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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod85

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod85 Module size 57 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 3983 ABLIM1 actin binding LIM protein 1 84448 ABLIM2 actin binding LIM protein family member 2 22885 ABLIM3 actin binding LIM protein family member 3 8851 CDK5R1 cyclin dependent kinase 5 regulatory subunit 1 1630 DCC DCC netrin 1 receptor 1826 DSCAM DS cell adhesion molecule 57453 DSCAML1 DS cell adhesion molecule like 1 9855 FARP2 FERM, ARH/RhoGEF and pleckstrin domain protein 2 2242 FES FES proto-oncogene, tyrosine kinase 84624 FNDC1 fibronectin type III domain containing 1 26762 HAVCR1 hepatitis A virus cellular receptor 1 9543 IGDCC3 immunoglobulin superfamily DCC subclass member 3 57722 IGDCC4 immunoglobulin superfamily DCC subclass member 4 57214 KIAA1199 cell migration inducing hyaluronidase 1 148930 KNCN kinocilin 4756 NEO1 neogenin 1 4745 NRP1 neural EGFL like 1 4753 NRP2 neural EGFL like 2 9423 NTN1 netrin 1 4917 NTN3 netrin 3 126147 NTN5 netrin 5 84628 NTNG1 netrin G2 84628 NTNG2 netrin G2 5361 PLXNA1 plexin A1 5362 PLXNA2 plexin A2 55558 PLXNA3 plexin A3 91584 PLXNA4 plexin A4 5364 PLXNB1 plexin B1 23654 PLXNB2 plexin B2 10154 PLXNC1 plexin C1 23129 PLXND1 plexin D1 283659 PRTG protogenin 10371 SEMA3A semaphorin 3A 10512 SEMA3C semaphorin 3C 223117 SEMA3D semaphorin 3D 9723 SEMA3E semaphorin 3E 6405 SEMA3F semaphorin 3F 56920 SEMA3G semaphorin 3G 64218 SEMA4A semaphorin 4A 10509 SEMA4B semaphorin 4B 54910 SEMA4C semaphorin 4C 10505 SEMA4F ssemaphorin 4F 57715 SEMA4G semaphorin 4G 9037 SEMA5A semaphorin 5A 54437 SEMA5B semaphorin 5B 57556 SEMA6A semaphorin 6A 10501 SEMA6B semaphorin 6B 10500 SEMA6C semaphorin 6C 80031 SEMA6D semaphorin 6D 8482 SEMA7A semaphorin 7A (John Milton Hagen blood group) 80723 SLC35G2 solute carrier family 35 member G2 440730 TRIM67 tripartite motif containing 67 90249 UNC5A unc-5 netrin receptor A 219699 UNC5B unc-5 netrin receptor B 8633 UNC5C unc-5 netrin receptor C 222643 UNC5CL unc-5 family C-terminal like 137970 UNC5D unc-5 netrin receptor D

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 4.49e-01 1.59e-14 Reactome Netrin mediated repulsion signals Developmental Biology 2.60e-01 1.05e-67 GO semaphorin-plexin signaling pathway biological_process 2.17e-01 2.84e-46 GO semaphorin receptor binding molecular_function 2.05e-01 2.83e-25 GO semaphorin receptor activity molecular_function 2.02e-01 2.83e-25 GO semaphorin receptor complex cellular_component 1.58e-01 1.41e-47 GO negative regulation of axon extension involved in axon guidance biological_process 8.13e-02 7.50e-41 GO chemorepellent activity molecular_function 7.23e-02 5.07e-17 Reactome CRMPs in Sema3A signaling Developmental Biology 7.17e-02 1.68e-20 Reactome Netrin-1 signaling Developmental Biology 2.44e-02 1.19e-17 Reactome SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion Developmental Biology 2.04e-02 2.43e-08 Reactome DSCAM interactions Developmental Biology 1.61e-02 4.09e-10 Reactome DCC mediated attractive signaling Developmental Biology 7.67e-03 9.17e-33 GO neuropilin binding 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 axon development 0e+00 0e+00 cell morphogenesis involved in differentiation 0e+00 0e+00 cell part morphogenesis 0e+00 0e+00 neuron projection development 0e+00 0e+00 cell morphogenesis 0e+00 0e+00 neuron projection morphogenesis 0e+00 0e+00 axon guidance 0e+00 0e+00 cell morphogenesis involved in neuron differentiation 0e+00 0e+00 neuron development 0e+00 0e+00 cell projection morphogenesis 0e+00 0e+00 neuron projection guidance 0e+00 0e+00 chemotaxis 0e+00 0e+00 axonogenesis 0e+00 0e+00 regulation of cell morphogenesis 0e+00 0e+00 regulation of neuron differentiation 0e+00 0e+00 regulation of axonogenesis 0e+00 0e+00 regulation of neuron projection development 0e+00 0e+00 regulation of cell projection organization 0e+00 0e+00 regulation of neurogenesis 0e+00 0e+00 semaphorin-plexin signaling pathway

