Clustering gene expression time series data using an infinite Gaussian process mixture model
Fig 2
DPGP clusters in H. salinarum H2O2-exposed gene expression trajectories.
(A–L) For each cluster, standardized log2 fold change in expression from pre-exposure levels is shown for each gene as well as the posterior cluster mean ±2 standard deviations. Control strain clusters are on left and ΔrosR clusters on right, organized to relate the ΔrosR clusters that correspond to each control cluster. Note that control cluster 5 had no corresponding ΔrosR cluster, but transcripts in this cluster instead distribute to a variety of ΔrosR clusters, none of which had a majority of cluster 5 transcripts. (M) Heatmap displays the proportion of DPGP samples from the Markov chain in which each gene (on the rows and columns) clusters with every other gene in the control strain. Rows and columns were clustered by Ward’s linkage. The predominant blocks of elevated co-clustering are labeled with the control cluster numbers to which the genes that compose the majority of the block belong. As indicated, cluster 6 is dispersed across multiple blocks, primarily the blocks for clusters 3 and 5. (N) Same as (M), except that values are replaced by the proportions in the ΔrosR strain instead of the control strain. Rows and columns ordered as in (M).