Combinatorial Use of Short Probes for Differential Gene Expression Profiling

Motivation: Gene chips or microarrays have made it possible to perform large-scale gene-expression experiments at the wholegenome level. To reduce the cost and identify genes that are differentially expressed between samples from hybridization signal intensity, we are proposing a suite of methods to use a relatively small number of short oligo probes for whole-genome or tissue-specific gene-expression studies. Results: We present methods to choose a set of short oligos to design a genome or tissue-specific biochip and then to solve a set of equations for gene-expression levels to determine genes that are differentially expressed between samples. The methods have been tested to define a set of 4,000 8mers as probes to identify genes that have fold changes for more than 6,000 identified yeast ORFs. These methods can also be expanded to design genome-specific or tissue-specific biochips for other organisms with full gene-sequence information.