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GeneChaser: Identifying all biological and clinical conditions in which genes of interest are differentially expressed

Rong Chen123, Rohan Mallelwar4, Ajit Thosar4, Shivkumar Venkatasubrahmanyam123 and Atul J Butte123*

Author Affiliations

1 Stanford Center for Biomedical Informatics Research, Department of Medicine, Stanford University School of Medicine, 251 Campus Drive, Stanford, CA 94305, USA

2 Department of Pediatrics, Stanford University School of Medicine, 251 Campus Drive, Stanford, CA 94305, USA

3 Lucile Packard Children's Hospital, 725 Welch Road, Palo Alto, CA 94304, USA

4 Optra Systems Pvt. Ltd, 1, "Dnyanesh", CTS No. 1179/3, Modern College Road, Shivajinagar, Pune, 411 005, India

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BMC Bioinformatics 2008, 9:548  doi:10.1186/1471-2105-9-548

Published: 18 December 2008



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.


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.

We performed a single gene search for Nanog and a multiple gene search for Nanog, Oct4, Sox2 and LIN28, 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.


We demonstrated that GeneChaser is a powerful tool to elucidate information on function, transcriptional regulation, drug-response and clinical implications for genes of interest.