title: Tools to covisualize and coanalyze proteomic data with genomes and transcriptomes: validation of genes and alternative mRNA splicing.
abstract: 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.
authors.affiliation: Systems Biology Initiative, The University of New South Wales , Sydney, New South Wales 2052, Australia.
authors.forename: Chi Nam Ignatius
authors.initials: CN
authors.lastname: Pang
authors.forename: Aidan P
authors.initials: AP
authors.lastname: Tay
authors.forename: Carlos
authors.initials: C
authors.lastname: Aya
authors.forename: Natalie A
authors.initials: NA
authors.lastname: Twine
authors.forename: Linda
authors.initials: L
authors.lastname: Harkness
authors.forename: Gene
authors.initials: G
authors.lastname: Hart-Smith
authors.forename: Samantha Z
authors.initials: SZ
authors.lastname: Chia
authors.forename: Zhiliang
authors.initials: Z
authors.lastname: Chen
authors.forename: Nandan P
authors.initials: NP
authors.lastname: Deshpande
authors.forename: Nadeem O
authors.initials: NO
authors.lastname: Kaakoush
authors.forename: Hazel M
authors.initials: HM
authors.lastname: Mitchell
authors.forename: Moustapha
authors.initials: M
authors.lastname: Kassem
authors.forename: Marc R
authors.initials: MR
authors.lastname: Wilkins
mesh_terms: D002167:Campylobacter / Q000235:genetics; D016678:Genome; D006801:Humans; D013058:Mass Spectrometry; D010748:Phosphopeptides / Q000235:genetics; D040901:Proteomics; D012326:RNA Splicing; D012333:RNA, Messenger / Q000235:genetics*; D012441:Saccharomyces cerevisiae / Q000235:genetics; D059467:Transcriptome
chemical_list: D010748:Phosphopeptides; D012333:RNA, Messenger