title: GEPIS--quantitative gene expression profiling in normal and cancer tissues.
abstract: BACKGROUND
  Expression profiling in diverse tissues is fundamental to understanding gene function as well as therapeutic target identification. The vast collection of expressed sequence tags (ESTs) and the associated tissue source information provides an attractive opportunity for studying gene expression.
  
  
  RESULTS
  To facilitate EST-based expression analysis, we developed GEPIS (gene expression profiling in silico), a tool that integrates EST and tissue source information to compute gene expression patterns in a large panel of normal and tumor samples. We found EST-based expression patterns to be consistent with published papers as well as our own experimental results. We also built a GEPIS Regional Atlas that depicts expression characteristics of all genes in a selected genomic region. This program can be adapted for large-scale screening for genes with desirable expression patterns, as illustrated by our large-scale mining for tissue- and tumor-specific genes.
  
  
  BACKGROUND
  The email server version of the GEPIS application is freely available at http://share.gene.com/share/gepis. An interactive version of GEPIS will soon be freely available at http://www.cgl.ucsf.edu/Research/genentech/gepis/. The source code, modules, data and gene lists can be downloaded at http://share.gene.com/share/gepis.
authors.affiliation: Department of Bioinformatics, Genentech Inc., South San Francisco, CA 94080, USA.
authors.forename: Yan
authors.initials: Y
authors.lastname: Zhang
authors.forename: David A
authors.initials: DA
authors.lastname: Eberhard
authors.forename: Gretchen D
authors.initials: GD
authors.lastname: Frantz
authors.forename: Patrick
authors.initials: P
authors.lastname: Dowd
authors.forename: Thomas D
authors.initials: TD
authors.lastname: Wu
authors.forename: Yan
authors.initials: Y
authors.lastname: Zhou
authors.forename: Colin
authors.initials: C
authors.lastname: Watanabe
authors.forename: Shiuh-Ming
authors.initials: SM
authors.lastname: Luoh
authors.forename: Paul
authors.initials: P
authors.lastname: Polakis
authors.forename: Kenneth J
authors.initials: KJ
authors.lastname: Hillan
authors.forename: William I
authors.initials: WI
authors.lastname: Wood
authors.forename: Zemin
authors.initials: Z
authors.lastname: Zhang
mesh_terms: D000465:Algorithms; D014408:Biomarkers, Tumor / Q000235:genetics; D002874:Chromosome Mapping / Q000379:methods*; D020224:Expressed Sequence Tags; D020869:Gene Expression Profiling / Q000379:methods*; D005820:Genetic Testing / Q000379:methods; D006801:Humans; D020407:Internet; D009369:Neoplasms / Q000175:diagnosis / Q000235:genetics*; D009862:Online Systems; D016415:Sequence Alignment / Q000379:methods; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software; D014584:User-Computer Interface
chemical_list: D014408:Biomarkers, Tumor