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However, there is a lack of genetic study of the internal mechanisms of PCOS. In this study we have identified core genes involved in the pathogenesis of PCOS by using bioinformatics analysis. For this study, the dataset GSE40400 was collected from the Gene Expression Omnibus (GEO) database. The differentially expressed genes (DEGs) were obtained by using the R package limma. We analysed the microarray dataset GSE40400 to identify DEGs of PCOS subjects with VD deficiency under oxidative stress. After applying the available numerical expression values, we 617 novel DEGS out of which 183 up-regulated and 434 were down-regulated). Out of them 144 novel DEGS related exclusively to oxidative stress (39 up-regulated and 105 down-regulated), 39 novel DEGS related exclusively to vitamin D deficiency (12 up-regulated and 27 down-regulated) and 160 novel DEGS related exclusively to oxidative stress and vitamin D deficiency (48 up-regulated and 112 down-regulated). 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New York, NY: Humana Press; 2016. p. 93–110. https://doi.org/ 10.1007/978-1-4939- 3578-9_5" }, { "key": "ref12", "doi": "10.1007/0-387-29362-0_23", "unstructured": "Smyth Gordon K. Limma: linear models for microarray data. In: Bioinformatics and computational biology solutions using R and Bioconductor. New York, NY: Springer; 2005. p. 397–420" }, { "key": "ref13", "doi": "10.1016/s0166-4328(01)00297-2", "unstructured": "Y. Benjamini, D. Drai, G. Elmer, N. Kafkafi, I. Golani, Controlling the false discovery rate in behavior genet ics research, Behavioural Brain Research. 125 (2001) 279–284. https://doi.org/10.1016/S0166-4328(01)00297-2" }, { "key": "ref14", "doi": "10.1093/bioinformatics/bti448", "unstructured": "Yudi P, Stefan M, Serge K, Arief G, Ploner A. False discovery rate, sensitivity and sample size for microarray studies. Bioinformatics 2005;21(13):3017–24" }, { "key": "ref15", "doi": "10.1038/75556", "unstructured": "Michael A, Ball Catherine A, Blake Judith A, Botstein David, Butler Heather, Michael Cherry J, Allan P, Davis, et al. Gene ontology: tool for the unification of biology. Nat Genet. 2000;25(1):25" }, { "key": "ref16", "doi": "10.1093/nar/gkv1070", "unstructured": "Minoru K, Yoko S, Masayuki K, Miho F, Mao T. KEGG as a reference resource for gene and protein annotation. Nucleic Acids Res 2015;44: D457–62" }, { "key": "ref17", "doi": "10.1093/bioinformatics/bts251", "unstructured": "Jiao Xiaoli, Sherman Brad T, Huang Da Wei, Stephens Robert, Baseler Michael W, Clifford Lane H, Lempicki Richard A. DAVID-WS: a stateful web service to facilitate gene/protein list analysis. Bioinformatics 2012;28(13):1805–6. https://doi.org/ 10.1093/bioinformatics/bts251" }, { "key": "ref18", "doi": "10.1016/j.fertnstert.2010.09.032", "unstructured": "Azziz Ricardo, Dumesic Daniel A, Goodarzi Mark O. Polycystic ovary syndrome: an ancient disorder? Fertil Steril 2011;95(5):1544–8. https://doi.org/10.1016/j. fertnstert.2010.09.032" }, { "key": "ref19", "doi": "10.12659/msm.915320", "unstructured": "Yuanyuan Zhong, Wang Zeqin, Song Xiaojie, Liu Liping, Xiang Yun, Zhou Jieqiong. Proliferation of ovarian granulosa cells in polycystic ovarian syndrome is regulated by MicroRNA-24 by targeting wingless-type family member 2B (WNT2B). Med Sci Mon Int Med J Exp Clin Res 2019; 25:4553–9. https://doi.org/10.12659/ MSM.915320" }, { "key": "ref20", "doi": "10.2105/ajph.2004.045260", "unstructured": "Garland CF, Garland FC, Gorham ED et al., 2006. The role of vitamin D in Cancer prevention. Am. J Public Health. 96 (2): 252-261" }, { "key": "ref21", "doi": "10.1007/s00125-012-2529-x", "unstructured": "Dc Deleskog, A. Hilding K. Brismar, A. Hamsten, S. Efendic, and C. G. Ostenson. Low serum 25-hydroxyvitamin D level predicts progression to type 2 diabetes in individuals P a g e 211 | 10 with prediabetes but not with normal glucose tolerance. Diabetologia. 2012, 55: 1668–1678" }, { "key": "ref22", "doi": "10.1507/endocrj.47.383", "unstructured": "Maestro, J. Campion, N. D ´ avila, and C. Calle. Stimulation ´ by 1,25 dihydroxyvitamin D3 of insulin receptor expression and insulin responsiveness for glucose transport in U-937 human promonocytic cells. Endocrine Journal. 2000, 47(4): 383–391" }, { "key": "ref23", "doi": "10.1016/0143-4160(90)90031-o", "unstructured": "P. F. Wil liams, I. D. Caterson, G. J. Cooney, R. R. Zilkens, and J. R. Turtle. High affinity insulin binding and insulin receptor-effector coupling: modulation by Ca2+. Cell Calcium. 1990, 11(8): 547–556" }, { "key": "ref24", "doi": "10.1007/s00404-009-0958-7", "unstructured": "Yildizhan R, Kurdoglu M, Adali E, Kolusari A, Yildizhan B, S ahin HG, et al. Serum 25-hydroxyvitamin D concentrations in obese and non-obese women with polycystic ovary syndrome. Arch Gynecol Obstet. 