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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod315

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod315 Module size 37 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 389813 C9orf172 apical junction component 1 homolog 92359 CRB3 crumbs 3, cell polarity complex component 50848 F11R F11 receptor 55924 FAM212B inka box actin regulator 2 350383 GPR142 G protein-coupled receptor 142 26086 GPSM1 G protein signaling modulator 1 29899 GPSM2 G protein signaling modulator 2 150084 IGSF5 immunoglobulin superfamily member 5 10207 INADL PATJ, crumbs cell polarity complex component 387755 INSC INSC, spindle orientation adaptor protein 58494 JAM2 junctional adhesion molecule 2 83700 JAM3 junctional adhesion molecule 3 84063 KIRREL2 kirre like nephrin family adhesion molecule 2 79165 LENG1 leukocyte receptor cluster member 1 3996 LLGL1 LLGL1, scribble cell polarity complex component 3993 LLGL2 LLGL2, scribble cell polarity complex component 84708 LNX1 ligand of numb-protein X 1 222484 LNX2 ligand of numb-protein X 2 389125 MUSTN1 musculoskeletal, embryonic nuclear protein 1 8650 NUMB NUMB, endocytic adaptor protein 56288 PARD3 par-3 family cell polarity regulator 50855 PARD6A par-6 family cell polarity regulator alpha 84612 PARD6B par-6 family cell polarity regulator beta 84552 PARD6G par-6 family cell polarity regulator gamma 10076 PCP2 protein tyrosine phosphatase, receptor type U 10343 PKDREJ polycystin family receptor for egg jelly 9240 PNMA1 PNMA family member 1 10687 PNMA2 PNMA family member 2 29944 PNMA3 PNMA family member 3 84968 PNMA6A PNMA family member 6A 55228 PNMAL1 PNMA family member 8A 5584 PRKCI protein kinase C iota 5590 PRKCZ protein kinase C zeta 221935 SDK1 sidekick cell adhesion molecule 1 387914 SHISA2 shisa family member 2 152573 SHISA3 shisa family member 3 6953 TCP10 t-complex 10

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 1.18e-01 3.26e-03 Reactome SDK interactions Cell-Cell communication 9.25e-02 2.69e-14 Reactome Tight junction interactions Cell-Cell communication 7.93e-02 1.01e-08 Reactome TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) Signal Transduction 7.48e-02 5.63e-14 GO bicellular tight junction assembly biological_process 3.09e-02 1.14e-04 GO GDP-dissociation inhibitor activity molecular_function 4.40e-04 1.14e-04 GO Schmidt-Lanterman incisure 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 apical junction assembly 0.00e+00 0.00e+00 bicellular tight junction assembly 0.00e+00 0.00e+00 bicellular tight junction 0.00e+00 0.00e+00 cell-cell junction 0.00e+00 0.00e+00 apical junction complex 1.44e-10 1.18e-07 cell-cell junction assembly 3.25e-10 2.56e-07 cell-cell junction organization 4.05e-09 2.78e-06 cell junction assembly 1.39e-07 4.61e-05 apical part of cell 1.87e-07 1.01e-04 establishment or maintenance of cell polarity 2.47e-07 7.89e-05 cell cortex 1.03e-06 4.88e-04 establishment of cell polarity 3.75e-06 1.07e-03 PDZ domain binding 1.10e-05 2.85e-03 protein domain specific binding 2.81e-05 9.70e-03 transforming growth factor beta receptor signaling pathway 6.02e-05 1.33e-02 GTPase regulator activity 1.03e-04 2.01e-02 slit diaphragm 1.28e-04 3.60e-02 cell division 1.39e-04 3.86e-02 cellular response to transforming growth factor beta stimulus 1.47e-04 4.05e-02 response to transforming growth factor beta

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 CELL CELL JUNCTION ORGANIZATION 0.00e+00 0.00e+00 CELL CELL COMMUNICATION 0.00e+00 0.00e+00 TIGHT JUNCTION INTERACTIONS 0.00e+00 0.00e+00 CELL JUNCTION ORGANIZATION 0.00e+00 0.00e+00 TIGHT JUNCTION INTERACTIONS 1.01e-10 2.76e-08 CELL CELL COMMUNICATION 4.68e-10 1.19e-07 CELL CELL JUNCTION ORGANIZATION 1.07e-09 2.60e-07 CELL JUNCTION ORGANIZATION 1.14e-07 2.20e-05 TGF BETA RECEPTOR SIGNALING IN EMT EPITHELIAL TO MESENCHYMAL TRANSITION 1.22e-07 3.12e-05 TGF BETA RECEPTOR SIGNALING IN EMT EPITHELIAL TO MESENCHYMAL TRANSITION 1.67e-05 2.41e-03 SIGNALING BY TGF BETA RECEPTOR COMPLEX 4.30e-05 7.31e-03 SIGNALING BY TGF BETA RECEPTOR COMPLEX 5.17e-04 5.59e-02 INTEGRIN CELL SURFACE INTERACTIONS 7.73e-04 7.97e-02 CELL SURFACE INTERACTIONS AT THE VASCULAR WALL 1.39e-03 1.56e-01 CELL SURFACE INTERACTIONS AT THE VASCULAR WALL 2.63e-03 2.69e-01 INTEGRIN CELL SURFACE INTERACTIONS 1.08e-02 7.78e-01 P75NTR RECRUITS SIGNALLING COMPLEXES 1.08e-02 7.78e-01 P75NTR SIGNALS VIA NFKB 3.74e-02 1.00e+00 ACTIVATED NOTCH1 TRANSMITS SIGNAL TO THE NUCLEUS 4.04e-02 1.00e+00 P75NTR RECRUITS SIGNALLING COMPLEXES

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 2.18e-04 3.67e-01 intraventricular hemorrhage 3.49e-04 4.89e-01 abnormal cochlear hair cell stereociliary bundle morphology 4.54e-04 5.72e-01 abnormal cochlear hair cell morphology 1.70e-03 1.00e+00 dilated lateral ventricles 3.74e-03 1.00e+00 abnormal kinocilium morphology 3.74e-03 1.00e+00 obstructive hydrocephaly 5.61e-03 1.00e+00 enlarged esophagus 5.61e-03 1.00e+00 abnormal melanocyte morphology 5.61e-03 1.00e+00 small amniotic cavity 6.39e-03 1.00e+00 abnormal placental labyrinth vasculature morphology 7.47e-03 1.00e+00 increased placenta intervillous maternal lacunae size 7.48e-03 1.00e+00 increased neuronal precursor cell number 7.48e-03 1.00e+00 complete lethality during fetal growth through weaning 7.48e-03 1.00e+00 abnormal head fold morphology 7.48e-03 1.00e+00 absent heart tube 8.74e-03 1.00e+00 hydroencephaly 9.33e-03 1.00e+00 abnormal neuron differentiation 9.33e-03 1.00e+00 abnormal placenta fetal blood space morphology 9.33e-03 1.00e+00 abnormal placenta intervillous maternal lacunae morphology 9.34e-03 1.00e+00 small allantois

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

²FDR corrected p-value (Benjamini-Hochberg)