Figure 3

Conservation of IMMADs in C. briggsae . The frequencies of IMMADs in introns flanking alternate exons were compared between C. elegans MASS and SASS genes, as well as between groups of orthologous genes in C. briggsae. These analyses focused on genes with a conserved exon-intron structure and for which the definition of C. briggsae introns of interest was unambiguous (38 MASS and 187 SASS genes, see Methods for more details). A) General analyses with a motif pool including the 17 IMMADs initially identified with a larger sample of MASS and SASS genes in C. elegans (Table 1). As control, the frequency of a population of scrambled IMMADs was compared across the MASS and SASS genes in both species. MASS/SASS frequency ratios are reported. Fisher’s exact tests were performed to evaluate the IMMAD enrichment in the MASS group versus the SASS group. *p < .01 (indicating a ratio significantly different from one). ns, not significant. B) Separate analyses for each IMMAD. MASS/SASS frequency ratios for each IMMAD are reported. Note the log scale on the vertical axis. Fisher’s exact tests were performed to evaluate the specific IMMAD enrichments in the MASS group versus the SASS group. A Bonferroni correction for multiple comparisons was applied. *p < .01 (indicating a ratio significantly different from one). p-values are reported in Additional file 4. na, not applicable because there was no occurrence in the SASS group.