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 AXON GUIDANCE 0.00e+00 0.00e+00 SEMAPHORIN INTERACTIONS 0.00e+00 0.00e+00 OTHER SEMAPHORIN INTERACTIONS 0.00e+00 0.00e+00 DEVELOPMENTAL BIOLOGY 0.00e+00 0.00e+00 NETRIN1 SIGNALING 0.00e+00 0.00e+00 CRMPS IN SEMA3A SIGNALING 0.00e+00 0.00e+00 SEMA3A PLEXIN REPULSION SIGNALING BY INHIBITING INTEGRIN ADHESION 0.00e+00 0.00e+00 AXON GUIDANCE 0.00e+00 0.00e+00 SEMAPHORIN INTERACTIONS 0.00e+00 0.00e+00 OTHER SEMAPHORIN INTERACTIONS 0.00e+00 0.00e+00 NETRIN1 SIGNALING 5.37e-12 2.08e-09 SEMA3A PAK DEPENDENT AXON REPULSION 1.20e-11 3.50e-09 SEMA3A PLEXIN REPULSION SIGNALING BY INHIBITING INTEGRIN ADHESION 9.61e-11 2.63e-08 CRMPS IN SEMA3A SIGNALING 1.25e-09 3.01e-07 SEMA3A PAK DEPENDENT AXON REPULSION 1.32e-08 3.81e-06 DSCAM INTERACTIONS 2.09e-08 4.42e-06 DSCAM INTERACTIONS 8.11e-08 2.11e-05 DCC MEDIATED ATTRACTIVE SIGNALING 2.84e-07 5.30e-05 DCC MEDIATED ATTRACTIVE SIGNALING 4.55e-05 7.68e-03 ROLE OF DCC IN REGULATING APOPTOSIS

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 2.71e-09 8.07e-05 abnormal hippocampal mossy fiber morphology 1.85e-08 3.86e-04 ectopic cerebellar granule cells 2.48e-08 4.93e-04 abnormal trigeminal nerve morphology 2.70e-08 5.17e-04 abnormal amacrine cell morphology 7.06e-08 1.07e-03 abnormal axon guidance 8.56e-08 1.24e-03 abnormal neuronal migration 6.00e-07 6.05e-03 abnormal spinal cord dorsal column morphology 1.07e-06 9.14e-03 abnormal retinal inner plexiform layer morphology 1.11e-06 9.41e-03 abnormal anterior commissure morphology 3.47e-06 2.23e-02 abnormal pyramidal decussation morphology 1.28e-05 5.64e-02 abnormal neurite morphology 2.60e-05 9.35e-02 abnormal retinal ganglion cell morphology 3.28e-05 1.08e-01 abnormal corticospinal tract morphology 3.73e-05 1.17e-01 abnormal axon fasciculation 1.91e-04 3.39e-01 absent trochlear nerve 2.15e-04 3.64e-01 abnormal habenula morphology 3.84e-04 5.20e-01 ectopic Purkinje cell 3.90e-04 5.24e-01 abnormal cerebellar molecular layer 4.09e-04 5.37e-01 abnormal spinal nerve morphology 4.68e-04 5.84e-01 abnormal oculomotor nerve morphology

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

²FDR corrected p-value (Benjamini-Hochberg)