sequence motif of length k was defined as the fraction of subsets that contained any k-mer with enrichment score (χ2-value) higher than the tested motif. Correcting for multiple testing is not required as the p-value was defined relative to the most enriched k-mer for each sampled set. For sets of skipped exons from human brain- and testis-derived EST sequences, the test sets comprised 1,265 and 517 exons skipped in brain- and testis-derived ESTs, respectively, and the control sets comprised 12,527 and 8,634 exons constitutively included in human brain- and testis-derived ESTs, respectively. Candidate sequence motifs in skipped exons from brain and testis-derived ESTs with associated p-values less than 0.002 were retained. For the set of A5E and A3E events from human liver-derived EST sequences, the test set comprised 44 A3Es and 45 A5Es, and the control set comprised 1,619 A3Es and 1,481 A5Es identified using ESTs from all tissues excluding liver. In this analysis, A3Es and A5Es with extension sequences of less than 25 bases were excluded and sequences longer than 150 bases were truncated to 150 bases, by retaining the exon sequence segment closest to the internal alternative splice junction. Over-represented sequence motifs in A3Es and A5Es from liver-derived
