SNPExpress: integrated visualization of genome-wide genotypes, copy numbers and gene expression levels
<p>Abstract</p> <p>Background</p> <p>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 currentl...
| Main Authors: | , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
BMC
2008-01-01
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| Series: | BMC Genomics |
| Online Access: | http://www.biomedcentral.com/1471-2164/9/41 |
| _version_ | 1811250664982970368 |
|---|---|
| author | Horsman Sebastiaan Abbas Saman Geertsma-Kleinekoort Wendy MC Verhaak Roel GW Sanders Mathijs A van der Spek Peter J Löwenberg Bob Valk Peter JM |
| author_facet | Horsman Sebastiaan Abbas Saman Geertsma-Kleinekoort Wendy MC Verhaak Roel GW Sanders Mathijs A van der Spek Peter J Löwenberg Bob Valk Peter JM |
| author_sort | Horsman Sebastiaan |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>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.</p> <p>Results</p> <p>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.</p> <p>Conclusion</p> <p>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.</p> |
| first_indexed | 2024-04-12T16:08:04Z |
| format | Article |
| id | doaj.art-6e3575f1c5694188b91630ac572f66d7 |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-04-12T16:08:04Z |
| publishDate | 2008-01-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-6e3575f1c5694188b91630ac572f66d72022-12-22T03:25:59ZengBMCBMC Genomics1471-21642008-01-01914110.1186/1471-2164-9-41SNPExpress: integrated visualization of genome-wide genotypes, copy numbers and gene expression levelsHorsman SebastiaanAbbas SamanGeertsma-Kleinekoort Wendy MCVerhaak Roel GWSanders Mathijs Avan der Spek Peter JLöwenberg BobValk Peter JM<p>Abstract</p> <p>Background</p> <p>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.</p> <p>Results</p> <p>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.</p> <p>Conclusion</p> <p>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.</p>http://www.biomedcentral.com/1471-2164/9/41 |
| spellingShingle | Horsman Sebastiaan Abbas Saman Geertsma-Kleinekoort Wendy MC Verhaak Roel GW Sanders Mathijs A van der Spek Peter J Löwenberg Bob Valk Peter JM SNPExpress: integrated visualization of genome-wide genotypes, copy numbers and gene expression levels BMC Genomics |
| title | SNPExpress: integrated visualization of genome-wide genotypes, copy numbers and gene expression levels |
| title_full | SNPExpress: integrated visualization of genome-wide genotypes, copy numbers and gene expression levels |
| title_fullStr | SNPExpress: integrated visualization of genome-wide genotypes, copy numbers and gene expression levels |
| title_full_unstemmed | SNPExpress: integrated visualization of genome-wide genotypes, copy numbers and gene expression levels |
| title_short | SNPExpress: integrated visualization of genome-wide genotypes, copy numbers and gene expression levels |
| title_sort | snpexpress integrated visualization of genome wide genotypes copy numbers and gene expression levels |
| url | http://www.biomedcentral.com/1471-2164/9/41 |
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