Mathematical design of prokaryotic clone-based microarrays

This paper describes the development of two complementary equations for determining the genome coverage at the gene level. The first equation predicts the fraction of genes that is represented on the array in a detectable way and cover at least a set part (the minimal insert coverage) of the genomic fragment by which these genes are represented. The higher this minimal insert coverage, the larger the chance that changes in expression of a specific gene can be detected and attributed to that gene. The second equation predicts the fraction of genes that is represented in spots on the array that only represent genes from a single transcription unit, which information can be interpreted in a quantitative way.Validation of these equations shows that they form reliable tools supporting optimal design of prokaryotic clone-based microarrays.In the past decade, whole transcriptome comparison by microarray hybridizations has proven to be an effective tool for studying genome wide gene responses. The general approaches for the development of microarrays are based on the completely annotated genome sequence of an organism. Usually each spot on the array represents one open reading frame (ORF). Whereas this approach has clear advantages for strains for which the complete annotated genome sequence is available, it is not applicable to strains for which this is not the case.A method that allows for the rapid construction of microarrays for which the completely annotated genome sequence is not required is by the construction of a clone-based array. In this approach, a chromosomal DNA library is constructed from the strain of interest. From this library the genomic fragments, the inserts, are amplified from the clones by PCR with generic primers and spotted on the array-slide [1,2].The major differences between ORF-based and clone-based arrays with respect to the data interpretation are that in case of clone-based arrays the differential signals can only be linked to a specific gene