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Nucleic Acids Research Advance Access originally published online on April 27, 2007
Nucleic Acids Research 2007 35(Web Server issue):W81-W85; doi:10.1093/nar/gkm257
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Nucleic Acids Research, 2007, Vol. 35, No. suppl_2 W81-W85
© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Articles

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

Lucía Conde1, David Montaner1,2, Jordi Burguet-Castell1, Joaquín Tárraga1,2, Ignacio Medina1, Fátima Al-Shahrour1 and Joaquín Dopazo1,2,*

1Bioinformatics Department, Centro de Investigación Príncipe Felipe (CIPF) and 2Functional Genomics Node, INB, CIPF, Valencia 46013, Spain

*To whom correspondence should be addressed. Tel: +34 963289680; Fax: +34 963289701; Email: jdopazo{at}cipf.es

Received January 30, 2007. Revised March 28, 2007. Accepted April 8, 2007.

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.


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