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Bioinformatics Advance Access originally published online on April 6, 2005
Bioinformatics 2005 21(11):2766-2772; doi:10.1093/bioinformatics/bti416
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© The Author 2005. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions{at}oupjournals.org

Common denominator procedure: a novel approach to gene-expression data mining for identification of phenotype-specific genes

René Korn 1, Sascha Röhrig 1,*, Steffen Schulze-Kremer 2 and Ulrich Brinkmann 1

1Xantos Biomedicine AG Max-Lebsche-Platz 31, 81377 München, Germany
2Rechenzentrum der Universität Hannover Schloßwender Straße 5, 30159 Hannover, Germany

*To whom correspondence should be addressed.

Motivation: We have established a novel data mining procedure for the identification of genes associated with pre-defined phenotypes and/or molecular pathways. Based on the observation that these genes are frequently expressed in the same place or in close proximity at about the same time, we have devised an approach termed Common Denominator Procedure. One unusual feature of this approach is that the specificity and probability to identify genes linked to the desired phenotype/pathway increase with greater diversity of the input data.

Result: To show the feasibility of our approach, the Cancer Genome Anatomy Project expression data combined with a defined set of angiogenic factors was used to identify additional and novel angiogenesis-associated genes. A multitude of these additional genes were known to be associated with angiogenesis according to published data, verifying our approach. For some of the remaining candidate genes, application of a high-throughput functional genomics platform (XantoScreenTM) provided further experimental evidence for association with angiogenesis.

Availability: Software available on request from the authors.

Contact: s.roehrig{at}xantos.de


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