Document Detail


GEPIS--quantitative gene expression profiling in normal and cancer tissues.
MedLine Citation:
PMID:  15073007     Owner:  NLM     Status:  MEDLINE    
Abstract/OtherAbstract:
MOTIVATION: 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. AVAILABILITY: 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:
Yan Zhang; David A Eberhard; Gretchen D Frantz; Patrick Dowd; Thomas D Wu; Yan Zhou; Colin Watanabe; Shiuh-Ming Luoh; Paul Polakis; Kenneth J Hillan; William I Wood; Zemin Zhang
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Publication Detail:
Type:  Comparative Study; Evaluation Studies; Journal Article; Validation Studies     Date:  2004-04-08
Journal Detail:
Title:  Bioinformatics (Oxford, England)     Volume:  20     ISSN:  1367-4803     ISO Abbreviation:  Bioinformatics     Publication Date:  2004 Oct 
Date Detail:
Created Date:  2004-10-12     Completed Date:  2005-02-10     Revised Date:  2009-11-19    
Medline Journal Info:
Nlm Unique ID:  9808944     Medline TA:  Bioinformatics     Country:  England    
Other Details:
Languages:  eng     Pagination:  2390-8     Citation Subset:  IM    
Affiliation:
Department of Bioinformatics, Genentech Inc., South San Francisco, CA 94080, USA.
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MeSH Terms
Descriptor/Qualifier:
Algorithms*
Chromosome Mapping / methods*
Expressed Sequence Tags
Gene Expression Profiling / methods*
Genetic Testing / methods
Humans
Internet
Neoplasms / diagnosis,  genetics*
Online Systems
Sequence Alignment / methods
Sequence Analysis, DNA / methods*
Software*
Tumor Markers, Biological / genetics
User-Computer Interface*
Chemical
Reg. No./Substance:
0/Tumor Markers, Biological

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine


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