Fig. 5

Illustration of the relationship between the 61 RBMY transcripts predicted by IsoCon and shared by both samples. Transcripts are indexed from 1 to 61. The left part of the figure uses IGV^65,66 to visualize a multiple-alignment of the transcripts. Colored positions are positions with variability in the transcripts while grey regions depict conserved positions. Deletions are shown with a horizontal line, with a number indicating their length. The right part of the figure illustrates the relationship between the 61 transcripts as a graph. Vertices are transcripts (labelled with their indices). A vertex is boldfaced if it is predicted to be protein-coding. An edge between two transcripts means that they are potential isoforms from the same gene copy, i.e., they have only exon presence/absence differences. To simplify the visualization, some of the vertices are surrounded by boxes, and a double-edge between two boxes indicates that all pairs of transcripts, between the two boxes, are potential isoforms from the same gene copy. Each maximal clique (i.e. group of vertices) greater than four vertices is shown as a colored circle. The colors of the circles correspond to the rows in the multiple-alignment that are marked with a similarly-colored vertical bar. A maximal clique should be interpreted as all transcripts that potentially originate from the same gene copy