A novel microarray strategy for detecting genes and pathways in microbes with unsequenced genomes

Expression profile analysis of genes provides valuable information concerning the genetic response of cells to stimuli. We describe an adaptation of this technology that can be used to probe for the expression of specific families of genes in microbial species. In our method a combination of sets of oligonucleotide probes representing fingerprint sequences specific to protein families is used to identify the presence and expression levels of family homologs in a microbial cell. We demonstrate computationally, using exemplars, that when the cDNA complement from an organism is sequentially screened against a set of specific motif oligonucleotides, statistically significant information can be obtained concerning the expression of the corresponding genes. This method can be used to identify specific genes and pathways simultaneously in several organisms of interest even in the absence of sequence information from the organisms.