Co-expressed gene assessment based on the path consistency algorithm: Operon detention in Escherichia coli

The assessment of co-expressed genes is an initial step to investigate the gene regulatory system in a microarray analysis. We designed a simple method to assess co-expressed genes from the expression profiles, based on the path consistency (PC) algorithm, which systematically infers a causal graph. The PC algorithm is simply modified for the frequent occurrence of high correlations between expression profiles, which causes an accidental stop of the algorithm by the violation of a numerical calculation. By utilizing the flexible features of the algorithm, biological information about co-expressed genes can be introduced into the algorithm. The performance is illustrated by the application to the gene profiles of operons: 1168 gene profiles in 137 known operons in Escherichia coli. By the improved algorithm, more than 80% of the operons were correctly detected, and less than one gene per operon was falsely detected. The performance promises the wide feasibility of the present method for the assessment of co-expressed genes from microarray data on a genomic scale.