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Measuring similarities between gene expression profiles through new data transformations

Kyungpil Kim12, Shibo Zhang3, Keni Jiang3, Li Cai4, In-Beum Lee2, Lewis J Feldman3 and Haiyan Huang1*

Author Affiliations

1 Department of Statistics, University of California, Berkeley, USA

2 Department of Chemical Engineering, Pohang University of Science and Technology (POSTECH), Korea

3 Department of Plant and Microbial Biology, University of California, Berkeley, USA

4 Department of Biomedical Engineering, Rutgers University, USA

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BMC Bioinformatics 2007, 8:29  doi:10.1186/1471-2105-8-29

Published: 27 January 2007



Clustering methods are widely used on gene expression data to categorize genes with similar expression profiles. Finding an appropriate (dis)similarity measure is critical to the analysis. In our study, we developed a new measure for clustering the genes when the key factor is the shape of the profile, and when the expression magnitude should also be accounted for in determining the gene relationship. This is achieved by modeling the shape and magnitude parameters separately in a gene expression profile, and then using the estimated shape and magnitude parameters to define a measure in a new feature space.


We explored several different transformation schemes to construct the feature spaces that include a space whose features are determined by the mutual differences of the original expression components, a space derived from a parametric covariance matrix, and the principal component space in traditional PCA analysis. The former two are the newly proposed and the latter is explored for comparison purposes. The new measures we defined in these feature spaces were employed in a K-means clustering procedure to perform analyses. Applying these algorithms to a simulation dataset, a developing mouse retina SAGE dataset, a small yeast sporulation cDNA dataset, and a maize root affymetrix microarray dataset, we found from the results that the algorithm associated with the first feature space, named TransChisq, showed clear advantages over other methods.


The proposed TransChisq is very promising in capturing meaningful gene expression clusters. This study also demonstrates the importance of data transformations in defining an efficient distance measure. Our method should provide new insights in analyzing gene expression data. The clustering algorithms are available upon request.