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Fig. 3 | Genome Biology

Fig. 3

From: Characterizing the interplay between gene nucleotide composition bias and splicing

Fig. 3

Nucleotide composition bias and dependency for specific spliceosome components. a Nucleotide frequency (%) maps in different sets of exons and their flanking intronic sequences. b Minimum free energy (MFE) at the 5′ ss of sets of exons activated by different spliceosome-associated factors. MFEs were computed using 25 nucleotides within the exons and 25 nucleotides within the intron. The red line indicates the median values calculated for control exons. “*” corresponds to Student’s test FDR < 0.02 when comparing a set of exons activated by a spliceosome-associated factor to control (CTRL) exons. c Proportion (%) of exons activated by U1 snRNP–associated factors (U1 exons) or by U2 snRNP–associated factors (U2 exons) with two or more predicted BPs in a window corresponding to the last 100 nucleotides in their upstream intron. “$$” corresponds to χ2 test P < 10−16 when comparing U1 exons to U2 exons. d Boxplot of the number of TNA sequences in the last 50 nucleotides upstream introns of U1 exons and U2 exons. “$” corresponds to Wald’s test P value < 10−16 when comparing U1 exons to U2 exons. e Boxplot of the number of T-rich low-complexity sequences in a window between positions − 35 and − 75 upstream the 3′ ss of U1 exons and U2 exons. “$” corresponds to Wald’s test P value < 10−16 when comparing U1 exons to U2 exons. f Density of peaks obtained from publicly available U2AF2-CLIP datasets generated from HEK293T (left panel) or HeLa (right panel) cells and mapped upstream of U1 exons or U2 exons. The green arrows indicate peaks mapping upstream of the Py tract. g The V value is a representation of a P value calculated by comparing the proportion of GC exons and AT exons activated by individual spliceosome-associated factors (see the “Materials and methods” section). A V value above the dotted line that corresponds to log10 (0.05) is statically significant

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