Clustering after LOS normalization yields coarse biological program. The clustering of LOS normalized DFT transformed data using the flowClust approach with ten clusters is shown in panel A. The gray lines represent individual gene profiles, the solid colored line marks the cluster mean profile, and the dashed colored lines mark the 5% and 95% quantiles. For visualization the 12m transformed data are used. On the upper left corner of every profile plot, the cluster index is given followed by the number of genes in the corresponding cluster. The gray shaded area marks the dark period. The clusters are sorted by the mean phase angle ϕ. A graphical representation of the cluster-wise functional enrichment of the clustering, shown in A, is presented in panel B. The rows of this matrix correspond to biological functions whereas the columns correspond to clusters, where the color marks on the top match the colors used for the cluster mean profiles. The number of genes with the corresponding function is shown on the top of each cell and the enrichment p-value on the bottom. Furthermore, the enrichment p-value is color-coded in the cell background, marking highly significant enrichments in black and non-significant enrichments in white. The rows were rearranged to reveal the temporal ordering.
Lehmann et al. BMC Bioinformatics 2013 14:133 doi:10.1186/1471-2105-14-133