ArticleGenome research2011
Shotgun proteomics aids discovery of novel protein-coding genes, alternative splicing, and "resurrected" pseudogenes in the mouse genome.
Article in Genome research, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 60 papers.
What it found
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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
60 citing papers in PubMed, 132 citations in OpenAlex.
- From Genomic Fossils to Functional Elements: The Evolving Story of Pseudogenes.Advanced genetics (Hoboken, N.J.) · 2025Review
- Four classic "de novo" genes all have plausible homologs and likely evolved from retro-duplicated or pseudogenic sequences.Molecular genetics and genomics : MGG · 2024Article
- Identification of potential pseudogenes for predicting the prognosis of hepatocellular carcinoma.Journal of cancer research and clinical oncology · 2023Article
- Understanding Insulin in the Age of Precision Medicine and Big Data: Under-Explored Nature of Genomics.Biomolecules · 2023Review
- Evolution and function of developmentally dynamic pseudogenes in mammals.Genome biology · 2022Article
- Pseudogenes and Liquid Phase Separation in Epigenetic Expression.Frontiers in oncology · 2022Review
- Discovering the N-Terminal Methylome by Repurposing of Proteomic Datasets.Journal of proteome research · 2021Article
- Long-read cDNA sequencing identifies functional pseudogenes in the human transcriptome.Genome biology · 2021Article
- Pseudogenes: Four Decades of Discovery.Methods in molecular biology (Clifton, N.J.) · 2021Article
- Advances in Proteomics Allow Insights Into Neuronal Proteomes.Frontiers in molecular neuroscience · 2021Review
- UBB pseudogene 4 encodes functional ubiquitin variants.Nature communications · 2020Article
- Overcoming challenges and dogmas to understand the functions of pseudogenes.Nature reviews. Genetics · 2020Review
- Pseudogene Associated Recurrent Gene Fusion in Prostate Cancer.Neoplasia (New York, N.Y.) · 2019Article
- Article
- Progress and Challenges in Ocean Metaproteomics and Proposed Best Practices for Data Sharing.Journal of proteome research · 2019Review
- Alternative Splicing and Protein Diversity: Plants Versus Animals.Frontiers in plant science · 2019Review
- Improvements to the Rice Genome Annotation Through Large-Scale Analysis of RNA-Seq and Proteomics Data Sets.Molecular & cellular proteomics : MCP · 2019Article
- Detection of Proteome Diversity Resulted from Alternative Splicing is Limited by Trypsin Cleavage Specificity.Molecular & cellular proteomics : MCP · 2018Article
- Proteogenomics from a bioinformatics angle: A growing field.Mass spectrometry reviews · 2017Review
- Impact of Alternative Splicing on the Human Proteome.Cell reports · 2017Article
Corrections and comments
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Authors and funding
11 authors at 1 institution in 1 country.
Funding
Abstract
Recent advances in proteomic mass spectrometry (MS) offer the chance to marry high-throughput peptide sequencing to transcript models, allowing the validation, refinement, and identification of new protein-coding loci. We present a novel pipeline that integrates highly sensitive and statistically robust peptide spectrum matching with genome-wide protein-coding predictions to perform large-scale gene validation and discovery in the mouse genome for the first time. In searching an excess of 10 million spectra, we have been able to validate 32%, 17%, and 7% of all protein-coding genes, exons, and splice boundaries, respectively. Moreover, we present strong evidence for the identification of multiple alternatively spliced translations from 53 genes and have uncovered 10 entirely novel protein-coding genes, which are not covered in any mouse annotation data sources. One such novel protein-coding gene is a fusion protein that spans the Ins2 and Igf2 loci to produce a transcript encoding the insulin II and the insulin-like growth factor 2-derived peptides. We also report nine processed pseudogenes that have unique peptide hits, demonstrating, for the first time, that they are not just transcribed but are translated and are therefore resurrected into new coding loci. This work not only highlights an important utility for MS data in genome annotation but also provides unique insights into the gene structure and propagation in the mouse genome. All these data have been subsequently used to improve the publicly available mouse annotation available in both the Vega and Ensembl genome browsers (http://vega.sanger.ac.uk).
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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.