Dataset Information

PCOSKB_R2: a database of genes, diseases, pathways, and networks associated with polycystic ovary syndrome.

ABSTRACT: PolyCystic Ovary Syndrome KnowledgeBase (PCOSKB_R2) is a manually curated database with information on 533 genes, 145 SNPs, 29 miRNAs, 1,150 pathways, and 1,237 diseases associated with PCOS. This data has been retrieved based on evidence gleaned by critically reviewing literature and related records available for PCOS in databases such as KEGG, DisGeNET, OMIM, GO, Reactome, STRING, and dbSNP. Since PCOS is associated with multiple genes and comorbidities, data mining algorithms for comorbidity prediction and identification of enriched pathways and hub genes are integrated in PCOSKB_R2, making it an ideal research platform for PCOS. PCOSKB_R2 is freely accessible at http://www.pcoskb.bicnirrh.res.in/ .

SUBMITTER: Sharma M

PROVIDER: S-EPMC7477240 | biostudies-literature | 2020 Sep

REPOSITORIES: biostudies-literature

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Publications

PCOSKB<sub>R2</sub>: a database of genes, diseases, pathways, and networks associated with polycystic ovary syndrome.

Sharma Mridula M Barai Ram Shankar RS Kundu Indra I Bhaye Sameeksha S Pokar Khushal K Idicula-Thomas Susan S

Scientific reports 20200907 1

PolyCystic Ovary Syndrome KnowledgeBase (PCOSKB<sub>R2</sub>) is a manually curated database with information on 533 genes, 145 SNPs, 29 miRNAs, 1,150 pathways, and 1,237 diseases associated with PCOS. This data has been retrieved based on evidence gleaned by critically reviewing literature and related records available for PCOS in databases such as KEGG, DisGeNET, OMIM, GO, Reactome, STRING, and dbSNP. Since PCOS is associated with multiple genes and comorbidities, data mining algorithms for co ...[more]

PMID: 32895427

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Project description:Polycystic Ovary Syndrome (PCOS) is a multifactorial syndrome with reproductive, endocrine, and metabolic symptoms, affecting about 10% women of reproductive age. Pathogenesis of the syndrome is poorly understood with genetic and fetal origins being the focus of the conundrum. Genetic predisposition of PCOS has been confirmed by candidate gene studies and Genome-Wide Association Studies (GWAS). Recently, the expression of PCOS candidate genes across gestation has been studied in human and bovine fetal ovaries. The current study sought to identify potential upstream regulators and mechanisms associated with PCOS candidate genes. Using RNA sequencing data of bovine fetal ovaries (62-276 days, n = 19), expression of PCOS candidate genes across gestation was analysed using Partek Flow. A supervised heatmap of the expression data of all 24,889 genes across gestation was generated. Most of the PCOS genes fell into one of four clusters according to their expression patterns. Some genes correlated negatively (early genes; C8H9orf3, TOX3, FBN3, GATA4, HMGA2, and DENND1A) and others positively (late genes; FDFT1, LHCGR, AMH, FSHR, ZBTB16, and PLGRKT) with gestational age. Pathways associated with PCOS candidate genes and genes co-expressed with them were determined using Ingenuity pathway analysis (IPA) software as well as DAVID Bioinformatics Resources for KEGG pathway analysis and Gene Ontology databases. Genes expressed in the early cluster were mainly involved in mitochondrial function and oxidative phosphorylation and their upstream regulators included PTEN, ESRRG/A and MYC. Genes in the late cluster were involved in stromal expansion, cholesterol biosynthesis and steroidogenesis and their upstream regulators included TGFB1/2/3, TNF, ERBB2/3, VEGF, INSIG1, POR, and IL25. These findings provide insight into ovarian development of relevance to the origins of PCOS, and suggest that multiple aetiological pathways might exist for the development of PCOS.

Dataset Information

PCOSKB_R2: a database of genes, diseases, pathways, and networks associated with polycystic ovary syndrome.

Publications

PCOSKB<sub>R2</sub>: a database of genes, diseases, pathways, and networks associated with polycystic ovary syndrome.

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OmicsDI is part of the ELIXIR infrastructure

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Dataset Information

PCOSKBR2: a database of genes, diseases, pathways, and networks associated with polycystic ovary syndrome.

Publications

PCOSKB<sub>R2</sub>: a database of genes, diseases, pathways, and networks associated with polycystic ovary syndrome.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets

PCOSKB_R2: a database of genes, diseases, pathways, and networks associated with polycystic ovary syndrome.