Genes co-regulated with the SPI-2 type III secretion system as determined by cluster analysis.

The CLR edge strengths (as z-scores between pairs of genes using a cutoff of 5 standard deviations) were used as a distance matrix for hierarchical clustering [20]. Gene pairs which had no edge above the threshold indicated above were assigned a 0. The clusters were chosen at a maximum separating distance (between clusters) of 0.02 and 0.015 for the regulator and GSE2456 networks respectively. These values were chosen using the elbow criterion choosing the minimum number of clusters that explains the maximum amount of variance in the data. This was performed for each network and a cluster that contained the SPI-2 genes was identified.
Genes were grouped into categories based on known function listed on Clusters of Orthologous Groups (COGs) in NCBI.