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CGH datamining

Monday 16 June 2008

CGH-Profiler (#16042799#)

CGH-Profiler is a program that supports the analysis of genomic aberrations measured by Comparative Genomic Hybridisation (CGH). Comparative genomic hybridisation (CGH) is a well-established, molecular cytogenetic method that allows the detection of chromosomal imbalances in entire genomes.

CGH-Profiler circumvents the semantic ISCN description by importing data from different CGH system vendors and by directly transferring the data into a table format that is readily accessible for subsequent statistical analysis.

CGH-profiler comes with different consistency checks, calculates various statistics and automatically assigns a median copy number ratio to each chromosomal band.Import of CGH profiles from different CGH system vendors is already supported; its extension to other systems can be readily achieved through Perl scripts.

CGH profiler can also be used to analyse comparative expressed sequence hybridisation (CESH) data.

CESH reveals gene expression patterns according to chromosomal locations in a similar manner as CGH detects chromosomal imbalances.

References

- Schubert F, Tausch B, Joos S, Eils R. CGH-Profiler: data mining based on genomic aberration profiles. BMC Bioinformatics. 2005 Jul 25;6:188.PMID: #16042799#