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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod15

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod15 Module size 69 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 59 ACTA2 actin, alpha 2, smooth muscle, aorta 345651 ACTBL2 actin, beta like 2 70 ACTC1 actin, alpha, cardiac muscle 1 71 ACTG1 actin gamma 1 72 ACTG2 actin, gamma 2, smooth muscle, enteric 170487 ACTL10 actin like 10 10881 ACTL7A actin like 7A 10880 ACTL7B actin like 7B 81569 ACTL8 actin like 8 284382 ACTL9 actin like 9 10097 ACTR2 ARP2 actin related protein 2 homolog 10096 ACTR3 ARP3 actin related protein 3 homolog 57180 ACTR3B ARP3 actin related protein 3 homolog B 653857 ACTR3C ARP3 actin related protein 3 homolog C 139741 ACTRT1 actin related protein T1 140625 ACTRT2 actin related protein T2 84517 ACTRT3 actin related protein T3 116987 AGAP1 ArfGAP with GTPase domain, ankyrin repeat and PH domain 1 116988 AGAP3 ArfGAP with GTPase domain, ankyrin repeat and PH domain 3 119016 AGAP4 ArfGAP with GTPase domain, ankyrin repeat and PH domain 4 729092 AGAP5 ArfGAP with GTPase domain, ankyrin repeat and PH domain 5 414189 AGAP6 ArfGAP with GTPase domain, ankyrin repeat and PH domain 6 653268 AGAP7 ArfGAP with GTPase domain, ankyrin repeat and PH domain 7, pseudogene 119016 AGAP8 ArfGAP with GTPase domain, ankyrin repeat and PH domain 4 822 CAPG capping actin protein, gelsolin like 829 CAPZA1 capping actin protein of muscle Z-line subunit alpha 1 830 CAPZA2 capping actin protein of muscle Z-line subunit alpha 2 93661 CAPZA3 capping actin protein of muscle Z-line subunit alpha 3 832 CAPZB capping actin protein of muscle Z-line subunit beta 1072 CFL1 cofilin 1 1073 CFL2 cofilin 2 79789 CLMN calmin 1264 CNN1 calponin 1 1265 CNN2 calponin 2 1266 CNN3 calponin 3 28988 DBNL drebrin like 11034 DSTN destrin, actin depolymerizing factor 23301 EHBP1 EH domain binding protein 1 254102 EHBP1L1 EH domain binding protein 1 like 1 83481 EPPK1 epiplakin 1 645027 EVPLL envoplakin like 56776 FMN2 formin 2 10634 GAS2L1 growth arrest specific 2 like 1 246176 GAS2L2 growth arrest specific 2 like 2 9535 GMFG glia maturation factor gamma 3936 LCP1 lymphocyte cytosolic protein 1 55604 LRRC16A capping protein regulator and myosin 1 linker 1 23499 MACF1 microtubule-actin crosslinking factor 1 64780 MICAL1 microtubule associated monooxygenase, calponin and LIM domain containing 1 9645 MICAL2 microtubule associated monooxygenase, calponin and LIM domain containing 2 57553 MICAL3 microtubule associated monooxygenase, calponin and LIM domain containing 3 85377 MICALL1 MICAL like 1 79778 MICALL2 MICAL like 2 683007 NPIP MIA SH3 domain ER export factor 3 23117 NPIPL3 nuclear pore complex interacting protein family member B3 5216 PFN1 profilin 1 5357 PLS1 plastin 1 5358 PLS3 plastin 3 6525 SMTN smoothelin 219537 SMTNL1 smoothelin like 1 342527 SMTNL2 smoothelin like 2 92521 SPECC1 sperm antigen with calponin homology and coiled-coil domains 1 23384 SPECC1L sperm antigen with calponin homology and coiled-coil domains 1 like 84501 SPIRE2 spire type actin nucleation factor 2 161176 SYNE3 spectrin repeat containing nuclear envelope family member 3 6876 TAGLN transgelin 8407 TAGLN2 transgelin 2 29114 TAGLN3 transgelin 3 11344 TWF2 twinfilin actin binding protein 2

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 4.80e-01 2.41e-16 GO actin filament depolymerization biological_process 4.02e-01 1.41e-11 GO F-actin capping protein complex cellular_component 1.80e-01 1.09e-08 GO actin filament bundle cellular_component 1.38e-01 6.11e-08 GO Arp2/3 protein complex cellular_component 8.17e-02 5.03e-10 GO filamentous actin cellular_component 6.71e-02 2.43e-06 GO actin filament network formation biological_process 4.33e-02 3.44e-04 GO cytoskeletal anchoring at nuclear membrane biological_process 4.24e-02 1.45e-06 GO actomyosin structure organization biological_process 3.57e-02 3.44e-04 GO intermediate filament binding molecular_function 1.85e-02 3.75e-05 GO intermediate filament cytoskeleton organization biological_process 1.08e-02 7.29e-15 GO actin cytoskeleton organization biological_process 9.40e-04 4.76e-06 GO actin cortical patch cellular_component

