Back to main page

DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod301

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod301 Module size 36 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 392636 AGMO alkylglycerol monooxygenase 11161 C14orf1 ergosterol biosynthesis 28 homolog 199920 C1orf168 FYN binding protein 2 10826 C5orf4 fatty acid hydroxylase domain containing 2 9023 CH25H cholesterol 25-hydroxylase 51004 COQ6 coenzyme Q6, monooxygenase 1583 CYP11A1 cytochrome P450 family 11 subfamily A member 1 57404 CYP20A1 cytochrome P450 family 20 subfamily A member 1 51302 CYP39A1 cytochrome P450 family 39 subfamily A member 1 1595 CYP51A1 cytochrome P450 family 51 subfamily A member 1 1581 CYP7A1 cytochrome P450 family 7 subfamily A member 1 9420 CYP7B1 cytochrome P450 family 7 subfamily B member 1 1582 CYP8B1 cytochrome P450 family 8 subfamily B member 1 1718 DHCR24 24-dehydrocholesterol reductase 1717 DHCR7 7-dehydrocholesterol reductase 117278 EBP EBP, cholestenol delta-isomerase 79152 FA2H fatty acid 2-hydroxylase 2222 FDFT1 farnesyl-diphosphate farnesyltransferase 1 158160 HSD17B7 hydroxysteroid 17-beta dehydrogenase 7 pseudogene 2 80270 HSD3B7 hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 7 8564 KMO kynurenine 3-monooxygenase 3930 LBR lamin B receptor 4047 LSS lanosterol synthase 6307 MSMO1 methylsterol monooxygenase 1 137682 NDUFAF6 NADH:ubiquinone oxidoreductase complex assembly factor 6 50814 NSDHL NAD(P) dependent steroid dehydrogenase-like 5740 PTGIS prostaglandin I2 synthase 6309 SC5DL sterol-C5-desaturase 93517 SDR42E1 short chain dehydrogenase/reductase family 42E, member 1 100288072 SDR42E2 short chain dehydrogenase/reductase family 42E, member 2 10280 SIGMAR1 sigma non-opioid intracellular receptor 1 6713 SQLE squalene epoxidase 134429 STARD4 StAR related lipid transfer domain containing 4 7108 TM7SF2 transmembrane 7 superfamily member 2 27346 TMEM97 transmembrane protein 97 7264 TSTA3 tissue specific transplantation antigen P35B

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 3.53e-01 1.69e-10 GO 3-beta-hydroxy-delta5-steroid dehydrogenase activity molecular_function 3.35e-01 3.58e-06 Reactome Sterols are 12-hydroxylated by CYP8B1 Metabolism 2.28e-01 1.33e-27 Reactome Cholesterol biosynthesis Metabolism 1.66e-01 9.43e-19 GO sterol biosynthetic process biological_process 1.34e-01 2.42e-15 Reactome Endogenous sterols Metabolism 1.10e-01 8.74e-12 Reactome Synthesis of bile acids and bile salts via 27-hydroxycholesterol Metabolism 5.57e-02 2.58e-08 Reactome Cholesterol biosynthesis via desmosterol Metabolism 5.51e-02 2.58e-08 Reactome Cholesterol biosynthesis via lathosterol Metabolism 1.97e-02 8.94e-12 GO bile acid biosynthetic process biological_process 1.32e-02 1.98e-24 GO cholesterol biosynthetic process biological_process 9.12e-03 1.79e-39 Reactome Metabolism of steroids Metabolism 2.29e-03 1.14e-17 GO iron ion binding molecular_function

