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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod107

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod107 Module size 32 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 23400 ATP13A2 ATPase cation transporting 13A2 79572 ATP13A3 ATPase 13A3 84239 ATP13A4 ATPase 13A4 344905 ATP13A5 ATPase 13A5 22883 CLSTN1 calsyntenin 1 64084 CLSTN2 calsyntenin 2 9746 CLSTN3 calsyntenin 3 1942 EFNA1 ephrin A1 1943 EFNA2 ephrin A2 1944 EFNA3 ephrin A3 1945 EFNA4 ephrin A4 1946 EFNA5 ephrin A5 1947 EFNB1 ephrin B1 1948 EFNB2 ephrin B2 1949 EFNB3 ephrin B3 2041 EPHA1 EPH receptor A1 2042 EPHA3 EPH receptor A3 2043 EPHA4 EPH receptor A4 2044 EPHA5 EPH receptor A5 285220 EPHA6 EPH receptor A6 2045 EPHA7 EPH receptor A7 2046 EPHA8 EPH receptor A8 2047 EPHB1 EPH receptor B1 2048 EPHB2 EPH receptor B2 2049 EPHB3 EPH receptor B3 2050 EPHB4 EPH receptor B4 2051 EPHB6 EPH receptor B6 23024 PDZRN3 PDZ domain containing ring finger 3 29951 PDZRN4 PDZ domain containing ring finger 4 23025 UNC13A unc-13 homolog A 440279 UNC13C unc-13 homolog C 85446 ZFHX2 zinc finger homeobox 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 5.66e-01 1.61e-41 GO transmembrane-ephrin receptor activity molecular_function 1.04e-01 5.98e-22 GO ephrin receptor binding molecular_function 9.20e-02 1.16e-45 Reactome EPH-ephrin mediated repulsion of cells Developmental Biology 4.98e-02 2.93e-06 GO positive regulation of synaptic transmission biological_process 3.74e-02 3.14e-18 Reactome Ephrin signaling Developmental Biology 3.32e-02 1.13e-04 GO synaptic vesicle docking biological_process 3.19e-02 2.64e-07 GO ATP hydrolysis coupled cation transmembrane transport biological_process 1.57e-02 1.41e-04 GO synaptic vesicle priming biological_process 1.36e-02 1.41e-04 GO synaptic vesicle maturation biological_process 5.08e-03 1.55e-11 GO positive regulation of synapse assembly biological_process

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 ephrin receptor signaling pathway 0.00e+00 0.00e+00 transmembrane receptor protein tyrosine kinase signaling pathway 0.00e+00 0.00e+00 enzyme linked receptor protein signaling pathway 0.00e+00 0.00e+00 peptidyl-tyrosine phosphorylation 0.00e+00 0.00e+00 protein tyrosine kinase activity 0.00e+00 0.00e+00 transmembrane receptor protein tyrosine kinase activity 0.00e+00 0.00e+00 protein kinase activity 0.00e+00 0.00e+00 phosphotransferase activity, alcohol group as acceptor 0.00e+00 0.00e+00 ephrin receptor activity 0.00e+00 0.00e+00 ephrin receptor binding 0.00e+00 0.00e+00 transmembrane-ephrin receptor activity 1.18e-12 8.14e-10 GPI-linked ephrin receptor activity 5.89e-11 5.01e-08 axon guidance 6.07e-11 5.15e-08 neuron projection guidance 1.35e-10 1.10e-07 regulation of synapse assembly 9.18e-10 6.87e-07 positive regulation of synapse assembly 1.40e-09 1.02e-06 axon development 2.23e-09 1.12e-06 axon guidance receptor activity 4.07e-09 2.79e-06 cell morphogenesis involved in differentiation 5.19e-09 3.50e-06 regulation of synapse organization

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 1.49e-10 7.97e-06 abnormal axon morphology 1.70e-08 3.65e-04 abnormal axon pruning 1.45e-06 1.15e-02 abnormal anterior commissure pars posterior morphology 2.94e-06 1.99e-02 abnormal axon guidance 1.58e-05 6.44e-02 abnormal sensory neuron innervation pattern 4.85e-05 1.39e-01 abnormal cranial neural crest cell migration 9.23e-05 2.14e-01 hypospadia 1.53e-04 2.98e-01 abnormal anogenital distance 2.06e-04 3.55e-01 thick mitral valve cusps 2.06e-04 3.55e-01 abnormal optic tract morphology 3.64e-04 5.02e-01 abnormal central pattern generator function 3.82e-04 5.20e-01 abnormal corticospinal tract morphology 3.84e-04 5.20e-01 thick aortic valve 3.87e-04 5.22e-01 abnormal anterior cardinal vein morphology 4.43e-04 5.65e-01 absent myocardial trabeculae 8.18e-04 8.02e-01 abnormal cardiac epithelial to mesenchymal transition 8.21e-04 8.04e-01 abnormal glutamate-mediated receptor currents 1.13e-03 9.65e-01 anencephaly 1.15e-03 9.76e-01 abnormal excitatory postsynaptic potential 1.32e-03 1.00e+00 abnormal endocardium morphology

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

²FDR corrected p-value (Benjamini-Hochberg)