Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2007 Jul;35(Web Server issue):W81-5.
doi: 10.1093/nar/gkm257. Epub 2007 Apr 27.

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

Lucía Conde  1 , David Montaner, Jordi Burguet-Castell, Joaquín Tárraga, Ignacio Medina, Fátima Al-Shahrour, Joaquín Dopazo
Affiliations

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

Lucía Conde et al. Nucleic Acids Res. 2007 Jul.

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.

PubMed Disclaimer

Figures

Figure 1.
Figure 1.
Human chromosome 18. Multiple myeloma (mm) cell line SK-MM-2 (see text) with copy number estimation (blue line) and gene expression values (grey bars). The isowindow segmentation method was used to estimate significant alterations in copy number.
Figure 2.
Figure 2.
The two zoom options in the breakpoint on the extreme closest to the centromer of the amplicon detected in 18q21.1 in one of the mm cases studied. The two probes form the array shown in the figure (the ones corresponding to SERPINB3 and CDH19) are green because all of them represent amplifications. The blue line represents the copy number estimation. (A) ISACGH viewer, (B) DAS server.
See this image and copyright information in PMC

References

    1. Bassett AS, Chow EW, Weksberg R. Chromosomal abnormalities and schizophrenia. Am. J. Med. Genet. 2000;97:45–51. - PMC - PubMed
    1. Albertson DG, Pinkel D. Genomic microarrays in human genetic disease and cancer. Hum. Mol. Genet. 2003;12:R145–R152. - PubMed
    1. Kallioniemi A, Kallioniemi OP, Sudar D, Rutovitz D, Gray JW, Waldman F, Pinkel D. Comparative genomic hybridization for molecular cytogenetic analysis of solid tumors. Science. 1992;258:818–821. - PubMed
    1. Mantripragada KK, Buckley PG, de Stahl TD, Dumanski JP. Genomic microarrays in the spotlight. Trends Genet. 2004;20:87–94. - PubMed
    1. Pinkel D, Albertson DG. Array comparative genomic hybridization and its applications in cancer. Nat. Genet. 2005;37(Suppl):S11–S17. - PubMed

Publication types