title: GeneChaser: identifying all biological and clinical conditions in which genes of interest are differentially expressed.
abstract: 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.
  
  
  CONCLUSIONS
  We demonstrated that GeneChaser is a powerful tool to elucidate information on function, transcriptional regulation, drug-response and clinical implications for genes of interest.
authors.affiliation: Stanford Center for Biomedical Informatics Research, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA. rchen1@stanford.edu
authors.forename: Rong
authors.initials: R
authors.lastname: Chen
authors.forename: Rohan
authors.initials: R
authors.lastname: Mallelwar
authors.forename: Ajit
authors.initials: A
authors.lastname: Thosar
authors.forename: Shivkumar
authors.initials: S
authors.lastname: Venkatasubrahmanyam
authors.forename: Atul J
authors.initials: AJ
authors.lastname: Butte
mesh_terms: D000818:Animals; D019295:Computational Biology / Q000379:methods*; D003198:Computer Simulation; D015870:Gene Expression; D020869:Gene Expression Profiling / Q000379:methods*; D005786:Gene Expression Regulation; D006801:Humans; D020407:Internet; D008288:Malaria / Q000235:genetics / Q000378:metabolism; D008297:Male; D051379:Mice; D008957:Models, Genetic; D009369:Neoplasms / Q000235:genetics / Q000378:metabolism; D020411:Oligonucleotide Array Sequence Analysis; D013094:Spermatozoa / Q000473:pathology