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Bioinformatics Advance Access published online on April 6, 2005
Bioinformatics, 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@oupjournals.org
Received February 3, 2005
Revised March 10, 2005
Accepted March 29, 2005

Article

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

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

* To whom correspondence should be addressed.
Sascha Röhrig, E-mail: s.roehrig{at}xantos.de


  Abstract

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 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 increases with greater diversity of the input data.

Result: To show the feasibility of our approach, the CGAP 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.


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