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Beyond Bioinformatics |
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Title |
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Incorporation of biological knowledge into distance for clustering genes |
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Authors |
Grzegorz M Boratyn1*, Susmita Datta2 and Somnath Datta2 |
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Affiliation |
1Clinical Proteomics Center, University of Louisville, Louisville, KY 40202; 2,3Department of Bioinformatics and Biostatistics, University of Louisville, Louisville, KY - 40202 |
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greg.boratyn@louisville.edu; * Corresponding author
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Article Type |
Prediction Model
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Date |
received December 09, 2006; accepted January 20, 2007; published online April 10, 2007
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Abstract |
In this paper we propose a data based algorithm to marry existing biological knowledge (e.g., functional annotations of genes) with experimental data (gene expression profiles) in creating an overall dissimilarity that can be used with any clustering algorithm that uses a general dissimilarity matrix. We explore this idea with two publicly available gene expression data sets and functional annotations where the results are compared with the clustering results that uses only the experimental data. Although more elaborate evaluations might be called for, the present paper makes a strong case for utilizing existing biological information in the clustering process.
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Availability |
Supplement is available at http://www.somnathdatta.org/Supp/Bioinformation/appendix.pdf
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Keywords
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knowledge; distance; clustering; genes; expression |
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Citation |
Boratyn et al., Bioinformation 1(10): 396-405 (2007)
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Edited by |
Susmita Datta
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ISSN |
0973-2063
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Publisher |
Biomedical Informatics Publishing Group
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Copyright |
Publisher
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Copyright Transfer Agreement |
The authors of published articles in Bioinformation automatically transfer the copyright to the publisher upon formal acceptance. However, the authors reserve right to use the information contained in the article for non commercial purposes.
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License |
This is an open-access article, which permits unrestricted use, distribution, and reproduction in any medium, for non-commercial purposes, provided the original author and source are credited.
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