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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod240

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod240 Module size 71 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 10863 ADAM28 ADAM metallopeptidase domain 28 8754 ADAM9 ADAM metallopeptidase domain 9 81792 ADAMTS12 ADAM metallopeptidase with thrombospondin type 1 motif 12 11093 ADAMTS13 ADAM metallopeptidase with thrombospondin type 1 motif 13 120425 AMICA1 junction adhesion molecule like 27329 ANGPTL3 angiopoietin like 3 54518 APBB1IP amyloid beta precursor protein binding family B member 1 interacting protein 81575 APOLD1 apolipoprotein L domain containing 1 9564 BCAR1 BCAR1, Cas family scaffold protein 826 CAPNS1 calpain small subunit 1 9607 CARTPT CART prepropeptide 831 CAST calpastatin 858 CAV2 caveolin 2 977 CD151 CD151 molecule (Raph blood group) 30835 CD209 CD209 molecule 960 CD44 CD44 molecule (Indian blood group) 100909977 CD47 leukocyte surface antigen CD47-like 967 CD63 CD63 molecule 3732 CD82 CD82 molecule 928 CD9 CD9 molecule 634 CEACAM1 carcinoembryonic antigen related cell adhesion molecule 1 90273 CEACAM3 carcinoembryonic antigen related cell adhesion molecule 21 4680 CEACAM6 carcinoembryonic antigen related cell adhesion molecule 6 1087 CEACAM7 carcinoembryonic antigen related cell adhesion molecule 7 1179 CLCA1 chloride channel accessory 1 10332 CLEC4M C-type lectin domain family 4 member M 2017 CTTN cortactin 3491 CYR61 cysteine rich angiogenic inducer 61 1834 DSPP dentin sialophosphoprotein 10085 EDIL3 EGF like repeats and discoidin domains 3 11082 ESM1 endothelial cell specific molecule 1 2170 FABP3 fatty acid binding protein 3 2335 FN1 fibronectin 1 3384 ICAM2 intercellular adhesion molecule 2 3385 ICAM3 intercellular adhesion molecule 3 3386 ICAM4 intercellular adhesion molecule 4 (Landsteiner-Wiener blood group) 7087 ICAM5 intercellular adhesion molecule 5 3611 ILK integrin linked kinase 3684 ITGAM integrin subunit alpha M 3688 ITGB1 integrin subunit beta 1 3689 ITGB2 integrin subunit beta 2 3690 ITGB3 integrin subunit beta 3 27074 LAMP3 lysosomal associated membrane protein 3 3987 LIMS1 LIM zinc finger domain containing 1 55679 LIMS2 LIM zinc finger domain containing 2 53353 LRP1B LDL receptor related protein 1B 4037 LRP3 LDL receptor related protein 3 8174 MADCAM1 mucosal vascular addressin cell adhesion molecule 1 4192 MDK midkine 8190 MIA MIA SH3 domain containing 4635 MLC1 myosin light chain 4 59277 NTN4 netrin 4 55742 PARVA parvin alpha 29780 PARVB parvin beta 64098 PARVG parvin gamma 5310 PKD1 polycystin 1, transient receptor potential channel interacting 5376 PMP22 peripheral myelin protein 22 81706 PPP1R14C protein phosphatase 1 regulatory inhibitor subunit 14C 5621 PRNP prion protein 5747 PTK2 protein tyrosine kinase 2 11156 PTP4A3 protein tyrosine phosphatase type IVA, member 3 5829 PXN paxillin 286205 SCAI suppressor of cancer cell invasion 6403 SELP selectin P 6614 SIGLEC1 sialic acid binding Ig like lectin 1 10417 SPON2 spondin 2 7052 TGM2 transglutaminase 2 7094 TLN1 talin 1 7106 TSPAN4 tetraspanin 4 7399 USH2A usherin 7408 VASP vasodilator stimulated phosphoprotein

