ArticleBMC genomics2013
Whole human genome proteogenomic mapping for ENCODE cell line data: identifying protein-coding regions.
Article in BMC genomics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers, 1 of them a synthesis that pooled it.
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Who cites it
25 citing papers in PubMed, 1 synthesis or guideline pooled it.
- A meta-analysis of Hodgkin lymphoma reveals 19p13.3 TCF3 as a novel susceptibility locus.Nature communications · 2014Pooled it
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- Profiles of alternative splicing events in the diagnosis and prognosis of Gastric Cancer.Journal of Cancer · 2021Article
- Emerging role of long noncoding RNA-encoded micropeptides in cancer.Cancer cell international · 2020Review
- A hidden human proteome encoded by 'non-coding' genes.Nucleic acids research · 2019Article
- Translatomics: The Global View of Translation.International journal of molecular sciences · 2019Review
- Improvements to the Rice Genome Annotation Through Large-Scale Analysis of RNA-Seq and Proteomics Data Sets.Molecular & cellular proteomics : MCP · 2019Article
- ProteomeGenerator: A Framework for Comprehensive Proteomics Based on de Novo Transcriptome Assembly and High-Accuracy Peptide Mass Spectral Matching.Journal of proteome research · 2018Article
- Proteogenomics from a bioinformatics angle: A growing field.Mass spectrometry reviews · 2017Review
- Proteogenomics produces comprehensive and highly accurate protein-coding gene annotation in a complete genome assembly of Malassezia sympodialis.Nucleic acids research · 2017Article
- Evaluating the effect of database inflation in proteogenomic search on sensitive and reliable peptide identification.BMC genomics · 2016Article
- Proteogenomics: Integrating Next-Generation Sequencing and Mass Spectrometry to Characterize Human Proteomic Variation.Annual review of analytical chemistry (Palo Alto, Calif.) · 2016Review
- Improving GENCODE reference gene annotation using a high-stringency proteogenomics workflow.Nature communications · 2016Article
- proBAMsuite, a Bioinformatics Framework for Genome-Based Representation and Analysis of Proteomics Data.Molecular & cellular proteomics : MCP · 2016Article
- Top-down-assisted bottom-up method for homologous protein sequencing: hemoglobin from 33 bird species.Journal of the American Society for Mass Spectrometry · 2015Article
- Proteome sequencing goes deep.Current opinion in chemical biology · 2015Review
- The potential clinical impact of the release of two drafts of the human proteome.Expert review of proteomics · 2015Article
- Onco-proteogenomics: cancer proteomics joins forces with genomics.Nature methods · 2014Article
Corrections and comments
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Authors and funding
11 authors.
Funding
Abstract
backgroundProteogenomic mapping is an approach that uses mass spectrometry data from proteins to directly map protein-coding genes and could aid in locating translational regions in the human genome. In concert with the ENcyclopedia of DNA Elements (ENCODE) project, we applied proteogenomic mapping to produce proteogenomic tracks for the UCSC Genome Browser, to explore which putative translational regions may be missing from the human genome.
resultsWe generated ~1 million high-resolution tandem mass (MS/MS) spectra for Tier 1 ENCODE cell lines K562 and GM12878 and mapped them against the UCSC hg19 human genome, and the GENCODE V7 annotated protein and transcript sets. We then compared the results from the three searches to identify the best-matching peptide for each MS/MS spectrum, thereby increasing the confidence of the putative new protein-coding regions found via the whole genome search. At a 1% false discovery rate, we identified 26,472, 24,406, and 13,128 peptides from the protein, transcript, and whole genome searches, respectively; of these, 481 were found solely via the whole genome search. The proteogenomic mapping data are available on the UCSC Genome Browser at http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeUncBsuProt.
conclusionsThe whole genome search revealed that ~4% of the uniquely mapping identified peptides were located outside GENCODE V7 annotated exons. The comparison of the results from the disparate searches also identified 15% more spectra than would have been found solely from a protein database search. Therefore, whole genome proteogenomic mapping is a complementary method for genome annotation when performed in conjunction with other searches.
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