2009, 280: 559–63" }, { "key": "ref25", "doi": "10.1017/s002202991700067x", "unstructured": "Bae H., Jeong C. H., Cheng W. N., Hong K., Seo H. G., Han S. G. Oxidative stress induced inflammatory responses and effects of N-acetylcysteine in bovine mammary alveolar cells. Journal of Dairy Research. 2017, 84(4): 418–425" } ], "record": { "registrant": "Longman Publishers", "registered": "2026-09-10", "updated": "2026-09-20", "issue_number": 1, "source": "crossref-api", "source_agency": "Crossref (member 25296)" } }, "url_after": "https://www.jst.org.in/index.php/pub/article/view/620", "sha256_before": null, "sha256_after": "2a148fce86594155365d38060c7c6e3362ca782e8270d60106610e139022a989" }, { "seq": 2, "kind": "update", "at": "2026-09-29 23:59:57", "by": "Administrator (admin)", "by_kind": "user", "note": "record re-read from api.crossref.org", "changes": [ { "path": "container.titles.0.value", "from": "Journal of Science & Technology", "to": "Journal of Science & Technology" } ], "record_after": { "format": "smartscholars-doi-metadata/1.0", "doi": "10.46243/jst.2021.v6.i04.pp206-215", "referent": "Creation", "type": "JournalArticle", "structural_type": "Digital", "modes": [ "Visual" ], "characters": [ "Language" ], "titles": [ { "value": "Identification of differentially expressed signature genes of PCOS under vitamin D deficiency and oxidative stress: A bioinformatics Analysis", "type": "PrincipalTitle", "lang": "en" } ], "identifiers": [ { "type": "DOI", "value": "10.46243/jst.2021.v6.i04.pp206-215" } ], "agents": [ { "role": "author", "name": { "given": "Aurobinda", "family": "Das" }, "sequence": "first" }, { "role": "author", "name": { "given": "Pallavi", "family": "Mishra" }, "sequence": "additional" }, { "role": "publisher", "name": { "org": "Longman Publishers" } } ], "dates": { "published": "2021-08-31", "date_type": "PublicationDate", "online": "2021-08-31" }, "language": "en", "container": { "type": "Journal", "titles": [ { "value": "Journal of Science & Technology", "type": "PrincipalTitle" } ], "identifiers": [ { "type": "ISSN", "value": "2456-5660", "medium": "electronic" } ], "volume": "06", "issue": "04", "pages": { "first": "206", "last": "215" } }, "links": [ { "url": "https://www.jst.org.in/index.php/pub/article/view/620", "return_type": "text/html", "primary": true }, { "url": "https://www.jst.org.in/index.php/pub/article/download/620/554", "purpose": "text-mining", "return_type": "application/pdf" }, { "url": "https://www.jst.org.in/index.php/pub/article/download/620/2807", "purpose": "text-mining", "return_type": "application/xml" }, { "url": "https://www.jst.org.in/index.php/pub/article/view/620/554", "purpose": "similarity-checking" } ], "abstract": { "value": "Polycystic ovary syndrome (PCOS) is one of the most common hormonal disorders in women of reproductive age. However, there is a lack of genetic study of the internal mechanisms of PCOS. In this study we have identified core genes involved in the pathogenesis of PCOS by using bioinformatics analysis. For this study, the dataset GSE40400 was collected from the Gene Expression Omnibus (GEO) database. The differentially expressed genes (DEGs) were obtained by using the R package limma. We analysed the microarray dataset GSE40400 to identify DEGs of PCOS subjects with VD deficiency under oxidative stress. After applying the available numerical expression values, we 617 novel DEGS out of which 183 up-regulated and 434 were down-regulated). Out of them 144 novel DEGS related exclusively to oxidative stress (39 up-regulated and 105 down-regulated), 39 novel DEGS related exclusively to vitamin D deficiency (12 up-regulated and 27 down-regulated) and 160 novel DEGS related exclusively to oxidative stress and vitamin D deficiency (48 up-regulated and 112 down-regulated). The functional analysis was carried out by using DAVID database and software tools for the identified up-regulated and down-regulated DEGs.", "lang": "en" }, "license": { "url": "https://creativecommons.org/licenses/by/4.0", "start": "2021-08-31", "applies_to": "vor" }, "references": [ { "key": "ref1", "doi": "10.4103/0971-5916.166527", "unstructured": "Fd Ming-Wei Lin and Meng-Hsing Wu. The role of vitamin D in Polycystic ovary syndrome, Indian J Med Res. 2015 Sep, 142(3): 238–240" }, { "key": "ref2", "doi": "10.1093/humupd/dmr001", "unstructured": "de Groot PC, Dekkers OM, Romijn JA, Dieben SW & Helmerhorst FM. PCOS, coronary heart disease, stroke and the influence of obesity: a systematic review and meta-analysis. Human Reproduction Update. 2011, 17: 495–500" }, { "key": "ref3", "doi": "10.1100/2012/741861", "unstructured": "Mishra P, Samanta L. Oxidative stress and heart failure in altered thyroid states. 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