Sequence specific sensitivity of oligonucleotide probes
نویسندگان
چکیده
Gene expression analysis by means of high-density-oligonucleotide-array chips is based on the sequence specific binding of mRNA to oligonucleotide probes and its measurement using fluorescence labels. The sensitivity of a probe to detect a certain amount of target mRNA considerably varies among the about 400.000 probes, which are covalently attached to a typical Affymetrix chip. We present a model which describes the probe intensities as a function of their sequence. The effect of a given base at each position of the probe sequence was specified in terms of a general set of nearest neighbour sensitivity parameters. Consequences of our results for gene expression analysis and chip design were discussed.
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