIOPTERIN BH4 SYNTHESIS RECYCLING SALVAGE AND REGULATION 3.66e-06 7.48e-04 GLYCOGEN BREAKDOWN GLYCOGENOLYSIS 4.83e-06 7.62e-04 GLYCOGEN BREAKDOWN GLYCOGENOLYSIS 5.26e-06 8.24e-04 KINESINS 7.71e-06 1.50e-03 CREB PHOSPHORYLATION THROUGH THE ACTIVATION OF CAMKII 7.95e-06 1.55e-03 RAS ACTIVATION UOPN CA2 INFUX THROUGH NMDA RECEPTOR 8.43e-06 1.27e-03 SMOOTH MUSCLE CONTRACTION 9.85e-06 1.47e-03 CREB PHOSPHORYLATION THROUGH THE ACTIVATION OF CAMKII 1.14e-05 1.68e-03 ENOS ACTIVATION AND REGULATION 1.20e-05 1.76e-03 MHC CLASS II ANTIGEN PRESENTATION 1.25e-05 2.35e-03 SMOOTH MUSCLE CONTRACTION 1.46e-05 2.72e-03 TETRAHYDROBIOPTERIN BH4 SYNTHESIS RECYCLING SALVAGE AND REGULATION 1.84e-05 2.64e-03 RAS ACTIVATION UOPN CA2 INFUX THROUGH NMDA RECEPTOR 3.63e-05 4.98e-03 MUSCLE CONTRACTION 4.26e-05 7.26e-03 KINESINS 5.75e-05 9.47e-03 MHC CLASS II ANTIGEN PRESENTATION 5.93e-05 9.73e-03 ENOS ACTIVATION AND REGULATION 6.69e-05 1.08e-02 CREB PHOSPHORYLATION THROUGH THE ACTIVATION OF RAS

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 1.58e-04 3.05e-01 abnormal heart septum morphology 2.10e-04 3.59e-01 abnormal eye electrophysiology 3.90e-04 5.24e-01 short sperm flagellum 7.68e-04 7.71e-01 abnormal cerebellar Purkinje cell layer 1.29e-03 1.00e+00 abnormal vesicle-mediated transport 3.75e-03 1.00e+00 multifocal hepatic necrosis 4.17e-03 1.00e+00 decreased brain weight 5.61e-03 1.00e+00 abnormal cerebellum lobule morphology 5.62e-03 1.00e+00 decreased skin turgor 6.43e-03 1.00e+00 increased liver weight 7.48e-03 1.00e+00 abnormal prostate gland ventral lobe morphology 7.48e-03 1.00e+00 lung situs inversus 9.34e-03 1.00e+00 increased cardiac stroke volume 9.34e-03 1.00e+00 delayed male fertility 9.34e-03 1.00e+00 delayed fertility 9.34e-03 1.00e+00 increased prostate gland weight 9.41e-03 1.00e+00 abnormal hippocampus morphology 1.12e-02 1.00e+00 decreased CD8-positive, alpha-beta memory T cell number 1.12e-02 1.00e+00 decreased CD4-positive, alpha-beta memory T cell number 1.12e-02 1.00e+00 abnormal intestinal peristalsis

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

²FDR corrected p-value (Benjamini-Hochberg)