PCA of D. melanogaster gene features. Results of PCA of frequencies of sequence words within gene features in Dm chromosome arms. Chromosomes colour-coded, and gene features indicated by symbols as follows: green = X, magenta = 3R, brown = 2R, blue = 3L, yellow = 2L; ∇ = promoter, Δ = 5'UTR, □ = CDS, O = intron, + = 3'UTR, × = intergenic. (A) Scatter plot of PCA first component scores of the gene features versus their AT contents. (B), (C) and (D): 1st vs 2nd, 3rd vs 4th and 5th vs 6th component score plots (R2cum = 0.774, 0.923 and 0.954, respectively) of the AT-normalized analysis of 2-6 mer frequencies in gene features.
Philip et al. BMC Genomics 2012 13:97 doi:10.1186/1471-2164-13-97