Tools to Covisualize and Coanalyze Proteomic Data with Genomes and Transcriptomes: Validation of Genes and Alternative mRNA Splicing

Direct links between proteomic and
genomic/transcriptomic data
are not frequently made, partly because of lack of appropriate bioinformatics
tools. To help address this, we have developed the PG Nexus pipeline.
The PG Nexus allows users to covisualize peptides in the context of
genomes or genomic contigs, along with RNA-seq reads. This is done
in the Integrated Genome Viewer (IGV). A Results Analyzer reports
the precise base position where LC–MS/MS-derived peptides cover
genes or gene isoforms, on the chromosomes or contigs where this occurs.
In prokaryotes, the PG Nexus pipeline facilitates the validation of
genes, where annotation or gene prediction is available, or the discovery
of genes using a “virtual protein”-based unbiased approach.
We illustrate this with a comprehensive proteogenomics analysis of
two strains of Campylobacter concisus. For higher eukaryotes, the PG Nexus facilitates gene validation
and supports the identification of mRNA splice junction boundaries
and splice variants that are protein-coding. This is illustrated with
an analysis of splice junctions covered by human phosphopeptides,
and other examples of relevance to the Chromosome-Centric Human Proteome
Project. The PG Nexus is open-source and available from https://github.com/IntersectAustralia/ap11_Samifier. It has been integrated into Galaxy and made available in the Galaxy
tool shed.