ArticleNucleic acids research2019
RPFdb v2.0: an updated database for genome-wide information of translated mRNA generated from ribosome profiling.
Article in Nucleic acids research, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
37 citing papers in PubMed.
- riboCIRC v2.0: an expanded resource for translatable CircRNAs.Nucleic acids research · 2026Article
- Translation Signature Scores: Data-Driven Approach to Assess Evidence for Active Translation.Methods in molecular biology (Clifton, N.J.) · 2026Article
- RiboMicrobe: An Integrated Translatome Atlas for Microorganism.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Deep generative optimization of mRNA codon sequences for enhanced mRNA translation and therapeutic efficacy.Nature communications · 2025Article
- A pan-cancer atlas of therapeutic T cell targets.bioRxiv : the preprint server for biology · 2025Article
- Identification of Small Open Reading Frame-encoded Proteins in the Human Genome.Genomics, proteomics & bioinformatics · 2025Article
- Emerging role of endogenous peptides encoded by non-coding RNAs in cancer biology.Non-coding RNA research · 2025Review
- MHC-I-presented non-canonical antigens expand the cancer immunotherapy targets in acute myeloid leukemia.Scientific data · 2024Article
- Polyglutamine-mediated ribotoxicity disrupts proteostasis and stress responses in Huntington's disease.Nature cell biology · 2024Article
- CancerProteome: a resource to functionally decipher the proteome landscape in cancer.Nucleic acids research · 2024Article
- Interchromosomal Colocalization with Parental Genes Is Linked to the Function and Evolution of Mammalian Retrocopies.Molecular biology and evolution · 2023Article
- What Can Ribo-Seq, Immunopeptidomics, and Proteomics Tell Us About the Noncanonical Proteome?Molecular & cellular proteomics : MCP · 2023Article
- What can Ribo-seq and proteomics tell us about the non-canonical proteome?bioRxiv : the preprint server for biology · 2023Article
- IEAtlas: an atlas of HLA-presented immune epitopes derived from non-coding regions.Nucleic acids research · 2023Article
- Ribo-uORF: a comprehensive data resource of upstream open reading frames (uORFs) based on ribosome profiling.Nucleic acids research · 2023Article
- Peptidomics Methods Applied to the Study of Flower Development.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Evolution and function of developmentally dynamic pseudogenes in mammals.Genome biology · 2022Article
- Short open reading frame genes in innate immunity: from discovery to characterization.Trends in immunology · 2022Review
- Novel open reading frames in human accelerated regions and transposable elements reveal new leads to understand schizophrenia and bipolar disorder.Molecular psychiatry · 2022Article
- FusionGDB 2.0: fusion gene annotation updates aided by deep learning.Nucleic acids research · 2022Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
RPFdb (http://www.rpfdb.org or http://sysbio.sysu.edu.cn/rpfdb) is a public database for hosting, analyzing and visualizing ribosome profiling (ribo-seq) data. Since its initial release in 2015, the amount of new ribo-seq data has been considerably enlarged with the increasing popularity of ribo-seq technique. Here, we describe an updated version, RPFdb v2.0, which brings significant data expansion, feature improvements, and functionality optimization: (i) RPFdb v2.0 currently hosts 2884 ribo-seq datasets from 293 studies, covering 29 different species, in comparison with 777 datasets from 82 studies and 8 species in the previous version; (ii) A refined analysis pipeline with multi-step quality controls has been applied to improve the pre-processing and alignment of ribo-seq data; (iii) New functional modules have been added to provide actively translated open reading frames (ORFs) information for each ribo-seq data; (iv) More features have been made available to increase database usability. With these additions and enhancements, RPFdb v2.0 will represent a more valuable and comprehensive database for the gene regulation community.
Indexed as
Identifiers
What OpenQuestion 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 OpenQuestion graph.