ArticleNucleic acids research2017
RCAS: an RNA centric annotation system for transcriptome-wide regions of interest.
Article in Nucleic acids research, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed.
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- PDGFRα signaling regulates Srsf3 transcript binding to affect PI3K signaling and endosomal trafficking.bioRxiv : the preprint server for biology · 2024Article
- Denaturing purifications demonstrate that PRC2 and other widely reported chromatin proteins do not appear to bind directly to RNA in vivo.Molecular cell · 2024Article
- hnRNP A1 dysfunction alters RNA splicing and drives neurodegeneration in multiple sclerosis (MS).Nature communications · 2024Article
- Matrin3 regulates mitotic spindle dynamics by controlling alternative splicing of CDC14B.Cell reports · 2023Article
- Global role of IGF2BP1 in controlling the expression of Wnt/β-catenin-regulated genes in colorectal cancer cells.Frontiers in cell and developmental biology · 2023Article
- Control of immediate early gene expression by CPEB4-repressor complex-mediated mRNA degradation.Genome biology · 2022Article
- The Role of m6A RNA Methylation in Cancer: Implication for Nature Products Anti-Cancer Research.Frontiers in pharmacology · 2022Review
- Dynamic regulation and key roles of ribonucleic acid methylation.Frontiers in cellular neuroscience · 2022Review
- deepEA: a containerized web server for interactive analysis of epitranscriptome sequencing data.Plant physiology · 2021Article
- The p53-induced RNA-binding protein ZMAT3 is a splicing regulator that inhibits the splicing of oncogenic CD44 variants in colorectal carcinoma.Genes & development · 2021Article
- Recent advances in functional annotation and prediction of the epitranscriptome.Computational and structural biotechnology journal · 2021Review
- Galaxy CLIP-Explorer: a web server for CLIP-Seq data analysis.GigaScience · 2020Article
- MoAIMS: efficient software for detection of enriched regions of MeRIP-Seq.BMC bioinformatics · 2020Article
- FLASH: ultra-fast protocol to identify RNA-protein interactions in cells.Nucleic acids research · 2020Article
- gprofiler2 -- an R package for gene list functional enrichment analysis and namespace conversion toolset g:Profiler.F1000Research · 2020Article
- RNAmod: an integrated system for the annotation of mRNA modifications.Nucleic acids research · 2019Article
- omniCLIP: probabilistic identification of protein-RNA interactions from CLIP-seq data.Genome biology · 2018Article
- The SMAD2/3 interactome reveals that TGFβ controls mNature · 2018Article
Corrections and comments
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
In the field of RNA, the technologies for studying the transcriptome have created a tremendous potential for deciphering the puzzles of the RNA biology. Along with the excitement, the unprecedented volume of RNA related omics data is creating great challenges in bioinformatics analyses. Here, we present the RNA Centric Annotation System (RCAS), an R package, which is designed to ease the process of creating gene-centric annotations and analysis for the genomic regions of interest obtained from various RNA-based omics technologies. The design of RCAS is modular, which enables flexible usage and convenient integration with other bioinformatics workflows. RCAS is an R/Bioconductor package but we also created graphical user interfaces including a Galaxy wrapper and a stand-alone web service. The application of RCAS on published datasets shows that RCAS is not only able to reproduce published findings but also helps generate novel knowledge and hypotheses. The meta-gene profiles, gene-centric annotation, motif analysis and gene-set analysis provided by RCAS provide contextual knowledge which is necessary for understanding the functional aspects of different biological events that involve RNAs. In addition, the array of different interfaces and deployment options adds the convenience of use for different levels of users. RCAS is available at http://bioconductor.org/packages/release/bioc/html/RCAS.html and http://rcas.mdc-berlin.de.
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Registered trials
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