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 4.07e-01 2.25e-10 Reactome Localization of the PINCH-ILK-PARVIN complex to focal adhesions Cell-Cell communication 2.17e-01 4.95e-16 Reactome Cell-extracellular matrix interactions Cell-Cell communication 2.00e-01 1.50e-11 Reactome p130Cas linkage to MAPK signaling for integrins Hemostasis#Signal Transduction 8.66e-02 2.97e-07 GO wound healing, spreading of cells biological_process 5.90e-02 1.84e-27 GO integrin binding molecular_function 5.76e-02 1.27e-05 GO cell-cell adhesion via plasma-membrane adhesion molecules biological_process 3.58e-02 5.46e-04 GO opsonization biological_process 3.47e-02 2.22e-17 Reactome Integrin cell surface interactions Extracellular matrix organization 3.02e-02 5.46e-04 GO phospholipid homeostasis biological_process 2.89e-02 1.29e-20 GO cell-matrix adhesion biological_process 1.87e-02 3.40e-19 GO integrin-mediated signaling pathway biological_process 1.63e-02 8.30e-04 GO intracellular transport of virus biological_process 1.55e-02 6.81e-04 GO dendritic spine maintenance biological_process 1.19e-02 6.32e-08 GO leukocyte cell-cell adhesion biological_process 1.17e-02 7.50e-05 Reactome CD209 (DC-SIGN) signaling Immune System 9.58e-03 1.18e-02 Reactome Uptake and function of diphtheria toxin Disease 8.92e-03 8.30e-04 GO virion binding molecular_function 8.85e-03 6.81e-04 GO profilin binding molecular_function 9.93e-05 3.88e-05 GO platelet alpha granule membrane 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 0.00e+00 0.00e+00 integrin-mediated signaling pathway 0.00e+00 0.00e+00 integrin binding 1.53e-21 1.11e-18 cell adhesion molecule binding 8.05e-19 7.71e-16 cell-matrix adhesion 1.73e-17 1.64e-14 cell-substrate adhesion 2.86e-16 2.70e-13 single organismal cell-cell adhesion 7.44e-15 5.19e-12 protein complex binding 1.08e-14 1.01e-11 cell-cell adhesion 4.36e-12 2.48e-09 focal adhesion 5.10e-12 2.89e-09 cell-substrate adherens junction 6.22e-12 3.51e-09 cell-substrate junction 1.34e-11 7.45e-09 adherens junction 1.66e-11 1.48e-08 extracellular matrix organization 1.76e-11 1.57e-08 extracellular structure organization 9.10e-10 6.81e-07 cell migration 1.02e-09 7.60e-07 endocytosis 1.82e-08 1.14e-05 cell junction assembly 2.58e-08 1.59e-05 leukocyte cell-cell adhesion 4.60e-07 1.55e-04 collagen binding 8.48e-07 2.51e-04 secretory granule membrane

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 INTEGRIN CELL SURFACE INTERACTIONS 0.00e+00 0.00e+00 INTEGRIN CELL SURFACE INTERACTIONS 1.86e-10 4.95e-08 CELL EXTRACELLULAR MATRIX INTERACTIONS 1.95e-10 5.17e-08 CELL CELL COMMUNICATION 2.67e-10 6.97e-08 P130CAS LINKAGE TO MAPK SIGNALING FOR INTEGRINS 4.54e-10 1.16e-07 CELL JUNCTION ORGANIZATION 5.93e-10 2.00e-07 CELL EXTRACELLULAR MATRIX INTERACTIONS 5.53e-09 1.24e-06 CELL SURFACE INTERACTIONS AT THE VASCULAR WALL 1.37e-08 3.94e-06 P130CAS LINKAGE TO MAPK SIGNALING FOR INTEGRINS 1.72e-08 3.68e-06 INTEGRIN ALPHAIIB BETA3 SIGNALING 1.77e-08 3.78e-06 IMMUNOREGULATORY INTERACTIONS BETWEEN A LYMPHOID AND A NON LYMPHOID CELL 2.90e-08 6.05e-06 GRB2 SOS PROVIDES LINKAGE TO MAPK SIGNALING FOR INTERGRINS 5.92e-08 1.19e-05 PLATELET AGGREGATION PLUG FORMATION 2.62e-07 6.42e-05 CELL CELL COMMUNICATION 3.18e-07 7.69e-05 CELL SURFACE INTERACTIONS AT THE VASCULAR WALL 5.00e-07 1.18e-04 INTEGRIN ALPHAIIB BETA3 SIGNALING 5.82e-07 1.05e-04 PLATELET ACTIVATION SIGNALING AND AGGREGATION 5.83e-07 1.36e-04 CELL JUNCTION ORGANIZATION 7.10e-07 1.64e-04 GRB2 SOS PROVIDES LINKAGE TO MAPK SIGNALING FOR INTERGRINS 1.63e-06 3.55e-04 PLATELET AGGREGATION PLUG FORMATION

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 2.56e-05 9.27e-02 abnormal leukocyte adhesion 3.60e-05 1.15e-01 thick myocardium 6.46e-05 1.69e-01 abnormal platelet physiology 7.47e-05 1.86e-01 abnormal leukocyte migration 1.48e-04 2.93e-01 abnormal neutrophil physiology 1.49e-04 2.94e-01 abnormal leukocyte tethering or rolling 1.68e-04 3.15e-01 hemorrhage 2.88e-04 4.38e-01 decreased keratinocyte migration 6.18e-04 6.84e-01 abnormal amnion morphology 6.40e-04 6.98e-01 impaired neutrophil recruitment 8.04e-04 7.93e-01 failure of chorioallantoic fusion 8.75e-04 8.35e-01 increased angiogenesis 8.91e-04 8.42e-01 abnormal platelet activation 8.97e-04 8.46e-01 abnormal physiological neovascularization 9.81e-04 8.94e-01 abnormal cell adhesion 1.01e-03 9.05e-01 abnormal cellular extravasation 1.02e-03 9.10e-01 abnormal heart development 1.53e-03 1.00e+00 small amniotic cavity 1.55e-03 1.00e+00 abnormal dorsal aorta morphology 2.45e-03 1.00e+00 failure of atrioventricular cushion closure

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

²FDR corrected p-value (Benjamini-Hochberg)