GEPIS--quantitative gene expression profiling in normal and cancer tissues.
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.
Zhang
Yan
Y
Department of Bioinformatics, Genentech Inc., South San Francisco, CA 94080, USA.
Eberhard
David A
DA
Frantz
Gretchen D
GD
Dowd
Patrick
P
Wu
Thomas D
TD
Zhou
Yan
Y
Watanabe
Colin
C
Luoh
Shiuh-Ming
SM
Polakis
Paul
P
Hillan
Kenneth J
KJ
Wood
William I
WI
Zhang
Zemin
Z
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
D014408:Biomarkers, Tumor