GeneHub-GEPIS: digital expression profiling for normal and cancer tissues based on an integrated gene database
| Autor: | Robert Baertsch, William I. Wood, Zemin Zhang, Yan Zhang, Shiuh-Ming Luoh, Lawrence S. Hon |
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| Rok vydání: | 2007 |
| Předmět: |
Sequence analysis
Biology computer.software_genre Online Systems Genome User-Computer Interface Neoplasms Gene expression Biomarkers Tumor Genetics Humans Genetic Testing Gene Expressed Sequence Tags Internet Expressed sequence tag Database Gene Expression Profiling Chromosome Mapping Sequence Analysis DNA Articles Gene Annotation Gene expression profiling Human genome Sequence Alignment computer Algorithms Software |
| Zdroj: | Nucleic Acids Research |
| ISSN: | 1362-4962 0305-1048 |
| DOI: | 10.1093/nar/gkm381 |
| Popis: | GeneHub-GEPIS is a web application that performs digital expression analysis in human and mouse tissues based on an integrated gene database. Using aggregated expressed sequence tag (EST) library information and EST counts, the application calculates the normalized gene expression levels across a large panel of normal and tumor tissues, thus providing rapid expression profiling for a given gene. The backend GeneHub component of the application contains pre-defined gene structures derived from mRNA transcript sequences from major databases and includes extensive cross references for commonly used gene identifiers. ESTs are then linked to genes based on their precise genomic locations as determined by GMAP. This genome-based approach reduces incorrect matches between ESTs and genes, thus minimizing the noise seen with previous tools. In addition, the gene-centric design makes it possible to add several important features, including text searching capabilities, the ability to accept diverse input values, expression analysis for microRNAs, basic gene annotation, batch analysis and linking between mouse and human genes. GeneHub-GEPIS is available at http://www.cgl.ucsf.edu/Research/genentech/genehub-gepis/ or http://www.gepis.org/. |
| Databáze: | OpenAIRE |
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