Tools to covisualize and coanalyze proteomic data with genomes and transcriptomes

Validation of genes and Alternative mRNA splicing

Chi Nam Ignatius Pang, Aidan P. Tay, Carlos Aya, Natalie A. Twine, Linda Harkness, Gene Hart-Smith, Samantha Z. Chia, Zhiliang Chen, Nandan P. Deshpande, Nadeem O. Kaakoush, Hazel M. Mitchell, Moustapha Kassem, Marc R. Wilkins*

*Corresponding author for this work

Research output: Contribution to journalArticle

33 Citations (Scopus)


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 ap11-Samifier. It has been integrated into Galaxy and made available in the Galaxy tool shed.

Original languageEnglish
Pages (from-to)84-98
Number of pages15
JournalJournal of Proteome Research
Issue number1
Publication statusPublished - 3 Jan 2014
Externally publishedYes


  • alternative splicing
  • data integration
  • RNA-seq
  • splice-junction peptides
  • visualization

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