ArticleGenomics2011
The discovery of novel protein-coding features in mouse genome based on mass spectrometry data.
Article in Genomics, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
8 citing papers in PubMed, 22 citations in OpenAlex.
- ProGeo-neo: a customized proteogenomic workflow for neoantigen prediction and selection.BMC medical genomics · 2020Article
- Impact of Alternative Splicing on the Human Proteome.Cell reports · 2017Article
- Proteogenomics produces comprehensive and highly accurate protein-coding gene annotation in a complete genome assembly of Malassezia sympodialis.Nucleic acids research · 2017Article
- An Analysis of the Sensitivity of Proteogenomic Mapping of Somatic Mutations and Novel Splicing Events in Cancer.Molecular & cellular proteomics : MCP · 2016Article
- Onco-proteogenomics: cancer proteomics joins forces with genomics.Nature methods · 2014Article
- Integrating genomic, transcriptomic, and interactome data to improve Peptide and protein identification in shotgun proteomics.Journal of proteome research · 2014Review
- Discovery and mass spectrometric analysis of novel splice-junction peptides using RNA-Seq.Molecular & cellular proteomics : MCP · 2013Article
- Article
Corrections and comments
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Authors and funding
12 authors at 4 institutions in 3 countries.
Funding
Abstract
Identifying protein-coding genes in eukaryotic genomes remains a challenge in post-genome era due to the complex gene models. We applied a proteogenomics strategy to detect un-annotated protein-coding regions in mouse genome. High-accuracy tandem mass spectrometry (MS/MS) data from diverse mouse samples were generated by LTQ-Orbitrap mass spectrometer in house. Two searchable diagnostic proteomic datasets were constructed, one with all possible encoding exon junctions, and the other with all putative encoding exons, for the discovery of novel exon splicing events and novel uninterrupted protein-coding regions. Altogether 29,586 unique peptides were identified. Aligning backwards to the mouse genome, the translation of 4471 annotated genes was validated by the known peptides; and 172 genic events were defined in mouse genome by the novel peptides. The approach in the current work can provide substantial evidences for eukaryote genome annotation in encoding genes.
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What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.