Transition matrix of expression pattern changes associated with domestication. The eight magnitude-independent expression patterns recovered by partitioning around medoids clustering found among differentially expressed genes in yucatanense are shown in red down the left side, with the same patterns found in domesticated TM-1 shown across the top in black. Lines represent the mean expression at each time point among all genes exhibiting each pattern. The blocks of the matrix contain the number of genes switching expression pattern during the transformation of wild into domesticated cotton. The diagonal represents genes that did not change expression pattern between TM-1 and yucatanense, but which experience a statistically significant shift in magnitude at one or more time points.