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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod188

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod188 Module size 41 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 150709 ANKAR ankyrin and armadillo repeat containing 114898 C1QTNF2 C1q and TNF related 2 10518 CIB2 calcium and integrin binding family member 2 117286 CIB3 calcium and integrin binding family member 3 83716 CRISPLD2 cysteine rich secretory protein LCCL domain containing 2 1523 CUX1 cut like homeobox 1 23316 CUX2 cut like homeobox 2 79645 EFCAB1 EF-hand calcium binding domain 1 146330 FBXL16 F-box and leucine rich repeat protein 16 55612 FERMT1 fermitin family member 1 3208 HPCA hippocalcin 3241 HPCAL1 hippocalcin like 1 51440 HPCAL4 hippocalcin like 4 11141 IL1RAPL1 interleukin 1 receptor accessory protein like 1 9657 IQCB1 IQ motif containing B1 10788 IQGAP2 IQ motif containing GTPase activating protein 2 128239 IQGAP3 IQ motif containing GTPase activating protein 3 30820 KCNIP1 potassium voltage-gated channel interacting protein 1 30819 KCNIP2 potassium voltage-gated channel interacting protein 2 30818 KCNIP3 potassium voltage-gated channel interacting protein 3 80333 KCNIP4 potassium voltage-gated channel interacting protein 4 23026 MYO16 myosin XVI 80179 MYO19 myosin XIX 4640 MYO1A myosin IA 4430 MYO1B myosin IB 4642 MYO1D myosin ID 4643 MYO1E myosin IE 4542 MYO1F myosin IF 64005 MYO1G myosin IG 283446 MYO1H myosin IH 4646 MYO6 myosin VI 23413 NCS1 neuronal calcium sensor 1 654790 PCP4L1 Purkinje cell protein 4 like 1 54922 RASIP1 Ras interacting protein 1 1827 RCAN1 regulator of calcineurin 1 10231 RCAN2 regulator of calcineurin 2 11123 RCAN3 RCAN family member 3 357 SHROOM2 shroom family member 2 55898 UNC45A unc-45 myosin chaperone A 146862 UNC45B unc-45 myosin chaperone B 7447 VSNL1 visinin like 1

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 3.31e-01 5.66e-10 Reactome Phase 1 - inactivation of fast Na+ channels Muscle contraction 1.36e-01 1.64e-15 GO myosin complex cellular_component 2.22e-02 4.87e-08 GO regulation of potassium ion transmembrane transport biological_process 2.18e-02 1.27e-05 GO positive regulation of dendrite morphogenesis biological_process 2.12e-02 2.32e-04 Reactome RHO GTPases activate IQGAPs Signal Transduction 1.47e-02 1.20e-11 GO motor activity molecular_function 8.89e-03 6.75e-06 GO actin filament-based movement 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 myosin complex 0.00e+00 0.00e+00 motor activity 1.64e-11 1.07e-08 actin binding 5.81e-10 3.19e-07 calmodulin binding 2.94e-09 1.25e-06 actin cytoskeleton 1.19e-08 5.36e-06 actin filament binding 1.86e-08 8.12e-06 calcium-dependent protein serine/threonine phosphatase regulator activity 2.69e-08 1.14e-05 microfilament motor activity 2.13e-07 7.71e-05 calcium ion binding 6.66e-07 3.28e-04 regulation of calcineurin-NFAT signaling cascade 2.44e-06 1.08e-03 regulation of potassium ion transmembrane transport 2.94e-06 1.27e-03 regulation of potassium ion transport 9.66e-06 3.75e-03 calcium-mediated signaling 2.07e-05 7.40e-03 regulation of calcium-mediated signaling 2.62e-05 5.91e-03 filamentous actin 2.94e-05 1.01e-02 cardiac conduction 4.57e-05 1.48e-02 second-messenger-mediated signaling 5.74e-05 1.28e-02 potassium channel regulator activity 7.70e-05 2.33e-02 positive regulation of dendrite morphogenesis 9.16e-05 1.82e-02 actin filament

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 3.42e-03 2.97e-01 GAP JUNCTION DEGRADATION 3.44e-03 3.35e-01 GAP JUNCTION DEGRADATION 5.16e-03 4.69e-01 TRAFFICKING OF AMPA RECEPTORS 6.05e-03 5.35e-01 SIGNALING BY FGFR1 FUSION MUTANTS 6.06e-03 5.36e-01 SIGNALING BY FGFR1 MUTANTS 6.07e-03 5.37e-01 SIGNALING BY FGFR MUTANTS 8.25e-03 6.28e-01 GAP JUNCTION TRAFFICKING 8.29e-03 6.90e-01 SIGNALING BY FGFR IN DISEASE 1.50e-02 1.00e+00 SIGNALING BY FGFR1 MUTANTS 1.50e-02 1.00e+00 SIGNALING BY FGFR1 FUSION MUTANTS 1.51e-02 1.00e+00 SIGNALING BY FGFR MUTANTS 1.85e-02 1.00e+00 SIGNALING BY FGFR IN DISEASE 2.05e-02 1.00e+00 TRAFFICKING OF AMPA RECEPTORS 3.09e-02 1.00e+00 NEUROTRANSMITTER RECEPTOR BINDING AND DOWNSTREAM TRANSMISSION IN THE POSTSYNAPTIC CELL 3.33e-02 1.00e+00 GAP JUNCTION TRAFFICKING

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 3.74e-03 1e+00 abnormal renal glomerular filtration rate 3.77e-03 1e+00 decreased cochlear hair cell stereocilia number 5.61e-03 1e+00 leukocyturia 5.62e-03 1e+00 hemoglobinuria 5.63e-03 1e+00 fused outer hair cell stereocilia 5.64e-03 1e+00 absent cochlear nerve compound action potential 7.49e-03 1e+00 podocyte microvillus transformation 7.51e-03 1e+00 absent organ of Corti 7.51e-03 1e+00 detached tectorial membrane 7.51e-03 1e+00 fused inner hair cell stereocilia 7.51e-03 1e+00 abnormal otolithic membrane morphology 7.52e-03 1e+00 utricular macular degeneration 7.52e-03 1e+00 vestibular ganglion degeneration 7.52e-03 1e+00 abnormal external male genitalia morphology 9.38e-03 1e+00 decreased vestibular hair cell number 9.38e-03 1e+00 abnormal outer hair cell kinocilium morphology 9.49e-03 1e+00 increased urine protein level 1.12e-02 1e+00 cochlear degeneration 1.12e-02 1e+00 abnormal T cell apoptosis 1.12e-02 1e+00 abnormal neural tube ventricular layer morphology

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

²FDR corrected p-value (Benjamini-Hochberg)