Overlay Tool© for aCGHViewer©: An Analysis Module Built for aCGHViewer© used to Perform Comparisons of Data Derived from Different Microarray Platforms
The Overlay Tool© has been developed to combine high throughput data derived from various microarray platforms. This tool analyzes high-resolution correlations between gene expression changes and either copy number abnormalities (CNAs) or loss of heterozygosity events detected using array comparativ...
| Main Authors: | , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
SAGE Publishing
2007-01-01
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| Series: | Cancer Informatics |
| Subjects: | |
| Online Access: | http://la-press.com/article.php?article_id=324 |
| _version_ | 1811333460023836672 |
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| author | Ken C. Lo Ganesh Shankar Yaron Turpaz Dione Bailey Michael R. Rossi Tania Burkhardt Ping Liang John K. Cowell |
| author_facet | Ken C. Lo Ganesh Shankar Yaron Turpaz Dione Bailey Michael R. Rossi Tania Burkhardt Ping Liang John K. Cowell |
| author_sort | Ken C. Lo |
| collection | DOAJ |
| description | The Overlay Tool© has been developed to combine high throughput data derived from various microarray platforms. This tool analyzes high-resolution correlations between gene expression changes and either copy number abnormalities (CNAs) or loss of heterozygosity events detected using array comparative genomic hybridization (aCGH). Using an overlay analysis which is designed to be performed using data from multiple microarray platforms on a single biological sample, the Overlay Tool© identifi es potentially important genes whose expression profiles are changed as a result of losses, gains and amplifi cations in the cancer genome. In addition, the Overlay Tool© will incorporate loss of heterozygosity (LOH) probability data into this overlay procedure. To facilitate this analysis, we developed an application which computationally combines two or more high throughput datasets (e.g. aCGH/expression) into a single categorized dataset for visualization and interrogation using a gene-centric approach. As such, data from virtually any microarray platform can be incorporated without the need to remap entire datasets individually. The resultant categorized (overlay) data set can be conveniently viewed using our in-house visualization tool, aCGHViewer© (Shankar et al. 2006), which serves as a conduit to public databases such as UCSC and NCBI, to rapidly investigate genes of interest. |
| first_indexed | 2024-04-13T16:53:12Z |
| format | Article |
| id | doaj.art-996ea937aec44953be950f3be1fd50fd |
| institution | Directory Open Access Journal |
| issn | 1176-9351 |
| language | English |
| last_indexed | 2024-04-13T16:53:12Z |
| publishDate | 2007-01-01 |
| publisher | SAGE Publishing |
| record_format | Article |
| series | Cancer Informatics |
| spelling | doaj.art-996ea937aec44953be950f3be1fd50fd2022-12-22T02:38:53ZengSAGE PublishingCancer Informatics1176-93512007-01-013307319Overlay Tool© for aCGHViewer©: An Analysis Module Built for aCGHViewer© used to Perform Comparisons of Data Derived from Different Microarray PlatformsKen C. LoGanesh ShankarYaron TurpazDione BaileyMichael R. RossiTania BurkhardtPing LiangJohn K. CowellThe Overlay Tool© has been developed to combine high throughput data derived from various microarray platforms. This tool analyzes high-resolution correlations between gene expression changes and either copy number abnormalities (CNAs) or loss of heterozygosity events detected using array comparative genomic hybridization (aCGH). Using an overlay analysis which is designed to be performed using data from multiple microarray platforms on a single biological sample, the Overlay Tool© identifi es potentially important genes whose expression profiles are changed as a result of losses, gains and amplifi cations in the cancer genome. In addition, the Overlay Tool© will incorporate loss of heterozygosity (LOH) probability data into this overlay procedure. To facilitate this analysis, we developed an application which computationally combines two or more high throughput datasets (e.g. aCGH/expression) into a single categorized dataset for visualization and interrogation using a gene-centric approach. As such, data from virtually any microarray platform can be incorporated without the need to remap entire datasets individually. The resultant categorized (overlay) data set can be conveniently viewed using our in-house visualization tool, aCGHViewer© (Shankar et al. 2006), which serves as a conduit to public databases such as UCSC and NCBI, to rapidly investigate genes of interest.http://la-press.com/article.php?article_id=324Overlay AnalysisMicroarrayACGHexpression profilingCNAsaCGHViewer. |
| spellingShingle | Ken C. Lo Ganesh Shankar Yaron Turpaz Dione Bailey Michael R. Rossi Tania Burkhardt Ping Liang John K. Cowell Overlay Tool© for aCGHViewer©: An Analysis Module Built for aCGHViewer© used to Perform Comparisons of Data Derived from Different Microarray Platforms Cancer Informatics Overlay Analysis Microarray ACGH expression profiling CNAs aCGHViewer. |
| title | Overlay Tool© for aCGHViewer©: An Analysis Module Built for aCGHViewer© used to Perform Comparisons of Data Derived from Different Microarray Platforms |
| title_full | Overlay Tool© for aCGHViewer©: An Analysis Module Built for aCGHViewer© used to Perform Comparisons of Data Derived from Different Microarray Platforms |
| title_fullStr | Overlay Tool© for aCGHViewer©: An Analysis Module Built for aCGHViewer© used to Perform Comparisons of Data Derived from Different Microarray Platforms |
| title_full_unstemmed | Overlay Tool© for aCGHViewer©: An Analysis Module Built for aCGHViewer© used to Perform Comparisons of Data Derived from Different Microarray Platforms |
| title_short | Overlay Tool© for aCGHViewer©: An Analysis Module Built for aCGHViewer© used to Perform Comparisons of Data Derived from Different Microarray Platforms |
| title_sort | overlay tool c for acghviewer c an analysis module built for acghviewer c used to perform comparisons of data derived from different microarray platforms |
| topic | Overlay Analysis Microarray ACGH expression profiling CNAs aCGHViewer. |
| url | http://la-press.com/article.php?article_id=324 |
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