PCOSBase: a manually curated database of polycystic ovarian syndrome

Abstract Polycystic ovarian syndrome (PCOS) is one of the main causes of infertility and affects 5–20% women of reproductive age. Despite the increased prevalence of PCOS, the mechanisms involved in its pathogenesis and pathophysiology remains unclear. The expansion of omics on studying the mechanisms of PCOS has lead into vast amounts of proteins related to PCOS resulting to a challenge in collating and depositing this deluge of data into one place. A knowledge-based repository named as PCOSBase was developed to systematically store all proteins related to PCOS. These proteins were compiled from various online databases and published expression studies. Rigorous criteria were developed to identify those that were highly related to PCOS. They were manually curated and analysed to provide additional information on gene ontologies, pathways, domains, tissue localizations and diseases that associate with PCOS. Other proteins that might interact with PCOS-related proteins identified from this study were also included. Currently, 8185 PCOS-related proteins were identified and assigned to 13 237 gene ontology vocabulary, 1004 pathways, 7936 domains, 29 disease classes, 1928 diseases, 91 tissues and 320 472 interactions. All publications related to PCOS are also indexed in PCOSBase. Data entries are searchable in the main page, search, browse and datasets tabs. Protein advanced search is provided to search for specific proteins. To date, PCOSBase has the largest collection of PCOS-related proteins. PCOSBase aims to become a self-contained database that can be used to further understand the PCOS pathogenesis and towards the identification of potential PCOS biomarkers. Database URL: http://pcosbase.org

[1]  Evan Bolton,et al.  Database resources of the National Center for Biotechnology Information , 2017, Nucleic Acids Res..

[2]  Peggy Hall,et al.  The NHGRI GWAS Catalog, a curated resource of SNP-trait associations , 2013, Nucleic Acids Res..

[3]  Janos X. Binder,et al.  DISEASES: Text mining and data integration of disease–gene associations , 2014, bioRxiv.

[4]  Pak Chung Sham,et al.  GWASdb v2: an update database for human genetic variants identified by genome-wide association studies , 2015, Nucleic Acids Res..

[5]  P. Stenson,et al.  The Human Gene Mutation Database: building a comprehensive mutation repository for clinical and molecular genetics, diagnostic testing and personalized genomic medicine , 2013, Human Genetics.

[6]  Silvio C. E. Tosatto,et al.  InterPro in 2017—beyond protein family and domain annotations , 2016, Nucleic Acids Res..

[7]  G. von Heijne,et al.  Tissue-based map of the human proteome , 2015, Science.

[8]  Núria Queralt-Rosinach,et al.  DisGeNET: a comprehensive platform integrating information on human disease-associated genes and variants , 2016, Nucleic Acids Res..

[9]  P. Claman.  Men at risk: occupation and male infertility. , 2004, Fertility and sterility.

[10]  Doron Lancet,et al.  MalaCards: an amalgamated human disease compendium with diverse clinical and genetic annotation and structured search , 2016, Nucleic Acids Res..

[11]  Alexander R. Pico,et al.  WikiPathways: Pathway Editing for the People , 2008, PLoS biology.

[12]  Hans-Dieter Pohlenz,et al.  PhenomicDB: a multi-species genotype/phenotype database for comparative phenomics , 2005, Bioinform..

[13]  Revised 2003 consensus on diagnostic criteria and long-term health risks related to polycystic ovary syndrome. , 2004, Fertility and sterility.

[14]  Gregory D. Schuler,et al.  Database resources of the National Center for Biotechnology Information: update , 2004, Nucleic acids research.

[15]  Robert Petryszak,et al.  ArrayExpress update—simplifying data submissions , 2014, Nucleic Acids Res..

[16]  Ram Shankar Barai,et al.  PCOSKB: A KnowledgeBase on genes, diseases, ontology terms and biochemical pathways associated with PolyCystic Ovary Syndrome , 2015, Nucleic Acids Res..

[17]  Gautier Koscielny,et al.  Open Targets: a platform for therapeutic target identification and validation , 2016, Nucleic Acids Res..

[18]  Tatiana A. Tatusova,et al.  Gene: a gene-centered information resource at NCBI , 2014, Nucleic Acids Res..

[19]  B. Fauser,et al.  Revised 2003 consensus on diagnostic criteria and long-term health risks related to polycystic ovary syndrome (PCOS). , 2004, Human reproduction.

[20]  The Uniprot Consortium,et al.  UniProt: a hub for protein information , 2014, Nucleic Acids Res..

[21]  Xin Li,et al.  PCOS and obesity: insulin resistance might be a common etiology for the development of type I endometrial carcinoma. , 2014, American journal of cancer research.

[22]  A. Dunaif,et al.  Ovarian hypertension: polycystic ovary syndrome. , 2011, Endocrinology and metabolism clinics of North America.

[23]  François Schiettecatte,et al.  OMIM.org: Online Mendelian Inheritance in Man (OMIM®), an online catalog of human genes and genetic disorders , 2014, Nucleic Acids Res..

[24]  F. Petraglia,et al.  Genetic, hormonal and metabolic aspects of PCOS: an update , 2016, Reproductive Biology and Endocrinology.

[25]  Wei Xu,et al.  The disease and gene annotations (DGA): an annotation resource for human disease , 2012, Nucleic Acids Res..

[26]  Martin H. Schaefer,et al.  HIPPIE v2.0: enhancing meaningfulness and reliability of protein–protein interaction networks , 2016, Nucleic Acids Res..

[27]  Minoru Kanehisa,et al.  KEGG as a reference resource for gene and protein annotation , 2015, Nucleic Acids Res..

[28]  H. Teede,et al.  Polycystic ovary syndrome , 2016, Nature Reviews Disease Primers.

[29]  Dhanashree S. Kelkar,et al.  Proteomics of follicular fluid from women with polycystic ovary syndrome suggests molecular defects in follicular development. , 2015, The Journal of clinical endocrinology and metabolism.

[30]  I. Passos,et al.  Polycystic ovary syndrome and mental disorders: a systematic review and exploratory meta-analysis , 2016, Neuropsychiatric disease and treatment.

[31]  R. Fox,et al.  A View from the Web , 1997, Journal of the Royal Society of Medicine.

[32]  Juancarlos Chan,et al.  Gene Ontology Consortium: going forward , 2014, Nucleic Acids Res..

[33]  K. Tai,et al.  Functional microarray analysis of differentially expressed genes in granulosa cells from women with polycystic ovary syndrome related to MAPK/ERK signaling , 2015, Scientific Reports.