Figure 4

GC skew in equivalent substitutions. (a-d) Median intensity difference vs. mispair orientation for equivalent mispairs in yeast (a, c) and human (b, d). For each mispair, the base listed first is contained in the array-bound oligo, while the second is its presumed counterpart in solution. Mispairs are plotted in the order shown in Table 2. Boxes represent inter-quartile range (i.e. middle 50% of intensity values for each mispair lie between upper and lower bounds). Figure gives mispair skew for all assayed regions (a, b), and for high-intensity (c, d) spots only. (e, f) Median intensity difference vs. GC effect in yeast (e) and human (f): plots those substitutions which increase GC content of oligo (GC+, left side of graph), those with no effect on GC content (GC =, middle) and those decreasing GC content of oligo (GC-, right). (g) Absolute value of the GC skew between equivalent mispairs presented in (a-f), with average skew by species and subset. (h) Intensity as a function of the longest length of a homopolymer nucleotide run contained within the sequence of an oligonucleotide probe. A (blue), C (black), G (green) and T (red) are displayed. Human PM data is shown here.