For each histone modification, e.g. H3K36me3, we deem it as present or absent in the region centred over the exon and the regions preceding and succeeding depending on if the histone modification pileup in such region is higher than a defined cut-off. This cut-off is specific for each histone modification since they were sequenced at difference depths.

(A) Rules predicting ‘spliced out’. Any each histone modification that occurs in any rule is labelled on the outer ring, and co-occurrence with other histone modifications are illustrated by ribbons across the circle. The width of the ribbon correlates to the number of rules where the two modifications co-occur as attributes. Colouring of the ribbons indicates ranking of number of rules with the given pair over the whole model with the lower 75% coloured in grey. The colours of the inner ring correspond to the colour in the outer ring in the other end of a given ribbon. The figure labels are ‘I’: H2BK5me1, ‘II’: H3K36me3, ‘III’: H3K4me1, ‘IV’: H3K9me1, ‘V’: H3K9me2, ‘VI’: H3K9me3, ‘VII’: H3R2me1, ‘VIII’: H4K16ac, ‘IX’: H4K20me1, ‘X’: H4K91ac; S: succeeding the exon, P: preceding the exon, E: on the exon; 0: is absent, 1: is present (e.g. “A P0” is interpreted as “H2BK5me1 preceding the exon is absent”). (B) Same as (A) but for the rules predicting ‘included’ exons. Images was generated using Circos [29].

The footprints are centred on intron-exon junctions (I/E) with examples of rules in the model from the (A) ‘Spliced out’ class (covers 358 exons, −6 pp accuracy gain over independent histone, referred to as S1 in Table 1), (B) ‘Spliced out’ (296, +5 pp, S3), (C) ‘Spliced out’ (260, +12 pp, S5) and (D) ‘Included’ (3738, −8 pp, I1). The number of reads normalized to sequence depth as left axis.