ArticleBioMed research international2016
Guitar: An R/Bioconductor Package for Gene Annotation Guided Transcriptomic Analysis of RNA-Related Genomic Features.
Article in BioMed research international, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 119 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
119 citing papers in PubMed.
- The novel regulatory influence of Argonaute 1 on messenger RNA 5-methylcytosine modification in Arabidopsis thaliana.The plant genome · 2026Article
- A DRACH Observed/Expected Metric Reveals the Evolutionary Landscape of Epitranscriptomic Regulation Across Bilateria.Annals of the New York Academy of Sciences · 2026Article
- The YTHDF proteins modulate Alzheimer's disease-associated brain gene signatures.Molecular neurodegeneration · 2026Article
- DREAMS illuminates spatial DNA and RNA modification landscapes.Nature cell biology · 2026Article
- mNature metabolism · 2026Article
- MoRNiNG: A Database of RNA Modification Sites Associated with RNA Secondary Structure Dynamics.Genomics, proteomics & bioinformatics · 2026Article
- Single-base resolution atlas reveals moderate conservation and regulatory diversity of m6A modifications across mammals.Nucleic acids research · 2026Article
- The epitranscriptomic m6A RNA modification modulates the synapse in ageing and in a mouse model of synucleinopathy.NPJ Parkinson's disease · 2026Article
- Systematic evaluation of computational tools for multitype RNA modification detection using nanopore direct RNA sequencing.Nature methods · 2026Article
- The mechanism of m6A methylation analysis of the transcriptome to regulate the diameter of Alpine Merino wool fiber.Animal bioscience · 2026Article
- Intermittent fasting inhibits Tp53-driven glioma through gut microbiota-mediated methionine-mNature communications · 2026Article
- Radiotherapy induces YTHDF2 in dendritic cells impairing cross-presentation and T cell function.The Journal of experimental medicine · 2026Article
- Multi-region mNature neuroscience · 2026Article
- NResearch (Washington, D.C.) · 2026Article
- Transcriptome-wide study of mRNAs modified by mAnimal biotechnology · 2025Article
- Stage-specific requirement for METTL3-dependent mCommunications biology · 2025Article
- Transcriptome-wide regulation of folate on neural mRNA mCommunications biology · 2025Article
- Graft-seq precisely maps RNA modifications via site-specific chemical grafting strategy.Cell reports methods · 2025Article
- Nanopore direct RNA sequencing of human transcriptomes reveals the complexity of mRNA modifications and crosstalk between regulatory features.Cell genomics · 2025Article
- Nat10 maintains the homeostasis of pluripotent and 2-cell-like states in mouse embryonic stem cells through mRNA cytidine acetylation.Nucleic acids research · 2025Article
59 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
8 authors.
Funding
Abstract
Biological features, such as genes and transcription factor binding sites, are often denoted with genome-based coordinates as the genomic features. While genome-based representation is usually very effective in correlating various biological features, it can be tedious to examine the relationship between RNA-related genomic features and the landmarks of RNA transcripts with existing tools due to the difficulty in the conversion between genome-based coordinates and RNA-based coordinates. We developed here an open source Guitar R/Bioconductor package for sketching the transcriptomic view of RNA-related biological features represented by genome based coordinates. Internally, Guitar package extracts the standardized RNA coordinates with respect to the landmarks of RNA transcripts, with which hundreds of millions of RNA-related genomic features can then be efficiently analyzed within minutes. We demonstrated the usage of Guitar package in analyzing posttranscriptional RNA modifications (5-methylcytosine and N6-methyladenosine) derived from high-throughput sequencing approaches (MeRIP-Seq and RNA BS-Seq) and show that RNA 5-methylcytosine (m(5)C) is enriched in 5'UTR. The newly developed Guitar R/Bioconductor package achieves stable performance on the data tested and revealed novel biological insights. It will effectively facilitate the analysis of RNA methylation data and other RNA-related biological features in the future.
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.