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


BACKGROUND
Code for the formulae can be obtained (R code) via http://www.panix.com/~derwisch/hannes/longrun
Hüsing
Johannes
J
Institut für Medizinische Informatik, Biometrie und Epidemiologie, Universitätsklinikum Essen, Hufelandstrasse 55, D-45122 Essen, Germany. johannes.huesing@medizin.uni-essen.de
Zeschnigk
Michael
M
Boes
Tanja
T
Jöckel
Karl-Heinz
KH
D002874:Chromosome Mapping / Q000379:methods*; D002875:Chromosomes / Q000235:genetics; D002893:Chromosomes, Human, Pair 3; D004252:DNA Mutational Analysis / Q000379:methods*; D030561:Databases, Nucleic Acid; D020869:Gene Expression Profiling / Q000379:methods*; D020868:Gene Silencing; D006801:Humans; D008545:Melanoma / Q000235:genetics; D009006:Monosomy / Q000235:genetics; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*; D014604:Uveal Neoplasms / Q000235:genetics