Journal
BIOINFORMATICS
Volume 24, Issue 7, Pages 1014-1015Publisher
OXFORD UNIV PRESS
DOI: 10.1093/bioinformatics/btn067
Keywords
-
Categories
Funding
- NCI NIH HHS [U24 CA126554, 1U24 CA126554] Funding Source: Medline
- NIGMS NIH HHS [R01 GM082798-01, R01 GM082798] Funding Source: Medline
Ask authors/readers for more resources
Accurate estimation of DNA copy numbers from array comparative genomic hybridization (CGH) data is important for characterizing the cancer genome. An important part of this process is the segmentation of the log-ratios between the sample and control DNA along the chromosome into regions of different copy numbers. However, multiple algorithms are available in the literature for this procedure and the results can vary substantially among these. Thus, a visualization tool that can display the segmented profiles from a number of methods can be helpful to the biologist or the clinician to ascertain that a feature of interest did not arise as an artifact of the algorithm. Such a tool also allows the methodologist to easily contrast his method against others. We developed a web-based tool that applies a number of popular algorithms to a single array CGH profile entered by the user. It generates a heatmap panel of the segmented profiles for each method as well as a consensus profile. The clickable heatmap can be moved along the chromosome and zoomed in or out. It also displays the time that each algorithm took and provides numerical values of the segmented profiles for download. The web interface calls algorithms written in the statistical language R. We encourage developers of new algorithms to submit their routines to be incorporated into the website.
Authors
I am an author on this paper
Click your name to claim this paper and add it to your profile.
Reviews
Recommended
No Data Available