Fig. 2

Hierarchical cluster analysis of the top 500 most variable transcripts selected by edgeR in the needles (N) and bark (B) treated with methyl jasmonate (MJ) and artificial bark stripping (strip) and control (C), 7 (T7), 14 (T14) and 21 (T21) days after treatment application. Transcripts (rows) and time/part/treatment categories (columns) were clustered using Euclidean distance. The Z-score is calculated by subtracting the trimmed mean of the M-value of the individual from the grand mean of all the individuals and then dividing by the standard deviation. Trimmed Means of M values are estimated in edgeR by where highly expressed genes and those that have a large variation of expression are excluded, whereupon a weighted average of the subset of genes is used to calculate a normalization factor. Colouration; yellow = mean expression, blue = expression below the mean and red = expression above the mean. The categories on the x-axis were re-arranged based on similarity