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


RESULTS
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 (XantoScreen) provided further experimental evidence for association with angiogenesis.
Korn
René
R
Xantos Biomedicine AG, Max-Lebsche-Platz 31, 81377 München, Germany.
Röhrig
Sascha
S
Schulze-Kremer
Steffen
S
Brinkmann
Ulrich
U
D042501:Angiogenic Proteins / Q000378:metabolism*; D003628:Database Management Systems; D030562:Databases, Protein; D020869:Gene Expression Profiling / Q000379:methods*; D015972:Gene Expression Regulation, Neoplastic; D015723:Gene Library; D006801:Humans; D016247:Information Storage and Retrieval / Q000379:methods*; D009363:Neoplasm Proteins / Q000378:metabolism; D009369:Neoplasms / Q000098:blood supply* / Q000235:genetics / Q000378:metabolism*; D009389:Neovascularization, Pathologic; D010641:Phenotype; D015398:Signal Transduction
D042501:Angiogenic Proteins; D009363:Neoplasm Proteins