{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,12]],"date-time":"2026-02-12T15:30:53Z","timestamp":1770910253800,"version":"3.50.1"},"reference-count":23,"publisher":"Springer Science and Business Media LLC","issue":"1","content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2008,12]]},"abstract":"<jats:title>Abstract<\/jats:title>\n          <jats:sec>\n            <jats:title>Background<\/jats:title>\n            <jats:p>The amount of gene expression data in the public repositories, such as NCBI Gene Expression Omnibus (GEO) has grown exponentially, and provides a gold mine for bioinformaticians, but has not been easily accessible by biologists and clinicians.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Results<\/jats:title>\n            <jats:p>We developed an automated approach to annotate and analyze all GEO data sets, including 1,515 GEO data sets from 231 microarray types across 42 species, and performed 12,658 group versus group comparisons of 24 GEO-specified types. We then built GeneChaser, a web server that enables biologists and clinicians without bioinformatics skills to easily identify biological and clinical conditions in which a gene or set of genes was differentially expressed. GeneChaser displays these conditions in graphs, gives statistical comparisons, allows sort\/filter functions and provides access to the original studies.<\/jats:p>\n            <jats:p>We performed a <jats:italic>single gene search<\/jats:italic> for <jats:italic>Nanog<\/jats:italic> and a <jats:italic>multiple gene search<\/jats:italic> for <jats:italic>Nanog<\/jats:italic>, <jats:italic>Oct4<\/jats:italic>, <jats:italic>Sox2<\/jats:italic> and <jats:italic>LIN28<\/jats:italic>, confirmed their roles in embryonic stem cell development, identified several drugs that regulate their expression, and suggested their potential roles in sex determination, abnormal sperm morphology, malaria infection, and cancer.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Conclusion<\/jats:title>\n            <jats:p>We demonstrated that GeneChaser is a powerful tool to elucidate information on function, transcriptional regulation, drug-response and clinical implications for genes of interest.<\/jats:p>\n          <\/jats:sec>","DOI":"10.1186\/1471-2105-9-548","type":"journal-article","created":{"date-parts":[[2008,12,19]],"date-time":"2008-12-19T07:14:40Z","timestamp":1229670880000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":30,"title":["GeneChaser: Identifying all biological and clinical conditions in which genes of interest are differentially expressed"],"prefix":"10.1186","volume":"9","author":[{"given":"Rong","family":"Chen","sequence":"first","affiliation":[]},{"given":"Rohan","family":"Mallelwar","sequence":"additional","affiliation":[]},{"given":"Ajit","family":"Thosar","sequence":"additional","affiliation":[]},{"given":"Shivkumar","family":"Venkatasubrahmanyam","sequence":"additional","affiliation":[]},{"given":"Atul J","family":"Butte","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2008,12,18]]},"reference":[{"key":"2533_CR1","doi-asserted-by":"crossref","unstructured":"Barrett T, Troup DB, Wilhite SE, Ledoux P, Rudnev D, Evangelista C, Kim IF, Soboleva A, Tomashevsky M, Edgar R: NCBI GEO: mining tens of millions of expression profiles\u2013database and tools update. Nucleic acids research 2007, (35 Database):D760\u2013765. 10.1093\/nar\/gkl887","DOI":"10.1093\/nar\/gkl887"},{"key":"2533_CR2","doi-asserted-by":"crossref","unstructured":"Parkinson H, Kapushesky M, Shojatalab M, Abeygunawardena N, Coulson R, Farne A, Holloway E, Kolesnykov N, Lilja P, Lukk M, et al.: ArrayExpress\u2013a public database of microarray experiments and gene expression profiles. Nucleic acids research 2007, (35 Database):D747\u2013750. 10.1093\/nar\/gkl995","DOI":"10.1093\/nar\/gkl995"},{"issue":"16","key":"2533_CR3","doi-asserted-by":"publisher","first-page":"6062","DOI":"10.1073\/pnas.0400782101","volume":"101","author":"AI Su","year":"2004","unstructured":"Su AI, Wiltshire T, Batalov S, Lapp H, Ching KA, Block D, Zhang J, Soden R, Hayakawa M, Kreiman G, et al.: A gene atlas of the mouse and human protein-encoding transcriptomes. 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