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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod164

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod164 Module size 47 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 10006 ABI1 abl interactor 1 10152 ABI2 abl interactor 2 393 ARHGAP4 Rho GTPase activating protein 4 10552 ARPC1A actin related protein 2/3 complex subunit 1A 10095 ARPC1B actin related protein 2/3 complex subunit 1B 10109 ARPC2 actin related protein 2/3 complex subunit 2 10094 ARPC3 actin related protein 2/3 complex subunit 3 297518 ARPC4 actin related protein 2/3 complex, subunit 4 100526693 ARPC4-TTLL3 ARPC4-TTLL3 readthrough 10092 ARPC5 actin related protein 2/3 complex subunit 5 81873 ARPC5L actin related protein 2/3 complex subunit 5 like 10458 BAIAP2 BAI1 associated protein 2 55845 BRK1 BRICK1, SCAR/WAVE actin nucleating complex subunit 23191 CYFIP1 cytoplasmic FMR1 interacting protein 1 26999 CYFIP2 cytoplasmic FMR1 interacting protein 2 1729 DIAPH1 diaphanous related formin 1 81624 DIAPH3 diaphanous related formin 3 23268 DNMBP dynamin binding protein 1793 DOCK1 dedicator of cytokinesis 1 139818 DOCK11 dedicator of cytokinesis 11 57572 DOCK6 dedicator of cytokinesis 6 85440 DOCK7 dedicator of cytokinesis 7 81704 DOCK8 dedicator of cytokinesis 8 23348 DOCK9 dedicator of cytokinesis 9 9844 ELMO1 engulfment and cell motility 1 63916 ELMO2 engulfment and cell motility 2 79767 ELMO3 engulfment and cell motility 3 55740 ENAH ENAH, actin regulator 54869 EPS8L1 EPS8 like 1 51466 EVL Enah/Vasp-like 2212 FCGR2A Fc fragment of IgG receptor IIa 10787 NCKAP1 NCK associated protein 1 3071 NCKAP1L NCK associated protein 1 like 51517 NCKIPSD NCK interacting protein with SH3 domain 345456 PFN3 profilin 3 8544 PIR pirin 65059 RAPH1 Ras association (RalGDS/AF-6) and pleckstrin homology domains 1 79626 TNFAIP8L2 TNF alpha induced protein 8 like 2 128434 VSTM2L V-set and transmembrane domain containing 2 like 7454 WAS Wiskott-Aldrich syndrome 8936 WASF1 WAS protein family member 1 10163 WASF2 WAS protein family member 2 10810 WASF3 WAS protein family member 3 8976 WASL Wiskott-Aldrich syndrome like 7456 WIPF1 WAS/WASL interacting protein family member 1 147179 WIPF2 WAS/WASL interacting protein family member 2 644150 WIPF3 WAS/WASL interacting protein family member 3

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 4.42e-01 3.81e-24 GO SCAR complex cellular_component 3.10e-01 3.80e-53 Reactome RHO GTPases Activate WASPs and WAVEs Signal Transduction 2.48e-01 2.14e-18 GO Arp2/3 protein complex cellular_component 9.15e-02 2.75e-13 GO actin polymerization or depolymerization biological_process 7.86e-02 5.62e-11 GO actin cortical patch cellular_component 5.19e-02 9.62e-11 GO positive regulation of actin nucleation biological_process 3.74e-02 6.84e-06 Reactome PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases Signal Transduction 2.20e-02 1.07e-12 GO actin filament polymerization biological_process 1.26e-02 5.46e-12 GO actin filament-based movement biological_process 1.17e-02 3.66e-45 Reactome Regulation of actin dynamics for phagocytic cup formation Immune System 8.83e-03 3.97e-04 GO guanyl-nucleotide exchange factor complex cellular_component 8.80e-03 1.48e-17 GO SH3 domain binding molecular_function 7.38e-03 1.38e-07 GO small GTPase mediated signal transduction biological_process 5.27e-03 3.60e-08 GO guanyl-nucleotide exchange factor 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 0e+00 0e+00 actin filament organization 0e+00 0e+00 immune response-activating signal transduction 0e+00 0e+00 actin polymerization or depolymerization 0e+00 0e+00 endocytosis 0e+00 0e+00 vascular endothelial growth factor receptor signaling pathway 0e+00 0e+00 immune response-regulating cell surface receptor signaling pathway 0e+00 0e+00 Fc-gamma receptor signaling pathway 0e+00 0e+00 Fc-gamma receptor signaling pathway involved in phagocytosis 0e+00 0e+00 Fc receptor signaling pathway 0e+00 0e+00 transmembrane receptor protein tyrosine kinase signaling pathway 0e+00 0e+00 Fc receptor mediated stimulatory signaling pathway 0e+00 0e+00 supramolecular fiber organization 0e+00 0e+00 immune response-activating cell surface receptor signaling pathway 0e+00 0e+00 phagocytosis 0e+00 0e+00 regulation of actin polymerization or depolymerization 0e+00 0e+00 positive regulation of supramolecular fiber organization 0e+00 0e+00 regulation of supramolecular fiber organization 0e+00 0e+00 actin nucleation 0e+00 0e+00 positive regulation of cellular component biogenesis 0e+00 0e+00 regulation of actin cytoskeleton organization

