Linked Life Data

18296463

Source:http://linkedlifedata.com/resource/pubmed/id/18296463

Statements in which the resource exists as a subject.
PredicateObject
rdf:type
lifeskim:mentions
pubmed:issue
7
pubmed:dateCreated
2008-3-27
pubmed:abstractText
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. AVAILABILITY: http://compbio.med.harvard.edu/CGHweb.
pubmed:grant
pubmed:commentsCorrections
pubmed:language
eng
pubmed:journal
pubmed:citationSubset
IM
pubmed:status
MEDLINE
pubmed:month
Apr
pubmed:issn
1367-4811
pubmed:author
pubmed:issnType
Electronic
pubmed:day
1
pubmed:volume
24
pubmed:owner
NLM
pubmed:authorsComplete
Y
pubmed:pagination
1014-5
pubmed:dateRevised
2010-8-9
pubmed:meshHeading
pubmed:year
2008
pubmed:articleTitle
CGHweb: a tool for comparing DNA copy number segmentations from multiple algorithms.
pubmed:affiliation
Harvard-Partners Center for Genetics and Genomics and Informatics Program, Children's Hospital, Boston, MA 02139, USA.
pubmed:publicationType
Journal Article, Research Support, N.I.H., Extramural