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 comparati...
| Main Authors: | , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
SAGE Publishing
2007-01-01
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| Series: | Cancer Informatics |
| Online Access: | https://doi.org/10.1177/117693510700300003 |
| _version_ | 1828193586839027712 |
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| author | Ken C. Lo Ganesh Shankar Yaron Turpaz Dione Bailey Michael R. Rossi Tania Burkhardt Ping Liang John K. Cowell Ph.D., D.Sc. FRCPath |
| author_facet | Ken C. Lo Ganesh Shankar Yaron Turpaz Dione Bailey Michael R. Rossi Tania Burkhardt Ping Liang John K. Cowell Ph.D., D.Sc. FRCPath |
| 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 © identifies potentially important genes whose expression profiles are changed as a result of losses, gains and amplifications 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 | 2024-04-12T09:10:49Z |
| format | Article |
| id | doaj.art-c9c9160ae5594a81b4e9ed6f5cc10805 |
| institution | Directory Open Access Journal |
| issn | 1176-9351 |
| language | English |
| last_indexed | 2024-04-12T09:10:49Z |
| publishDate | 2007-01-01 |
| publisher | SAGE Publishing |
| record_format | Article |
| series | Cancer Informatics |
| spelling | doaj.art-c9c9160ae5594a81b4e9ed6f5cc108052022-12-22T03:38:59ZengSAGE PublishingCancer Informatics1176-93512007-01-01310.1177/117693510700300003Overlay Tool for aCGHViewer: An Analysis Module Built for aCGHViewer used to Perform Comparisons of Data Derived from Different Microarray PlatformsKen C. Lo0Ganesh Shankar1Yaron Turpaz2Dione Bailey3Michael R. Rossi4Tania Burkhardt5Ping Liang6John K. Cowell Ph.D., D.Sc. FRCPath7Department of Cancer Genetics, Roswell Park Cancer Institute, Buffalo, NY 14263.Department of Cancer Genetics, Roswell Park Cancer Institute, Buffalo, NY 14263.Affymetrix, Inc. Santa Clara, CA 95051.Affymetrix, Inc. Santa Clara, CA 95051.Yale University School of Medicine, Department of Cancer Genetics, New Haven, CT 06520.Department of Cancer Genetics, Roswell Park Cancer Institute, Buffalo, NY 14263.Department of Cancer Genetics, Roswell Park Cancer Institute, Buffalo, NY 14263.Department of Cancer Genetics, Roswell Park Cancer Institute, Buffalo, NY 14263.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 © identifies potentially important genes whose expression profiles are changed as a result of losses, gains and amplifications 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.https://doi.org/10.1177/117693510700300003 |
| spellingShingle | Ken C. Lo Ganesh Shankar Yaron Turpaz Dione Bailey Michael R. Rossi Tania Burkhardt Ping Liang John K. Cowell Ph.D., D.Sc. FRCPath Overlay Tool for aCGHViewer: An Analysis Module Built for aCGHViewer used to Perform Comparisons of Data Derived from Different Microarray Platforms Cancer Informatics |
| 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 for acghviewer an analysis module built for acghviewer used to perform comparisons of data derived from different microarray platforms |
| url | https://doi.org/10.1177/117693510700300003 |
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