Nucleic Acids Research Advance Access published online on August 7, 2007
Nucleic Acids Research, doi:10.1093/nar/gkm549
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Methods Online |
Toward a universal microarray: prediction of gene expression through nearest-neighbor probe sequence identification
1Interdepartmental Program in Computational Biology and Bioinformatics 2Department of Molecular Biophysics and Biochemistry and 3Department of Computer Science, Yale University, USA
*To whom correspondence should be addressed. Tel: +1 203 432 8189; Fax: +1 203 432 6946; Email: mark.gerstein{at}yale.edu
Received March 12, 2007. Revised June 29, 2007. Accepted July 9, 2007.
A generic DNA microarray design applicable to any species would greatly benefit comparative genomics. We have addressed the feasibility of such a design by leveraging the great feature densities and relatively unbiased nature of genomic tiling microarrays. Specifically, we first divided each Homo sapiens Refseq-derived gene's spliced nucleotide sequence into all of its possible contiguous 25 nt subsequences. For each of these 25 nt subsequences, we searched a recent human transcript mapping experiment's probe design for the 25 nt probe sequence having the fewest mismatches with the subsequence, but that did not match the subsequence exactly. Signal intensities measured with each gene's nearest-neighbor features were subsequently averaged to predict their gene expression levels in each of the experiment's thirty-three hybridizations. We examined the fidelity of this approach in terms of both sensitivity and specificity for detecting actively transcribed genes, for transcriptional consistency between exons of the same gene, and for reproducibility between tiling array designs. Taken together, our results provide proof-of-principle for probing nucleic acid targets with off-target, nearest-neighbor features.