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 cholesterol metabolic process 0.00e+00 0.00e+00 lipid biosynthetic process 0.00e+00 0.00e+00 steroid metabolic process 0.00e+00 0.00e+00 alcohol metabolic process 0.00e+00 0.00e+00 steroid biosynthetic process 0.00e+00 0.00e+00 sterol metabolic process 0.00e+00 0.00e+00 sterol biosynthetic process 0.00e+00 0.00e+00 cholesterol biosynthetic process 0.00e+00 0.00e+00 oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen 0.00e+00 0.00e+00 oxidoreductase activity 0.00e+00 0.00e+00 iron ion binding 0.00e+00 0.00e+00 monooxygenase activity 0.00e+00 0.00e+00 oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen 3.16e-11 2.02e-08 heme binding 8.82e-11 5.41e-08 steroid hydroxylase activity 2.60e-10 2.07e-07 bile acid biosynthetic process 9.90e-10 7.39e-07 bile acid metabolic process 1.22e-08 5.49e-06 3-beta-hydroxy-delta5-steroid dehydrogenase activity 3.12e-08 1.90e-05 cholesterol biosynthetic process via lathosterol 3.12e-08 1.90e-05 cholesterol biosynthetic process via desmosterol

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 CHOLESTEROL BIOSYNTHESIS 0.00e+00 0.00e+00 CHOLESTEROL BIOSYNTHESIS 6.11e-12 2.36e-09 ENDOGENOUS STEROLS 2.13e-11 8.10e-09 SYNTHESIS OF BILE ACIDS AND BILE SALTS 2.71e-11 7.78e-09 ENDOGENOUS STEROLS 4.82e-11 1.79e-08 CYTOCHROME P450 ARRANGED BY SUBSTRATE TYPE 5.66e-11 1.59e-08 SYNTHESIS OF BILE ACIDS AND BILE SALTS 7.01e-11 1.94e-08 CYTOCHROME P450 ARRANGED BY SUBSTRATE TYPE 2.68e-10 9.33e-08 BILE ACID AND BILE SALT METABOLISM 4.38e-10 1.49e-07 PHASE1 FUNCTIONALIZATION OF COMPOUNDS 5.08e-10 1.29e-07 PHASE1 FUNCTIONALIZATION OF COMPOUNDS 6.05e-10 1.52e-07 BILE ACID AND BILE SALT METABOLISM 3.34e-08 6.94e-06 BIOLOGICAL OXIDATIONS 4.98e-08 1.33e-05 BIOLOGICAL OXIDATIONS 4.18e-06 8.46e-04 SYNTHESIS OF BILE ACIDS AND BILE SALTS VIA 24 HYDROXYCHOLESTEROL 8.07e-06 1.23e-03 SYNTHESIS OF BILE ACIDS AND BILE SALTS VIA 24 HYDROXYCHOLESTEROL 1.15e-05 2.18e-03 SYNTHESIS OF BILE ACIDS AND BILE SALTS VIA 7ALPHA HYDROXYCHOLESTEROL 2.29e-05 3.23e-03 SYNTHESIS OF BILE ACIDS AND BILE SALTS VIA 7ALPHA HYDROXYCHOLESTEROL 4.71e-03 3.91e-01 STEROID HORMONES 5.49e-03 4.93e-01 STEROID HORMONES

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 3.99e-06 2.44e-02 decreased intestinal cholesterol absorption 1.57e-05 6.42e-02 abnormal bile salt homeostasis 2.05e-05 7.70e-02 flaky skin 1.02e-04 2.29e-01 hyperkeratosis 1.97e-04 3.46e-01 abnormal cholesterol homeostasis 3.21e-04 4.69e-01 steatorrhea 7.52e-04 7.64e-01 abnormal bile composition 9.46e-04 8.74e-01 abnormal skin condition 1.20e-03 1.00e+00 abnormal bile salt level 1.20e-03 1.00e+00 dry skin 1.39e-03 1.00e+00 syndactyly 1.76e-03 1.00e+00 pericardial effusion 2.21e-03 1.00e+00 decreased cholesterol level 2.30e-03 1.00e+00 delayed hair appearance 2.58e-03 1.00e+00 abnormal lipid level 5.46e-03 1.00e+00 focal hair loss 5.49e-03 1.00e+00 abnormal epidermis stratum granulosum morphology 6.34e-03 1.00e+00 alopecia 6.36e-03 1.00e+00 hypoactivity 7.28e-03 1.00e+00 preweaning lethality

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

²FDR corrected p-value (Benjamini-Hochberg)