than transcript pairs that overlap less. As an example of the splice junction difference between two sets of transcripts, consider the set S1, consisting of transcripts (1,2) from Figure 4, and set S2, consisting of transcripts (3,4) from Figure 4. Using the notation introduced in Figure 4, SJD(S1,S2) = d(S1,S2) / t(S1,S2) = [d(1,3) + d(1,4) + d(2,3) + d(2,4)]/ [t(1,3) +t(1,4) + t(2,3) + t(2,4)] = [3 + 4 + 2 + 3]/ [3 + 4 + 4 + 5] = 12/16 = 0.75, reflecting a high level of dissimilarity between the isoforms in these sets, whereas the SJD falls to 0.57 for the more similar sets S1 = transcripts (1,2) versus S3 = transcripts (2,3). Note that in cases where multiple similar/identical transcripts occur in a given set, the SJD measure effectively weights the isoforms by their abundance, reflecting an average dissimilarity when comparing randomly chosen pairs of transcripts from the two tissues. For example, the SJD computed for the set S4 = (1,2,2,2,2), that is, one transcript aligning as transcript 1 in Figure 4 and four transcripts aligning as transcript 2, and the set S5 = (2,2,2,2,3) is 23/95 = 0.24, substantially lower than the SJD value