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 3.00e-06 4.84e-04 GENERATION OF SECOND MESSENGER MOLECULES 1.46e-05 2.13e-03 TCR SIGNALING 7.82e-05 1.02e-02 DCC MEDIATED ATTRACTIVE SIGNALING 1.21e-04 1.51e-02 FACTORS INVOLVED IN MEGAKARYOCYTE DEVELOPMENT AND PLATELET PRODUCTION 1.69e-04 2.48e-02 GENERATION OF SECOND MESSENGER MOLECULES 2.64e-04 3.05e-02 AXON GUIDANCE 8.07e-04 8.30e-02 SIGNALING BY ROBO RECEPTOR 8.99e-04 1.07e-01 TCR SIGNALING 9.94e-04 1.00e-01 NETRIN1 SIGNALING 1.23e-03 1.40e-01 DCC MEDIATED ATTRACTIVE SIGNALING 4.57e-03 4.24e-01 FACTORS INVOLVED IN MEGAKARYOCYTE DEVELOPMENT AND PLATELET PRODUCTION 7.65e-03 6.47e-01 SIGNALING BY ROBO RECEPTOR 1.24e-02 9.44e-01 NETRIN1 SIGNALING 1.29e-02 9.02e-01 THE ROLE OF NEF IN HIV1 REPLICATION AND DISEASE PATHOGENESIS 2.37e-02 1.00e+00 NEPHRIN INTERACTIONS 2.52e-02 1.00e+00 AXON GUIDANCE 3.76e-02 1.00e+00 ENOS ACTIVATION AND REGULATION 4.66e-02 1.00e+00 HOST INTERACTIONS OF HIV FACTORS

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 3.00e-04 4.47e-01 decreased T cell proliferation 4.21e-04 5.49e-01 abnormal cell migration 8.03e-04 7.93e-01 increased leukocyte cell number 1.10e-03 9.51e-01 increased neutrophil cell number 1.25e-03 1.00e+00 preweaning lethality 1.97e-03 1.00e+00 spleen hyperplasia 2.35e-03 1.00e+00 abnormal blastocyst morphology 3.56e-03 1.00e+00 abnormal endocardium morphology 3.86e-03 1.00e+00 embryonic lethality 4.48e-03 1.00e+00 increased interleukin-17 secretion 6.18e-03 1.00e+00 decreased lymphocyte cell number 6.51e-03 1.00e+00 extramedullary hematopoiesis 6.84e-03 1.00e+00 abnormal object recognition memory 8.97e-03 1.00e+00 abnormal dendritic cell antigen presentation 9.01e-03 1.00e+00 decreased circulating total protein level 9.18e-03 1.00e+00 thymus hypoplasia 9.35e-03 1.00e+00 abnormal pharyngeal arch development 9.35e-03 1.00e+00 decreased follicular dendritic cell number 9.35e-03 1.00e+00 abnormal regulatory T cell number 9.74e-03 1.00e+00 abnormal vasculogenesis

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

²FDR corrected p-value (Benjamini-Hochberg)