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dc.contributor.authorSchlaffner, CNen_US
dc.contributor.authorPirklbauer, GJen_US
dc.contributor.authorBender, Aen_US
dc.contributor.authorSteen, JAJen_US
dc.contributor.authorChoudhary, JSen_US
dc.coverage.spatialUnited Statesen_US
dc.date.accessioned2019-02-25T16:36:08Z
dc.date.issued2018-05-22en_US
dc.identifierhttps://www.ncbi.nlm.nih.gov/pubmed/29889196en_US
dc.identifier.citationJ Vis Exp, 2018, (135)en_US
dc.identifier.urihttps://repository.icr.ac.uk/handle/internal/3094
dc.identifier.eissn1940-087Xen_US
dc.identifier.doi10.3791/57633en_US
dc.description.abstractCross-talk between genes, transcripts, and proteins is the key to cellular responses; hence, analysis of molecular levels as distinct entities is slowly being extended to integrative studies to enhance the understanding of molecular dynamics within cells. Current tools for the visualization and integration of proteomics with other omics datasets are inadequate for large-scale studies. Furthermore, they only capture basic sequence identify, discarding post-translational modifications and quantitation. To address these issues, we developed PoGo to map peptides with associated post-translational modifications and quantification to reference genome annotation. In addition, the tool was developed to enable the mapping of peptides identified from customized sequence databases incorporating single amino acid variants. While PoGo is a command line tool, the graphical interface PoGoGUI enables non-bioinformatics researchers to easily map peptides to 25 species supported by Ensembl genome annotation. The generated output borrows file formats from the genomics field and, therefore, visualization is supported in most genome browsers. For large-scale studies, PoGo is supported by TrackHubGenerator to create web-accessible repositories of data mapped to genomes that also enable an easy sharing of proteogenomics data. With little effort, this tool can map millions of peptides to reference genomes within only a few minutes, outperforming other available sequence-identity based tools. This protocol demonstrates the best approaches for proteogenomics mapping through PoGo with publicly available datasets of quantitative and phosphoproteomics, as well as large-scale studies.en_US
dc.languageengen_US
dc.language.isoengen_US
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/en_US
dc.subjectGenomeen_US
dc.subjectGenomicsen_US
dc.subjectPeptidesen_US
dc.subjectProtein Processing, Post-Translationalen_US
dc.subjectProteomicsen_US
dc.titleA Fast and Quantitative Method for Post-translational Modification and Variant Enabled Mapping of Peptides to Genomes.en_US
dc.typeJournal Article
rioxxterms.versionofrecord10.3791/57633en_US
rioxxterms.licenseref.startdate2018-05-22en_US
rioxxterms.typeJournal Article/Reviewen_US
dc.relation.isPartOfJ Vis Expen_US
pubs.issue135en_US
pubs.notesNot knownen_US
pubs.organisational-group/ICR
pubs.publication-statusPublished onlineen_US
pubs.embargo.termsNot knownen_US
dc.contributor.icrauthorChoudhary, Jyotien_US


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