ISACGH: a web-based environment for the analysis of Array CGH and gene expression which includes functional profiling

TitleISACGH: a web-based environment for the analysis of Array CGH and gene expression which includes functional profiling
Publication TypeJournal Article
Year of Publication2007
AuthorsConde, L, Montaner, D, Burguet-Castell, J, Tarraga, J, Medina, I, Al-Shahrour, F, Dopazo, J
JournalNucleic Acids Res
Volume35
PaginationW81-5
KeywordsAnimals Cluster Analysis Computational Biology/*methods Computer Graphics Gene Expression Profiling/*methods Humans Internet Models; Genetic *Nucleic Acid Hybridization Oligonucleotide Array Sequence Analysis/*methods Programming Languages *Software Systems Integration User-Computer Interface
Abstract

We present the ISACGH, a web-based system that allows for the combination of genomic data with gene expression values and provides different options for functional profiling of the regions found. Several visualization options offer a convenient representation of the results. Different efficient methods for accurate estimation of genomic copy number from array-CGH hybridization data have been included in the program. Moreover, the connection to the gene expression analysis package GEPAS allows the use of different facilities for data pre-processing and analysis. A DAS server allows exporting the results to the Ensembl viewer where contextual genomic information can be obtained. The program is freely available at: http://isacgh.bioinfo.cipf.es or within http://www.gepas.org.

Notes

Conde, Lucia Montaner, David Burguet-Castell, Jordi Tarraga, Joaquin Medina, Ignacio Al-Shahrour, Fatima Dopazo, Joaquin Research Support, Non-U.S. Gov’t England Nucleic acids research Nucleic Acids Res. 2007 Jul;35(Web Server issue):W81-5. Epub 2007 Apr 27.

URLhttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=17468499