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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod244

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod244 Module size 31 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 407 ARR3 arrestin 3 680 BRS3 bombesin receptor subtype 3 114814 GNRHR2 gonadotropin releasing hormone receptor 2 (pseudogene) 2835 GPR12 G protein-coupled receptor 12 64582 GPR135 G protein-coupled receptor 135 124274 GPR139 G protein-coupled receptor 139 344561 GPR148 G protein-coupled receptor 148 285601 GPR150 G protein-coupled receptor 150 54328 GPR173 G protein-coupled receptor 173 11245 GPR176 G protein-coupled receptor 176 2842 GPR19 G protein-coupled receptor 19 2827 GPR3 G protein-coupled receptor 3 2863 GPR39 G protein-coupled receptor 39 9293 GPR52 G protein-coupled receptor 52 2830 GPR6 G protein-coupled receptor 6 83873 GPR61 G protein-coupled receptor 61 118442 GPR62 G protein-coupled receptor 62 81491 GPR63 G protein-coupled receptor 63 27201 GPR78 G protein-coupled receptor 78 10888 GPR83 G protein-coupled receptor 83 53831 GPR84 G protein-coupled receptor 84 54329 GPR85 G protein-coupled receptor 85 5956 OPN1LW opsin 1, long wave sensitive 2652 OPN1MW opsin 1, medium wave sensitive 728458 OPN1MW2 opsin 1, medium wave sensitive 2 23596 OPN3 opsin 3 6010 RHO rhodopsin 6094 ROM1 retinal outer segment membrane protein 1 10692 RRH retinal pigment epithelium-derived rhodopsin homolog 1755 SAG deleted in malignant brain tumors 1 10329 TMEM5 ribitol xylosyltransferase 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 1.35e-01 4.81e-17 GO G-protein coupled photoreceptor activity molecular_function 1.35e-01 4.81e-17 GO cellular response to light stimulus biological_process 1.22e-01 3.67e-07 GO arrestin family protein binding molecular_function 8.53e-02 6.63e-13 Reactome Opsins Signal Transduction 1.62e-02 1.31e-14 GO photoreceptor outer segment cellular_component 6.00e-03 3.21e-14 GO protein-chromophore linkage 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 detection of light stimulus 0.00e+00 0.00e+00 protein-chromophore linkage 0.00e+00 0.00e+00 phototransduction 0.00e+00 0.00e+00 non-motile cilium 0.00e+00 0.00e+00 photoreceptor cell cilium 0.00e+00 0.00e+00 photoreceptor outer segment 0.00e+00 0.00e+00 G-protein coupled receptor activity 0.00e+00 0.00e+00 photoreceptor activity 3.79e-11 3.28e-08 detection of abiotic stimulus 4.41e-10 3.42e-07 response to light stimulus 5.09e-10 3.92e-07 visual perception 5.60e-10 4.30e-07 sensory perception of light stimulus 4.06e-09 1.69e-06 cilium 5.19e-09 3.50e-06 response to radiation 9.76e-08 3.34e-05 photoreceptor outer segment membrane 1.18e-07 6.59e-05 detection of stimulus 1.24e-06 3.86e-04 neuropeptide receptor activity 7.85e-06 1.96e-03 ciliary membrane 9.21e-06 2.42e-03 gonadotropin-releasing hormone receptor activity 1.04e-05 2.70e-03 opsin binding

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 OPSINS 0.00e+00 0.00e+00 OPSINS 9.88e-10 3.26e-07 CLASS A1 RHODOPSIN LIKE RECEPTORS 9.89e-09 2.91e-06 GPCR LIGAND BINDING 6.21e-08 1.65e-05 G ALPHA I SIGNALLING EVENTS 8.26e-08 1.63e-05 G ALPHA I SIGNALLING EVENTS

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 6.82e-06 3.57e-02 abnormal retinal rod cell outer segment morphology 5.85e-05 1.59e-01 increased percent body fat 3.00e-04 4.47e-01 disorganized photoreceptor outer segment 3.01e-04 4.47e-01 abnormal ocular fundus morphology 6.26e-04 6.89e-01 abnormal rod electrophysiology 7.98e-04 7.91e-01 retinal rod cell degeneration 1.23e-03 1.00e+00 increased body weight 1.44e-03 1.00e+00 abnormal vision 1.57e-03 1.00e+00 short photoreceptor outer segment 1.87e-03 1.00e+00 excessive digestive secretion 2.99e-03 1.00e+00 obese 5.14e-03 1.00e+00 retinal degeneration 5.61e-03 1.00e+00 short estrous cycle 5.61e-03 1.00e+00 disorganized photoreceptor inner segment 5.61e-03 1.00e+00 decreased retinal rod cell number 5.62e-03 1.00e+00 disorganized retinal layers 5.82e-03 1.00e+00 thin retinal outer nuclear layer 6.81e-03 1.00e+00 decreased anxiety-related response 7.48e-03 1.00e+00 disorganized retinal outer nuclear layer 9.33e-03 1.00e+00 photosensitivity

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

²FDR corrected p-value (Benjamini-Hochberg)