Figure 4
From: Similarity-Based Segmentation of Multi-Dimensional Signals
Example Domain (chrI:300000..70000). A densely transcribed domain from chromosome I is shown, transcribed segments are shown separately and in reverse order for the forward (top) and reverse (bottom) strand. ‘total’ is a color-coded version of the total signal (sum over all time points), ‘read-counts’ are the individual time-points, ‘primseg’ are the primary segments which were used to split segmentation (Fig. 1), the shown segmentations are from top to bottom those indicated as 1, 3 and 5 in Fig. 2d. Segments were colored by calculating a cycle phase from the average segment read-count along a color wheel (Supp. Fig. S5), and color alpha was derived from a p-value (\(-{\mathrm{log}}_{2}(p)\)) for oscillation calculated by the rain R package49. Segments with \(p\ge 0.05\) are shown in black, where the alpha is derived from their total expression level. ‘ORF’ are the experimentally defined ORF-T transcripts from26 which were used in the parameter scan (Fig. 2), ‘gene’ and ‘dubious’ are annotated confirmed and dubious open reading frames in the yeast genome release R64.1.1. The ‘gene’ ORF are colored by a previous consensus definition of rhythmically co-transcribed gene cohorts in this experimental system23. The plot was generated using the genomeBrowser R script collection at https://gitlab.com/raim/genomeBrowser.