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 0e+00 0e+00 regulation of actin polymerization or depolymerization 0e+00 0e+00 regulation of protein complex disassembly 0e+00 0e+00 regulation of supramolecular fiber organization 0e+00 0e+00 negative regulation of supramolecular fiber organization 0e+00 0e+00 regulation of protein complex assembly 0e+00 0e+00 regulation of actin filament polymerization 0e+00 0e+00 regulation of actin filament length 0e+00 0e+00 regulation of actin cytoskeleton organization 0e+00 0e+00 regulation of actin filament depolymerization 0e+00 0e+00 regulation of cytoskeleton organization 0e+00 0e+00 regulation of actin filament-based process 0e+00 0e+00 regulation of cellular component size 0e+00 0e+00 actin filament organization 0e+00 0e+00 actin filament-based process 0e+00 0e+00 actin filament depolymerization 0e+00 0e+00 supramolecular fiber organization 0e+00 0e+00 actin cytoskeleton organization 0e+00 0e+00 actin cytoskeleton 0e+00 0e+00 actin binding 0e+00 0e+00 actin filament binding

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 3.07e-05 4.25e-03 ADVANCED GLYCOSYLATION ENDPRODUCT RECEPTOR SIGNALING 4.60e-04 5.04e-02 SMOOTH MUSCLE CONTRACTION 5.92e-04 7.47e-02 ADVANCED GLYCOSYLATION ENDPRODUCT RECEPTOR SIGNALING 1.28e-03 1.45e-01 SMOOTH MUSCLE CONTRACTION 2.20e-03 2.02e-01 FACTORS INVOLVED IN MEGAKARYOCYTE DEVELOPMENT AND PLATELET PRODUCTION 2.24e-03 2.06e-01 MUSCLE CONTRACTION 2.76e-03 2.80e-01 MUSCLE CONTRACTION 4.74e-03 3.93e-01 RESPONSE TO ELEVATED PLATELET CYTOSOLIC CA2 1.26e-02 8.86e-01 SEMA3A PAK DEPENDENT AXON REPULSION 1.36e-02 9.40e-01 PLATELET ACTIVATION SIGNALING AND AGGREGATION 1.57e-02 1.00e+00 RESPONSE TO ELEVATED PLATELET CYTOSOLIC CA2 1.82e-02 1.00e+00 CASPASE MEDIATED CLEAVAGE OF CYTOSKELETAL PROTEINS 2.17e-02 1.00e+00 INNATE IMMUNE SYSTEM 2.55e-02 1.00e+00 SEMA3A PAK DEPENDENT AXON REPULSION 2.91e-02 1.00e+00 FACTORS INVOLVED IN MEGAKARYOCYTE DEVELOPMENT AND PLATELET PRODUCTION 3.38e-02 1.00e+00 AXON GUIDANCE 3.55e-02 1.00e+00 CASPASE MEDIATED CLEAVAGE OF CYTOSKELETAL PROTEINS 4.11e-02 1.00e+00 SIGNALING BY ROBO RECEPTOR

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 1.35e-05 5.72e-02 decreased vasoconstriction 5.26e-05 1.48e-01 fused cornea and lens 9.71e-04 8.90e-01 enhanced wound healing 1.49e-03 1.00e+00 abnormal blood vessel physiology 2.04e-03 1.00e+00 abnormal systemic arterial blood pressure 3.42e-03 1.00e+00 abnormal sarcomere morphology 3.53e-03 1.00e+00 abnormal skeletal muscle fiber type ratio 3.75e-03 1.00e+00 distended duodenum 5.61e-03 1.00e+00 abnormal somite border morphology 5.61e-03 1.00e+00 thin cochlear hair cell stereocilia 6.75e-03 1.00e+00 abnormal cornea morphology 6.96e-03 1.00e+00 impaired hearing 7.48e-03 1.00e+00 short inner hair cell stereocilia 8.68e-03 1.00e+00 abnormal macrophage physiology 9.34e-03 1.00e+00 abnormal neural crest cell delamination 1.30e-02 1.00e+00 abnormal primary polar body morphology 1.30e-02 1.00e+00 ectopic bone formation 1.30e-02 1.00e+00 increased keratinocyte migration 1.31e-02 1.00e+00 decreased outer hair cell stereocilia number 1.31e-02 1.00e+00 increased diameter of femur

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

²FDR corrected p-value (Benjamini-Hochberg)