ArticleProteomics2014
Revisiting the identification of canonical splice isoforms through integration of functional genomics and proteomics evidence.
Article in Proteomics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed.
- The MEC-2E isoform with a large C-terminal completely rescues the touch sensation defect of C. elegans.Scientific reports · 2025Article
- RNA preservation in human dental pulp for transcriptomic profiling: a comparative multi-parameter study.Frontiers in dental medicine · 2025Article
- Long read sequencing to reveal the full complexity of a plant transcriptome by targeting both standard and long workflows.Plant methods · 2023Article
- An expectation-maximization framework for comprehensive prediction of isoform-specific functions.Bioinformatics (Oxford, England) · 2023Article
- Defining the characteristics of interferon-alpha-stimulated human genes: insight from expression data and machine learning.GigaScience · 2022Article
- Ranked choice voting for representative transcripts with TRaCE.Bioinformatics (Oxford, England) · 2021Article
- FINER: enhancing the prediction of tissue-specific functions of isoforms by refining isoform interaction networks.NAR genomics and bioinformatics · 2021Article
- Exploring the functional impact of alternative splicing on human protein isoforms using available annotation sources.Briefings in bioinformatics · 2019Review
- Network-based method for drug target discovery at the isoform level.Scientific reports · 2019Article
- PROTEOFORMER 2.0: Further Developments in the Ribosome Profiling-assisted Proteogenomic Hunt for New Proteoforms.Molecular & cellular proteomics : MCP · 2019Article
- Proteogenomics from a bioinformatics angle: A growing field.Mass spectrometry reviews · 2017Review
- N-terminal Proteomics Assisted Profiling of the Unexplored Translation Initiation Landscape in Arabidopsis thaliana.Molecular & cellular proteomics : MCP · 2017Article
- Annotation of Alternatively Spliced Proteins and Transcripts with Protein-Folding Algorithms and Isoform-Level Functional Networks.Methods in molecular biology (Clifton, N.J.) · 2017Article
- A proteogenomic approach to understand splice isoform functions through sequence and expression-based computational modeling.Briefings in bioinformatics · 2016Article
- ISOexpresso: a web-based platform for isoform-level expression analysis in human cancer.BMC genomics · 2016Article
- SpectroGene: A Tool for Proteogenomic Annotations Using Top-Down Spectra.Journal of proteome research · 2016Article
- Computational Inferences of the Functions of Alternative/Noncanonical Splice Isoforms Specific to HER2+/ER-/PR- Breast Cancers, a Chromosome 17 C-HPP Study.Journal of proteome research · 2015Article
- Functional Networks of Highest-Connected Splice Isoforms: From The Chromosome 17 Human Proteome Project.Journal of proteome research · 2015Article
- MI-PVT: A Tool for Visualizing the Chromosome-Centric Human Proteome.Journal of proteome research · 2015Article
- BreakSeek: a breakpoint-based algorithm for full spectral range INDEL detection.Nucleic acids research · 2015Article
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4 authors.
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Abstract
Canonical isoforms in different databases have been defined as the most prevalent, most conserved, most expressed, longest, or the one with the clearest description of domains or posttranslational modifications. In this article, we revisit these definitions of canonical isoforms based on functional genomics and proteomics evidence, focusing on mouse data. We report a novel functional relationship network-based approach for identifying the highest connected isoforms (HCIs). We show that 46% of these HCIs are not the longest transcripts. In addition, this approach revealed many genes that have more than one highly connected isoforms. Averaged across 175 RNA-seq datasets covering diverse tissues and conditions, 65% of the HCIs show higher expression levels than nonhighest connected isoforms at the transcript level. At the protein level, these HCIs highly overlap with the expressed splice variants, based on proteomic data from eight different normal tissues. These results suggest that a more confident definition of canonical isoforms can be made through integration of multiple lines of evidence, including HCIs defined by biological processes and pathways, expression prevalence at the transcript level, and relative or absolute abundance at the protein level. This integrative proteogenomics approach can successfully identify principal isoforms that are responsible for the canonical functions of genes.
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