ArticleNucleic acids research2021
OpenProt 2021: deeper functional annotation of the coding potential of eukaryotic genomes.
Article in Nucleic acids research, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 66 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.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
66 citing papers in PubMed.
- Dark matter matters: from noncoding RNA regulation to cancer immunity.Oncoimmunology · 2026Review
- Comprehensive annotation and analysis of human microproteins by human microprotein atlas platform.Communications chemistry · 2026Article
- Degradation Determinants Are Abundant in Human Noncanonical Proteins and Minor Annotated Isoforms.Genome biology and evolution · 2026Article
- Identification of Canonical and Alternative Proteins by Mass Spectrometry.Methods in molecular biology (Clifton, N.J.) · 2026Article
- RiboMicrobe: An Integrated Translatome Atlas for Microorganism.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Micropeptides in the oncological dark matter: decoding their roles in tumor progression and therapy resistance.Journal of translational medicine · 2025Review
- Proteomics-based characterization of ribosome heterogeneity in adult mouse organs.Cellular and molecular life sciences : CMLS · 2025Article
- Current Perspectives on Functional Involvement of Micropeptides in Virus-Host Interactions.International journal of molecular sciences · 2025Review
- Small open reading frame-encoded microproteins in cancer: identification, biological functions and clinical significance.Molecular cancer · 2025Review
- Enhanced Discovery of Alternative Proteins (AltProts) in Mouse Cardiac Development Using Data-Independent Acquisition (DIA) Proteomics.Analytical chemistry · 2025Article
- Discovery of diverse chimeric peptides in a eukaryotic proteome sets the stage for experimental validation of the mosaic translation hypothesis.Computational and structural biotechnology journal · 2025Article
- ChiMSource improves the accuracy of studies on novel amino acid sequences by predicting alternative sources of mass spectrometry-derived peptides.Computational and structural biotechnology journal · 2025Article
- A universal pipeline MosaicProt enables large-scale modeling and detection of chimeric protein sequences for studies on programmed ribosomal frameshifting.Computational and structural biotechnology journal · 2025Article
- Micropeptides Encoded by Noncoding RNAs: Biological Functions and Roles in Diseases.Research (Washington, D.C.) · 2025Review
- Proteomics Can Rise to the Challenge of Pseudogenes' Coding Nature.Journal of proteome research · 2024Review
- Article
- Small ORFs, Big Insights:Cells · 2024Review
- Deciphering the ghost proteome in ovarian cancer cells by deep proteogenomic characterization.Cell death & disease · 2024Article
- NMDtxDB: data-driven identification and annotation of human NMD target transcripts.RNA (New York, N.Y.) · 2024Article
- Comparison of Peptidomes Extracted from Healthy Tissue and Tumor Tissue of the Parotid Glands and Saliva Samples.International journal of molecular sciences · 2024Article
6 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
15 authors.
Funding
Abstract
OpenProt (www.openprot.org) is the first proteogenomic resource supporting a polycistronic annotation model for eukaryotic genomes. It provides a deeper annotation of open reading frames (ORFs) while mining experimental data for supporting evidence using cutting-edge algorithms. This update presents the major improvements since the initial release of OpenProt. All species support recent NCBI RefSeq and Ensembl annotations, with changes in annotations being reported in OpenProt. Using the 131 ribosome profiling datasets re-analysed by OpenProt to date, non-AUG initiation starts are reported alongside a confidence score of the initiating codon. From the 177 mass spectrometry datasets re-analysed by OpenProt to date, the unicity of the detected peptides is controlled at each implementation. Furthermore, to guide the users, detectability statistics and protein relationships (isoforms) are now reported for each protein. Finally, to foster access to deeper ORF annotation independently of one's bioinformatics skills or computational resources, OpenProt now offers a data analysis platform. Users can submit their dataset for analysis and receive the results from the analysis by OpenProt. All data on OpenProt are freely available and downloadable for each species, the release-based format ensuring a continuous access to the data. Thus, OpenProt enables a more comprehensive annotation of eukaryotic genomes and fosters functional proteomic discoveries.
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What Socratic holds
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.