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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod249

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod249 Module size 19 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 333 APLP1 amyloid beta precursor like protein 1 1663 CHL1 DEAD/H-box helicase 11 1272 CNTN1 contactin 1 6900 CNTN2 contactin 2 5067 CNTN3 contactin 3 152330 CNTN4 contactin 4 53942 CNTN5 contactin 5 27255 CNTN6 contactin 6 8506 CNTNAP1 contactin associated protein 1 26047 CNTNAP2 contactin associated protein like 2 79937 CNTNAP3 contactin associated protein like 3 728577 CNTNAP3B contactin associated protein like 3B 85445 CNTNAP4 contactin associated protein like 4 129684 CNTNAP5 contactin associated protein like 5 338094 FAM151A family with sequence similarity 151 member A 167555 FAM151B family with sequence similarity 151 member B 3897 L1CAM L1 cell adhesion molecule 23114 NFASC neurofascin 4897 NRCAM neuronal cell adhesion molecule

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 3.25e-01 1.32e-11 Reactome Neurofascin interactions Developmental Biology 4.47e-02 3.00e-07 GO dendrite self-avoidance biological_process 2.45e-02 3.19e-05 GO juxtaparanode region of axon cellular_component 1.58e-02 4.36e-07 GO axonal fasciculation biological_process 2.31e-03 2.55e-05 Reactome CHL1 interactions Developmental Biology 2.09e-03 4.36e-07 GO cell-cell adhesion mediator activity molecular_function 2.03e-03 6.17e-15 Reactome L1CAM interactions Developmental Biology 8.44e-04 2.04e-10 GO anchored component of 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 1.28e-09 9.40e-07 neuron projection development 3.05e-09 2.13e-06 neuronal ion channel clustering 1.30e-08 8.34e-06 neuron development 4.15e-08 2.48e-05 neuron recognition 4.53e-08 1.65e-05 anchored component of membrane 8.62e-08 4.93e-05 neuron maturation 8.64e-08 4.94e-05 axon guidance 9.05e-08 5.15e-05 neuron projection guidance 1.28e-07 7.11e-05 protein localization to juxtaparanode region of axon 1.57e-07 8.57e-05 neuron projection morphogenesis 1.80e-07 9.74e-05 cell projection morphogenesis 1.96e-07 6.35e-05 main axon 2.24e-07 1.19e-04 cell part morphogenesis 3.90e-07 2.00e-04 cell recognition 6.88e-07 3.38e-04 transmission of nerve impulse 1.04e-06 4.92e-04 axonogenesis 1.17e-06 5.49e-04 cell morphogenesis 1.51e-06 6.95e-04 axon development 1.87e-06 8.44e-04 axonal fasciculation 2.26e-06 1.00e-03 cell morphogenesis involved in neuron differentiation

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 L1CAM INTERACTIONS 5.82e-11 2.15e-08 L1CAM INTERACTIONS 9.82e-09 2.16e-06 AXON GUIDANCE 3.29e-08 9.04e-06 AXON GUIDANCE 5.72e-07 1.34e-04 DEVELOPMENTAL BIOLOGY 2.75e-04 3.16e-02 INTERACTION BETWEEN L1 AND ANKYRINS 7.16e-04 8.76e-02 INTERACTION BETWEEN L1 AND ANKYRINS 1.03e-02 8.15e-01 SIGNAL TRANSDUCTION BY L1 1.61e-02 1.00e+00 RECYCLING PATHWAY OF L1 1.65e-02 1.00e+00 RECYCLING PATHWAY OF L1 1.83e-02 1.00e+00 SIGNAL TRANSDUCTION BY L1 2.28e-02 1.00e+00 ACTIVATED NOTCH1 TRANSMITS SIGNAL TO THE NUCLEUS 2.55e-02 1.00e+00 ACTIVATED NOTCH1 TRANSMITS SIGNAL TO THE NUCLEUS 3.12e-02 1.00e+00 BASIGIN INTERACTIONS 3.75e-02 1.00e+00 BASIGIN INTERACTIONS 4.56e-02 1.00e+00 NCAM1 INTERACTIONS

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 1.12e-05 5.09e-02 decreased nerve conduction velocity 4.83e-05 1.39e-01 impaired limb coordination 6.86e-05 1.76e-01 abnormal spinal cord dorsal horn morphology 2.46e-04 3.97e-01 abnormal motor coordination/ balance 2.46e-04 3.97e-01 abnormal somatic nervous system physiology 3.86e-04 5.22e-01 abnormal cerebral cortex pyramidal cell morphology 3.98e-04 5.30e-01 abnormal axon morphology 6.01e-04 6.75e-01 abnormal limb posture 8.18e-04 8.02e-01 complete lethality at weaning 8.70e-04 8.33e-01 abnormal neurite morphology 8.71e-04 8.34e-01 increased grooming behavior 1.05e-03 9.25e-01 impaired coordination 1.76e-03 1.00e+00 abnormal axon guidance 1.87e-03 1.00e+00 long toenails 2.15e-03 1.00e+00 abnormal spatial learning 2.16e-03 1.00e+00 abnormal sensory neuron innervation pattern 2.17e-03 1.00e+00 abnormal response to new environment 3.74e-03 1.00e+00 abnormal node of Ranvier morphology 3.74e-03 1.00e+00 hypermyelination 3.74e-03 1.00e+00 enlarged fourth ventricle

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

²FDR corrected p-value (Benjamini-Hochberg)