SNPExpress: Integrated Visualization of Genome-wide Genotypes, Copy Numbers and Gene Expression Levels

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SNPExpress: Integrated Visualization of Genome-wide Genotypes, Copy Numbers and Gene Expression Levels

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dc.contributor.author Sanders, Mathijs A
dc.contributor.author Geertsma-Kleinekoort, Wendy MC
dc.contributor.author Abbas, Saman
dc.contributor.author Horsman, Sebastiaan
dc.contributor.author van der Spek, Peter J
dc.contributor.author Löwenberg, Bob
dc.contributor.author Valk, Peter JM
dc.contributor.author Verhaak, Roel
dc.date.accessioned 2011-04-26T02:14:48Z
dc.date.issued 2008
dc.identifier.citation Sanders, Mathijs A., Roel G. W. Verhaak, Wendy M. C. Geertsma-Kleinekoort, Saman Abbas, Sebastiaan Horsman, Peter J. van der Spek, Bob Löwenberg, and Peter J. M. Valk. 2008. SNPExpress: integrated visualization of genome-wide genotypes, copy numbers and gene expression levels. BMC Genomics 9: 41. en_US
dc.identifier.issn 1471-2164 en_US
dc.identifier.uri http://nrs.harvard.edu/urn-3:HUL.InstRepos:4875893
dc.description.abstract Background: Accurate analyses of comprehensive genome-wide SNP genotyping and gene expression data sets is challenging for many researchers. In fact, obtaining an integrated view of both large scale SNP genotyping and gene expression is currently complicated since only a limited number of appropriate software tools are available. Results: We present SNPExpress, a software tool to accurately analyze Affymetrix and Illumina SNP genotype calls, copy numbers, polymorphic copy number variations (CNVs) and Affymetrix gene expression in a combinatorial and efficient way. In addition, SNPExpress allows concurrent interpretation of these items with Hidden-Markov Model (HMM) inferred Loss-of-Heterozygosity (LOH)- and copy number regions. Conclusion: The combined analyses with the easily accessible software tool SNPExpress will not only facilitate the recognition of recurrent genetic lesions, but also the identification of critical pathogenic genes. en_US
dc.language.iso en_US en_US
dc.publisher BioMed Central en_US
dc.relation.isversionof doi:10.1186/1471-2164-9-41 en_US
dc.relation.hasversion http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2235842/pdf/ en_US
dash.license LAA
dc.title SNPExpress: Integrated Visualization of Genome-wide Genotypes, Copy Numbers and Gene Expression Levels en_US
dc.type Journal Article en_US
dc.description.version Version of Record en_US
dc.relation.journal BMC Genomics en_US
dash.depositing.author Verhaak, Roel
dc.date.available 2011-04-26T02:14:48Z
dash.affiliation.other HMS^Medicine-Brigham and Women's Hospital en_US

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