Fig. 4

Comprehensive map of protein peptides supports novel alternative splicing events in full-length MCF-7 transcriptome. a Histogram shows the distribution of peptide amino acid (aa) lengths that could be associated with either Gencode or PacBio transcript variants. b Scatter plot illustrates the number of unique peptide hits per gene based on PacBio (x-axis) or Gencode annotation (y-axis). Each dot represents a single gene locus based on matching of PacBio and Gencode genes. c Empirical cumulative distribution of relative peptide counts per gene for each peptide hit category. Genes with a single transcript annotation (single-transcript category) are shown in light blue. Multi-transcript genes with peptides matching to a subset of transcripts (sub-transcripts category) are shown in yellow. Multi-transcript genes with peptides matching to all annotated transcripts (all-transcripts category) are shown in brown. Multi-gene hits are shown in black. Dotted lines represent the cumulative distributions based on the Gencode annotation. d Bar charts illustrate the comparison of Gencode- or PacBio-based classification of Peptides. e Bar charts show the number of peptides derived from exon–exon junctions of transcripts. The number of peptides that match exon–exon junction of mutually inclusive (blue) or exclusive (yellow) exons. f Peptides with different classification matching to multiple transcripts of ITGB4. Black peptides are all-transcripts hits whereas, based on full-length MCF-7 transcriptome data, yellow peptides are only associated with a subset of transcripts. Exons are colored based on coupling networks, shown in red and blue