Figure 6.

De novo transcriptome variation. (a) The generalized HMM procedure for a chromosome region. Upper panel: the relative log intensity for four Col replicates (red) and four Van replicates (black) along chromosome positions. Blue bars, annotated genes. Middle panel: probe level p-value was obtained by one-sided two sample t-test between Col and Van. Emission and transition probability was estimated by the Baum-Welch algorithm. Lower panel: posterior probabilities of no difference (blue), greater Van expression (green), and greater Col expression (orange) were determined using the Forward-Backward algorithm. Black line: 0.99 posterior probability cutoff. (b) The distribution of the length of differential segment (white bars) and probes per differential segment (grey bars) for state 2 (upper panel) and state 3 (lower panel) segments.