| Abstract: |  This work examines the possibilities of alternative genomic probeset consolidation using the Affymetrix annotation data and utilizing them in conjunction with various publicly available databases of genomic sequences. The protein- and gene-based representations were compared by means of synonymous probesets' correlation, the accuracy of an automatic classifier built upon the two representations and the number of significantly differentially expressed units. It has been found that the protein-based probeset consolidation is a good alternative to the traditional gene-based one, increasing the within-unit correlation of measured data on the one hand, but causing a decrease in the overall number of usable probesets on the other hand.
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