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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod132

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod132 Module size 41 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 216 ALDH1A1 aldehyde dehydrogenase 1 family member A1 8854 ALDH1A2 aldehyde dehydrogenase 1 family member A2 158835 AWAT2 acyl-CoA wax alcohol acyltransferase 2 53630 BCMO1 beta-carotene oxygenase 1 83875 BCO2 beta-carotene oxygenase 2 622 BDH1 3-hydroxybutyrate dehydrogenase 1 84869 CBR4 carbonyl reductase 4 306504 CMAS tRNA methyltransferase 9B (putative) 26063 DECR2 2,4-dienoyl-CoA reductase 2 115817 DHRS1 dehydrogenase/reductase 1 79154 DHRS11 dehydrogenase/reductase 11 10202 DHRS2 dehydrogenase/reductase 2 9249 DHRS3 dehydrogenase/reductase 3 10901 DHRS4 dehydrogenase/reductase 4 317749 DHRS4L2 dehydrogenase/reductase 4 like 2 51635 DHRS7 dehydrogenase/reductase 7 25979 DHRS7B dehydrogenase/reductase 7B 201140 DHRS7C dehydrogenase/reductase 7C 10170 DHRS9 dehydrogenase/reductase 9 3248 HPGD 15-hydroxyprostaglandin dehydrogenase 54979 HRASLS2 HRAS like suppressor 2 374875 HSD11B1L hydroxysteroid 11-beta dehydrogenase 1 like 51170 HSD17B11 hydroxysteroid 17-beta dehydrogenase 11 345275 HSD17B13 hydroxysteroid 17-beta dehydrogenase 13 51171 HSD17B14 hydroxysteroid 17-beta dehydrogenase 14 7923 HSD17B8 hydroxysteroid 17-beta dehydrogenase 8 83693 HSDL1 hydroxysteroid dehydrogenase like 1 293711 LRAT HRAS-like suppressor family, member 5 140838 NANP N-acetylneuraminic acid phosphatase 55825 PECR peroxisomal trans-2-enoyl-CoA reductase 8228 PNPLA4 patatin like phospholipase domain containing 4 157506 RDH10 retinol dehydrogenase 10 51109 RDH11 retinol dehydrogenase 11 145226 RDH12 retinol dehydrogenase 12 8608 RDH16 retinol dehydrogenase 16 5959 RDH5 retinol dehydrogenase 5 50700 RDH8 retinol dehydrogenase 8 54884 RETSAT retinol saturase 114106 RPE65 beta-carotene oxygenase 1 195814 SDR16C5 short chain dehydrogenase/reductase family 16C member 5 121214 SDR9C7 short chain dehydrogenase/reductase family 9C member 7

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 2.84e-01 1.98e-36 GO retinol metabolic process biological_process 2.26e-01 5.51e-26 GO retinol dehydrogenase activity molecular_function 1.20e-01 4.54e-03 GO 15-hydroxyprostaglandin dehydrogenase (NAD+) activity molecular_function 1.14e-01 2.12e-11 GO estradiol 17-beta-dehydrogenase activity molecular_function 9.15e-02 5.87e-11 GO estrogen biosynthetic process biological_process 8.26e-02 6.57e-22 Reactome The canonical retinoid cycle in rods (twilight vision) Signal Transduction 3.37e-02 6.57e-22 Reactome RA biosynthesis pathway Signal Transduction

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 retinal metabolic process 0.00e+00 0.00e+00 hormone metabolic process 0.00e+00 0.00e+00 isoprenoid metabolic process 0.00e+00 0.00e+00 regulation of hormone levels 0.00e+00 0.00e+00 retinoid metabolic process 0.00e+00 0.00e+00 diterpenoid metabolic process 0.00e+00 0.00e+00 retinol metabolic process 0.00e+00 0.00e+00 alcohol metabolic process 0.00e+00 0.00e+00 oxidoreductase activity 0.00e+00 0.00e+00 oxidoreductase activity, acting on CH-OH group of donors 0.00e+00 0.00e+00 retinol dehydrogenase activity 0.00e+00 0.00e+00 oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor 0.00e+00 0.00e+00 NADP-retinol dehydrogenase activity 9.81e-13 6.79e-10 alcohol dehydrogenase (NADP+) activity 2.36e-11 1.52e-08 aldo-keto reductase (NADP) activity 1.16e-09 8.56e-07 cellular aldehyde metabolic process 5.79e-09 3.88e-06 retinoic acid metabolic process 1.27e-08 8.16e-06 visual perception 1.58e-08 1.00e-05 sensory perception of light stimulus 2.21e-08 9.56e-06 estradiol 17-beta-dehydrogenase activity

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 2.15e-06 3.56e-04 METABOLISM OF STEROID HORMONES AND VITAMINS A AND D 4.67e-05 7.84e-03 METABOLISM OF STEROID HORMONES AND VITAMINS A AND D 2.42e-03 2.51e-01 ETHANOL OXIDATION 5.84e-03 4.68e-01 ETHANOL OXIDATION 1.84e-02 1.00e+00 PHASE1 FUNCTIONALIZATION OF COMPOUNDS

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 2.03e-11 1.41e-06 delayed dark adaptation 3.80e-10 1.62e-05 abnormal vitamin A metabolism 7.05e-05 1.79e-01 abnormal eye electrophysiology 1.11e-04 2.42e-01 absent third pharyngeal arch 1.31e-04 2.71e-01 small forelimb buds 1.75e-04 3.23e-01 abnormal retinol level 1.85e-04 3.32e-01 retinal cone cell degeneration 2.41e-04 3.93e-01 abnormal frontonasal prominence morphology 2.60e-04 4.10e-01 retinal rod cell degeneration 3.26e-04 4.72e-01 absent pharyngeal arches 3.26e-04 4.72e-01 abnormal vagus ganglion morphology 3.70e-04 5.09e-01 abnormal maxillary prominence morphology 4.26e-04 5.52e-01 abnormal third pharyngeal arch artery morphology 4.78e-04 5.93e-01 abnormal glossopharyngeal ganglion morphology 4.98e-04 6.04e-01 abnormal retinal rod cell outer segment morphology 7.88e-04 7.83e-01 abnormal vestibulocochlear ganglion morphology 8.57e-04 8.25e-01 small otic vesicle 1.05e-03 9.25e-01 short photoreceptor outer segment 1.47e-03 1.00e+00 decreased somite size 1.58e-03 1.00e+00 abnormal heart tube morphology

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

²FDR corrected p-value (Benjamini-Hochberg)