TY - JOUR
T1 - GeneChaser
T2 - identifying all biological and clinical conditions in which genes of interest are differentially expressed.
AU - Chen, Rong
AU - Mallelwar, Rohan
AU - Thosar, Ajit
AU - Venkatasubrahmanyam, Shivkumar
AU - Butte, Atul J.
N1 - Funding Information:
This work was supported by Lucile Packard Foundation for Children's Health, US National Library of Medicine (K22 LM008261), National Institute of General Medical Sciences (R01 GM079719), Howard Hughes Medical Institute, and Pharmaceutical Research and Manufacturers of America Foundation. We thank Alex Skrenchuk from Stanford University for computer support, Valerie Natale for editing, and Kitch Wilson, Annie P. Chiang, Andy Kogelnik and Gavi Kohlberg from Stanford University for suggestions.
PY - 2008
Y1 - 2008
N2 - BACKGROUND: 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. RESULTS: 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. CONCLUSION: We demonstrated that GeneChaser is a powerful tool to elucidate information on function, transcriptional regulation, drug-response and clinical implications for genes of interest.
AB - BACKGROUND: 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. RESULTS: 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. CONCLUSION: We demonstrated that GeneChaser is a powerful tool to elucidate information on function, transcriptional regulation, drug-response and clinical implications for genes of interest.
UR - http://www.scopus.com/inward/record.url?scp=62349088493&partnerID=8YFLogxK
U2 - 10.1186/1471-2105-9-548
DO - 10.1186/1471-2105-9-548
M3 - Article
C2 - 19094235
AN - SCOPUS:62349088493
SN - 1471-2105
VL - 9
SP - 548
JO - BMC Bioinformatics
JF - BMC Bioinformatics
ER -