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Bioinformatics Vol. 19 no. 18 2003
pages 2335-2342
© 2003 Oxford University Press

Combining DNA expression with positional information to detect functional silencing of chromosomal regions

Johannes Hüsing 1,*, Michael Zeschnigk 2, Tanja Boes 1 and Karl-Heinz Jöckel 1

1 Institut für Medizinische Informatik, Biometrie und Epidemiologie and 2 Institut für Humangenetik, Universitätsklinikum Essen, Hufelandstraße 55, D-45122 Essen, Germany

Received on September 3, 2002 ; revised on April 7, 2003 ; accepted on May 8, 2003

Motivation: Loss of chromosomal material is often observed in cancer cells. In this situation the expression of genes is related to their position on the genome. Epigenetic phenomena may also silence several genes in the same region of a chromosome. While cytogenetic or other molecular genetic methods spot changes of DNA copy number, they cannot detect other causes of silencing.

Results: We propose a method that utilizes the link from expression information gained from high-density DNA microarrays to the gene locus according to current databases. Statistical methods adequate to spot conspicuous runs of non-expressed genes are introduced and compared to one another by merit of their power and robustness against false positives.

Availability: Code for the formulae can be obtained (R code) via http://www.panix.com/~derwisch/hannes/longrun

Contact: johannes.huesing{at}medizin.uni-essen.de

* To whom correspondence should be addressed.


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