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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod276

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod276 Module size 33 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 8756 ADAM7 ADAM metallopeptidase domain 7 338440 ANO9 anoctamin 9 320 APBA1 amyloid beta precursor protein binding family A member 1 9546 APBA3 amyloid beta precursor protein binding family A member 3 334 APLP2 amyloid beta precursor like protein 2 9311 ASIC3 acid sensing ion channel subunit 3 80262 C16orf70 chromosome 16 open reading frame 70 1448 CASK casein kappa 140880 CST11 cystatin 11 3758 KCNJ1 potassium voltage-gated channel subfamily J member 1 3768 KCNJ12 potassium voltage-gated channel subfamily J member 12 3769 KCNJ13 potassium voltage-gated channel subfamily J member 13 3770 KCNJ14 potassium voltage-gated channel subfamily J member 14 3772 KCNJ15 potassium voltage-gated channel subfamily J member 15 3773 KCNJ16 potassium voltage-gated channel subfamily J member 16 3759 KCNJ2 potassium voltage-gated channel subfamily J member 2 3761 KCNJ4 potassium voltage-gated channel subfamily J member 4 3764 KCNJ8 potassium voltage-gated channel subfamily J member 8 138307 LCN8 lipocalin 8 392399 LCN9 lipocalin 9 9211 LGI1 leucine rich glioma inactivated 1 8825 LIN7A lin-7 homolog A, crumbs cell polarity complex component 64130 LIN7B lin-7 homolog B, crumbs cell polarity complex component 55327 LIN7C lin-7 homolog C, crumbs cell polarity complex component 57555 NLGN2 neuroligin 2 54413 NLGN3 neuroligin 3 9369 NRXN3 neurexin 3 399968 PATE4 prostate and testis expressed 4 338879 RNASE10 ribonuclease A family member 10 (inactive) 653423 SPAG11A sperm associated antigen 11A 9825 SPATA2 spermatogenesis associated 2 643394 SPINK9 serine peptidase inhibitor, Kazal type 9 391253 SPINT4 serine peptidase inhibitor, Kunitz type 4

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 5.01e-01 9.92e-12 Reactome Classical Kir channels Neuronal System 1.90e-01 1.30e-20 GO inward rectifier potassium channel activity molecular_function 1.59e-01 1.01e-05 Reactome Potassium transport channels Neuronal System 7.09e-02 5.32e-10 Reactome Dopamine Neurotransmitter Release Cycle Neuronal System 6.69e-02 6.66e-16 Reactome Neurexins and neuroligins Neuronal System 1.92e-02 3.24e-06 GO neuron cell-cell adhesion biological_process 1.33e-02 3.70e-09 GO neurotransmitter secretion biological_process 2.23e-03 3.02e-04 GO small molecule binding molecular_function 8.16e-04 1.23e-17 GO potassium ion import 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 regulation of ion transport 0.00e+00 0.00e+00 regulation of ion transmembrane transport 0.00e+00 0.00e+00 potassium ion import 0.00e+00 0.00e+00 inward rectifier potassium channel activity 2.01e-11 1.78e-08 potassium ion transmembrane transport 5.34e-11 4.55e-08 potassium ion transport 5.54e-09 2.62e-06 voltage-gated potassium channel activity 6.67e-09 4.43e-06 monovalent inorganic cation transport 7.85e-09 3.63e-06 ligand-gated ion channel activity 1.60e-08 1.01e-05 metal ion transport 1.79e-08 7.84e-06 G-protein activated inward rectifier potassium channel activity 5.89e-08 2.34e-05 potassium channel activity 7.92e-08 3.09e-05 voltage-gated cation channel activity 8.66e-08 4.95e-05 neurotransmitter secretion 1.18e-07 3.97e-05 voltage-gated potassium channel complex 1.34e-07 4.47e-05 potassium channel complex 1.46e-07 8.01e-05 cation transmembrane transport 2.51e-07 8.96e-05 potassium ion transmembrane transporter activity 2.73e-07 1.43e-04 protein localization to basolateral plasma membrane 5.94e-07 1.96e-04 voltage-gated ion channel activity

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 POTASSIUM CHANNELS 0.00e+00 0.00e+00 INWARDLY RECTIFYING K CHANNELS 0.00e+00 0.00e+00 POTASSIUM CHANNELS 0.00e+00 0.00e+00 INWARDLY RECTIFYING K CHANNELS 1.97e-09 4.64e-07 NEURONAL SYSTEM 2.07e-09 6.55e-07 INHIBITION OF VOLTAGE GATED CA2 CHANNELS VIA GBETA GAMMA SUBUNITS 2.43e-09 7.59e-07 GABA B RECEPTOR ACTIVATION 3.29e-09 1.01e-06 NEURONAL SYSTEM 1.54e-08 4.40e-06 GABA RECEPTOR ACTIVATION 1.57e-08 3.37e-06 INHIBITION OF VOLTAGE GATED CA2 CHANNELS VIA GBETA GAMMA SUBUNITS 2.73e-08 5.71e-06 GABA B RECEPTOR ACTIVATION 3.24e-07 7.82e-05 NEUROTRANSMITTER RECEPTOR BINDING AND DOWNSTREAM TRANSMISSION IN THE POSTSYNAPTIC CELL 5.85e-07 1.06e-04 GABA RECEPTOR ACTIVATION 5.77e-06 1.15e-03 TRANSMISSION ACROSS CHEMICAL SYNAPSES 7.11e-06 1.09e-03 NEUROTRANSMITTER RECEPTOR BINDING AND DOWNSTREAM TRANSMISSION IN THE POSTSYNAPTIC CELL 4.36e-05 5.89e-03 TRANSMISSION ACROSS CHEMICAL SYNAPSES

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 3.49e-04 4.89e-01 wrinkled skin 5.49e-04 6.42e-01 abnormal glutamate-mediated receptor currents 8.45e-04 8.19e-01 abnormal behavior 9.83e-04 8.94e-01 abnormal maxilla morphology 1.59e-03 1.00e+00 palatal shelves fail to meet at midline 1.87e-03 1.00e+00 decreased skin turgor 3.25e-03 1.00e+00 decreased urine osmolality 4.19e-03 1.00e+00 increased T cell number 5.04e-03 1.00e+00 cleft secondary palate 5.52e-03 1.00e+00 decreased startle reflex 5.61e-03 1.00e+00 absent hair follicles 5.61e-03 1.00e+00 retrognathia 5.62e-03 1.00e+00 decreased renal glomerular filtration rate 5.62e-03 1.00e+00 stereotypic behavior 6.23e-03 1.00e+00 polyuria 7.48e-03 1.00e+00 reduced AMPA-mediated synaptic currents 8.42e-03 1.00e+00 abnormal miniature excitatory postsynaptic currents 8.63e-03 1.00e+00 abnormal motor coordination/ balance 9.33e-03 1.00e+00 increased excitatory postsynaptic current amplitude 9.34e-03 1.00e+00 decreased circulating interleukin-12 level

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

²FDR corrected p-value (Benjamini-Hochberg)