K-means clustering of tag types with similar expression trends. PoissonC with K = 10 (where K = number of clusters) was conducted over 100 iterations separately for each biological replicate (mice 13N, 15N, and 13R) and the results from the iterations were combined into consensus clusters shown here. Plotted on the x-axes are the long serial analysis of gene expression (LongSAGE) libraries representing different stages of prostate progression: AS, androgen-sensitive; RAD, responsive to androgen-deprivation; and CR, castration-recurrent. Plotted on the y-axes are the relative expression levels of each tag type, represented as a percentage of the total tag count (for a particular tag type) in all three LongSAGE libraries. Different colors represent different tag types. Each of the ten clusters for each biological replicate are labeled as such. 'No equivalent' indicates that a similar expression trend was not observed in the indicated biological replicate. Eleven expression patterns are evident in total and are labeled on the left. K-means clusters were amalgamated into five major expression trends: group 1, up during progression; group 2, down during progression; group 3, peak in the RAD stage; group 4, constant during progression; and group 5, valley in RAD stage.
Romanuik et al. BMC Medical Genomics 2010 3:43 doi:10.1186/1755-8794-3-43