ArticleJournal of proteome research2015
Most highly expressed protein-coding genes have a single dominant isoform.
Article in Journal of proteome research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 82 papers.
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Who cites it
82 citing papers in PubMed.
- Transitioning from Transcriptomics to Proteomics: Enhancing Mechanistic Accuracy in PBPK Modeling via Absolute Protein Abundances.CPT: pharmacometrics & systems pharmacology · 2026Article
- Profiling maize embryonic leaf development and discovering new genes using high-resolution spatial long-read isoform sequencing.Nature plants · 2026Article
- Integrating short-read and long-read single-cell transcriptomics of pig pituitary reveals mechanisms of high-altitude hypoxia adaptation.PLoS genetics · 2026Article
- Coding regions are rarely predefined in the eukaryotic genomes: a note on simplified models of gene architecture.BMC genomics · 2026Article
- Mammalian aging involves genome-wide splicing degeneration leading to functional decline.bioRxiv : the preprint server for biology · 2026Article
- Disease-associated genetic variants can cause missense effects in tissue-specific protein isoforms.Nature communications · 2026Article
- Pervasive non-triplet alternative splicing drives functional isoform diversity.Nature communications · 2026Article
- Glycolysis and glycolytic enzymes in acute myeloid leukemia: Warburg and beyond.Frontiers in pharmacology · 2026Review
- BOGO: A Proteome-Wide Gene Overexpression Platform for Discovering Rational Cancer Combination Therapies.bioRxiv : the preprint server for biology · 2025Article
- CoExpPhylo - a novel pipeline for biosynthesis gene discovery.BMC genomics · 2025Article
- Heterogeneous and novel transcript expression in single cells of patient-derived clear cell renal cell carcinoma organoids.Genome research · 2025Article
- Toward a comprehensive profiling of alternative splicing proteoform structures, interactions and functions.Current opinion in structural biology · 2025Review
- Isoform differences drive functional diversity of NHR-49.microPublication biology · 2025Article
- IsopretGO-analysing and visualizing the functional consequences of differential splicing.NAR genomics and bioinformatics · 2024Article
- Global impact of unproductive splicing on human gene expression.Nature genetics · 2024Article
- Detecting differential transcript usage in complex diseases with SPIT.Cell reports methods · 2024Article
- A cis-regulatory element regulates ERAP2 expression through autoimmune disease risk SNPs.Cell genomics · 2024Article
- Comparative analyses of dynamic transcriptome profiles highlight key response genes and dominant isoforms for muscle development and growth in chicken.Genetics, selection, evolution : GSE · 2023Article
- Global impact of aberrant splicing on human gene expression levels.bioRxiv : the preprint server for biology · 2023Article
- Detecting differential transcript usage in complex diseases with SPIT.bioRxiv : the preprint server for biology · 2023Article
22 more citing papers are in PubMed but not listed here.
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6 authors.
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Abstract
Although eukaryotic cells express a wide range of alternatively spliced transcripts, it is not clear whether genes tend to express a range of transcripts simultaneously across cells, or produce dominant isoforms in a manner that is either tissue-specific or regardless of tissue. To date, large-scale investigations into the pattern of transcript expression across distinct tissues have produced contradictory results. Here, we attempt to determine whether genes express a dominant splice variant at the protein level. We interrogate peptides from eight large-scale human proteomics experiments and databases and find that there is a single dominant protein isoform, irrespective of tissue or cell type, for the vast majority of the protein-coding genes in these experiments, in partial agreement with the conclusions from the most recent large-scale RNAseq study. Remarkably, the dominant isoforms from the experimental proteomics analyses coincided overwhelmingly with the reference isoforms selected by two completely orthogonal sources, the consensus coding sequence variants, which are agreed upon by separate manual genome curation teams, and the principal isoforms from the APPRIS database, predicted automatically from the conservation of protein sequence, structure, and function.
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