ArticleMolecular & cellular proteomics : MCP2016
Integrated Transcriptomic-Proteomic Analysis Using a Proteogenomic Workflow Refines Rat Genome Annotation.
Article in Molecular & cellular proteomics : MCP, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 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
17 citing papers in PubMed, 37 citations in OpenAlex.
- Introduction to Integrated Proteogenomic Pipeline for Dealing with Pathogenic Missense SNPs.Methods in molecular biology (Clifton, N.J.) · 2025Article
- PgxSAVy: A tool for comprehensive evaluation of variant peptide quality in proteogenomics - catching the (un)usual suspects.Computational and structural biotechnology journal · 2024Article
- Nematode gene annotation by machine-learning-assisted proteotranscriptomics enables proteome-wide evolutionary analysis.Genome research · 2023Article
- Integrated view and comparative analysis of baseline protein expression in mouse and rat tissues.PLoS computational biology · 2022Article
- Prospects and challenges of cancer systems medicine: from genes to disease networks.Briefings in bioinformatics · 2022Review
- AnnotaPipeline: An integrated tool to annotate eukaryotic proteins using multi-omics data.Frontiers in genetics · 2022Article
- Proteotranscriptomics - A facilitator in omics research.Computational and structural biotechnology journal · 2022Review
- Improving the Genome Annotation ofCurrent genomics · 2021Article
- Proteogenomic Analysis Provides Novel Insight into Genome Annotation and Nitrogen Metabolism inMicrobiology spectrum · 2021Article
- Fusion transcripts in normal human cortex increase with age and show distinct genomic features for single cells and tissues.Scientific reports · 2020Article
- SWATH-MS-facilitated proteomic profiling of fruit skin between Fuji apple and a red skin bud sport mutant.BMC plant biology · 2019Article
- Alternative splicing and translation play important roles in hypoxic germination in rice.Journal of experimental botany · 2019Article
- Peptimapper: proteogenomics workflow for the expert annotation of eukaryotic genomes.BMC genomics · 2019Article
- Proteins and Proteoforms: New Separation Challenges.Analytical chemistry · 2018Review
- Proteogenomic Analysis and Discovery of Immune Antigens inMolecular & cellular proteomics : MCP · 2017Article
- A Golden Age for Working with Public Proteomics Data.Trends in biochemical sciences · 2017Review
- A polarizing question: do M1 and M2 microglia exist?Nature neuroscience · 2016Review
Corrections and comments
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Authors and funding
5 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Proteogenomic re-annotation and mRNA splicing information can lead to the discovery of various protein forms for eukaryotic model organisms like rat. However, detection of novel proteoforms using mass spectrometry proteomics data remains a formidable challenge. We developed EuGenoSuite, an open source multiple algorithmic proteomic search tool and utilized it in our in-house integrated transcriptomic-proteomic pipeline to facilitate automated proteogenomic analysis. Using four proteogenomic pipelines (integrated transcriptomic-proteomic, Peppy, Enosi, and ProteoAnnotator) on publicly available RNA-sequence and MS proteomics data, we discovered 363 novel peptides in rat brain microglia representing novel proteoforms for 249 gene loci in the rat genome. These novel peptides aided in the discovery of novel exons, translation of annotated untranslated regions, pseudogenes, and splice variants for various loci; many of which have known disease associations, including neurological disorders like schizophrenia, amyotrophic lateral sclerosis, etc. Novel isoforms were also discovered for genes implicated in cardiovascular diseases and breast cancer for which rats are considered model organisms. Our integrative multi-omics data analysis not only enables the discovery of new proteoforms but also generates an improved reference for human disease studies in the rat model.
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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.