Comparison of array-based comparative genomic hybridization with gene expression-based regional expression biases to identify genetic abnormalities in hepatocellular carcinoma.docVIP

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Comparison of array-based comparative genomic hybridization with gene expression-based regional expression biases to identify genetic abnormalities in hepatocellular carcinoma.doc

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Comparison of array-based comparative genomic hybridization with gene expression-based regional expression biases to identify genetic abnormalities in hepatocellular carcinoma

BMC Genomics BioMedCentral Methodology article Open Access Comparison of array-based comparative genomic hybridization with gene expression-based regional expression biases to identify genetic abnormalities in hepatocellular carcinoma Kyle A Furge*1, Karl J Dykema1, Coral Ho2 and Xin Chen2,3,4 Address: 1Bioinformatics Special Program, Van Andel Research Institute, 333 Bostwick Ave. NE, Grand Rapids, MI 49503, USA, 2Dept of Pharmaceutical Sciences, University of California, S816 513 Parnassus Ave., San Francisco, CA 94143-0046, USA, 3Cancer Center, University of California, S816 513 Parnassus Ave., San Francisco, CA 94143-0046, USA and 4Liver Center, University of California, S816 513 Parnassus Ave., San Francisco, CA 94143-0046, USA Email: Kyle A Furge* - kyle.furge@; Karl J Dykema - karl.dykema@; Coral Ho - coralho@; Xin Chen - xinchen@ * Corresponding author Published: 09 May 2005 Received: 10 January 2005 Accepted: 09 May 2005 BMC Genomics 2005, 6:67 doi:10.1186/1471-2164-6-67 This article is available from: /1471-2164/6/67 ? 2005 Furge et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Abstract Background: Regional expression biases (REBs) are genetic intervals where gene expression is coordinately changed. For example, if a region of the genome is amplified, often the majority of genes that map within the amplified region show increased expression when compared to genes located in cytogenetically normal regions. As such, REBs have the potential to act as surrogates for cytogenetic data traditionally obtained using molecular technologies such as comparative genomic hybridization. However as REBs are identified using transcriptional information, detection of REBs may also identify local tran