aCGHviewer

A generic visualization tool for aCGH data

Ganesh Shankar, Michael R. Rossi, Devin E. McQuaid, Jeffrey M. Conroy, Daniel G. Gaile, John Kenneth Cowell, Norma J. Nowak, Ping Liang

Research output: Contribution to journalArticle

10 Citations (Scopus)

Abstract

Array-Comparative Genomic Hybridization (aCGH) is a powerful high throughput technology for detecting chromosomal copy number aberrations (CNAs) in cancer, aiming at identifying related critical genes from the affected genomic regions. However, advancing from a dataset with thousands of tabular lines to a few candidate genes can be an onerous and time-consuming process. To expedite the aCGH data analysis process, we have developed a user-friendly aCGH data viewer (aCGHViewer) as a conduit between the aCGH data tables and a genome browser. The data from a given aCGH analysis are displayed in a genomic view comprised of individual chromosome panels which can be rapidly scanned for interesting features. A chromosome panel containing a feature of interest can be selected to launch a detail window for that single chromosome. Selecting a data point of interest in the detail window launches a query to the UCSC or NCBI genome browser to allow the user to explore the gene content in the chromosomal region. Additionally, aCGHViewer can display aCGH and expression array data concurrently to visually correlate the two. aCGHViewer is a stand alone Java visualization application that should be used in conjunction with separate statistical programs. It operates on all major computer platforms and is freely available at http://falcon.roswellpark.org/aCGHview/.

Original languageEnglish (US)
Pages (from-to)36-43
Number of pages8
JournalCancer Informatics
Volume2
StatePublished - Jun 15 2006

Fingerprint

Comparative Genomic Hybridization
Chromosomes
Genome
Genes
Technology
Neoplasms

Keywords

  • Array-CGH
  • CNA
  • Gene expression
  • Visualization

ASJC Scopus subject areas

  • Oncology
  • Cancer Research

Cite this

Shankar, G., Rossi, M. R., McQuaid, D. E., Conroy, J. M., Gaile, D. G., Cowell, J. K., ... Liang, P. (2006). aCGHviewer: A generic visualization tool for aCGH data. Cancer Informatics, 2, 36-43.

aCGHviewer : A generic visualization tool for aCGH data. / Shankar, Ganesh; Rossi, Michael R.; McQuaid, Devin E.; Conroy, Jeffrey M.; Gaile, Daniel G.; Cowell, John Kenneth; Nowak, Norma J.; Liang, Ping.

In: Cancer Informatics, Vol. 2, 15.06.2006, p. 36-43.

Research output: Contribution to journalArticle

Shankar, G, Rossi, MR, McQuaid, DE, Conroy, JM, Gaile, DG, Cowell, JK, Nowak, NJ & Liang, P 2006, 'aCGHviewer: A generic visualization tool for aCGH data', Cancer Informatics, vol. 2, pp. 36-43.
Shankar G, Rossi MR, McQuaid DE, Conroy JM, Gaile DG, Cowell JK et al. aCGHviewer: A generic visualization tool for aCGH data. Cancer Informatics. 2006 Jun 15;2:36-43.
Shankar, Ganesh ; Rossi, Michael R. ; McQuaid, Devin E. ; Conroy, Jeffrey M. ; Gaile, Daniel G. ; Cowell, John Kenneth ; Nowak, Norma J. ; Liang, Ping. / aCGHviewer : A generic visualization tool for aCGH data. In: Cancer Informatics. 2006 ; Vol. 2. pp. 36-43.
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