Title |
Tools to Covisualize and Coanalyze Proteomic Data with Genomes and Transcriptomes: Validation of Genes and Alternative mRNA Splicing
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Published in |
Journal of Proteome Research, November 2013
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DOI | 10.1021/pr400820p |
Pubmed ID | |
Authors |
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 |
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. |
X Demographics
Geographical breakdown
Country | Count | As % |
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France | 3 | 20% |
United Kingdom | 3 | 20% |
Canada | 1 | 7% |
Spain | 1 | 7% |
Mexico | 1 | 7% |
United States | 1 | 7% |
Netherlands | 1 | 7% |
Unknown | 4 | 27% |
Demographic breakdown
Type | Count | As % |
---|---|---|
Members of the public | 9 | 60% |
Scientists | 5 | 33% |
Science communicators (journalists, bloggers, editors) | 1 | 7% |
Mendeley readers
Geographical breakdown
Country | Count | As % |
---|---|---|
United States | 4 | 3% |
France | 1 | <1% |
Italy | 1 | <1% |
Brazil | 1 | <1% |
Netherlands | 1 | <1% |
New Zealand | 1 | <1% |
United Kingdom | 1 | <1% |
Slovenia | 1 | <1% |
Singapore | 1 | <1% |
Other | 0 | 0% |
Unknown | 130 | 92% |
Demographic breakdown
Readers by professional status | Count | As % |
---|---|---|
Researcher | 43 | 30% |
Student > Ph. D. Student | 39 | 27% |
Other | 11 | 8% |
Student > Master | 11 | 8% |
Professor > Associate Professor | 10 | 7% |
Other | 19 | 13% |
Unknown | 9 | 6% |
Readers by discipline | Count | As % |
---|---|---|
Agricultural and Biological Sciences | 67 | 47% |
Biochemistry, Genetics and Molecular Biology | 33 | 23% |
Medicine and Dentistry | 6 | 4% |
Computer Science | 6 | 4% |
Immunology and Microbiology | 3 | 2% |
Other | 10 | 7% |
Unknown | 17 | 12% |