ArticleNucleic acids research2022
APPRIS: selecting functionally important isoforms.
Article in Nucleic acids research, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 57 papers.
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Who cites it
57 citing papers in PubMed.
- Review
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- Orthrus: toward evolutionary and functional RNA foundation models.Nature methods · 2026Article
- Predicting the translation efficiency of messenger RNA in mammalian cells.Nature biotechnology · 2026Article
- Developing a germline prostate cancer risk test incorporating rare and common variants, to inform clinical decisions: a route to precision oncology.Genome medicine · 2026Article
- Variant-resolved prediction of context-specific isoform variation with a graph-based attention model.Cell genomics · 2026Article
- Exonic enhancers are a widespread class of dual-function regulatory elements.Nature communications · 2026Article
- IsoProDB: an integrated map of human protein isoforms for accelerated research.Database : the journal of biological databases and curation · 2026Article
- ProteoformDB: an integrative database for functional roles of proteoforms.Database : the journal of biological databases and curation · 2026Article
- CpG Methylation-Driven Pleiotropic Spliced Isoforms of PRSS3 Facilitate Gastric Intratumor Heterogeneity and Metastasis.Cancer science · 2026Article
- PUS1 Drives Renal Cancer Progression by Preventing Formation of Endogenous Double-stranded RNAs.International journal of biological sciences · 2026Article
- The degradation of extended protein isoforms points to a misfiring translation initiation process.Molecular genetics and genomics : MGG · 2025Article
- Reconstructing Evolutionary Histories with Hierarchical Orthologous Groups.Journal of molecular evolution · 2025Review
- Recombination Suppression Drives Expansion of the Drosophila Dot Chromosome.Molecular biology and evolution · 2025Article
- An audit of the PeptideAtlas database uncovers evidence for repurposed pseudogenes and co-opted retroviral ORFs.BMC genomics · 2025Article
- Transcriptomics in the era of long-read sequencing.Nature reviews. Genetics · 2025Review
- Landscape of BRAF transcript variants in human cancer.Molecular oncology · 2025Article
- Orthrus: Towards Evolutionary and Functional RNA Foundation Models.bioRxiv : the preprint server for biology · 2025Article
- Systematic identification of exercise-induced anti-aging processes involving intron retention.The journals of gerontology. Series A, Biological sciences and medical sciences · 2025Article
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
APPRIS (https://appris.bioinfo.cnio.es) is a well-established database housing annotations for protein isoforms for a range of species. APPRIS selects principal isoforms based on protein structure and function features and on cross-species conservation. Most coding genes produce a single main protein isoform and the principal isoforms chosen by the APPRIS database best represent this main cellular isoform. Human genetic data, experimental protein evidence and the distribution of clinical variants all support the relevance of APPRIS principal isoforms. APPRIS annotations and principal isoforms have now been expanded to 10 model organisms. In this paper we highlight the most recent updates to the database. APPRIS annotations have been generated for two new species, cow and chicken, the protein structural information has been augmented with reliable models from the EMBL-EBI AlphaFold database, and we have substantially expanded the confirmatory proteomics evidence available for the human genome. The most significant change in APPRIS has been the implementation of TRIFID functional isoform scores. TRIFID functional scores are assigned to all splice isoforms, and APPRIS uses the TRIFID functional scores and proteomics evidence to determine principal isoforms when core methods cannot.
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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 Socratic graph.