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

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

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