ArticleBMC bioinformatics2016
Roar: detecting alternative polyadenylation with standard mRNA sequencing libraries.
Article in BMC bioinformatics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 papers.
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Who cites it
36 citing papers in PubMed.
- Foxg1 and companions: Not only transcription factors.Neural regeneration research · 2026Article
- Alternative cleavage and polyadenylation: key regulatory mechanisms in health and disease.RNA biology · 2025Review
- Computational methods for alternative polyadenylation and splicing in post-transcriptional gene regulation.Experimental & molecular medicine · 2025Review
- Benchmarking of methods that identify alternative polyadenylation events in single-/multiple-polyadenylation site genes.NAR genomics and bioinformatics · 2025Review
- Review
- Foxg1 regulates translation of neocortical neuronal genes, including the main NMDA receptor subunit gene, Grin1.BMC biology · 2024Article
- PolyAMiner-Bulk is a deep learning-based algorithm that decodes alternative polyadenylation dynamics from bulk RNA-seq data.Cell reports methods · 2024Article
- Extensible benchmarking of methods that identify and quantify polyadenylation sites from RNA-seq data.RNA (New York, N.Y.) · 2023Review
- REPAC: analysis of alternative polyadenylation from RNA-sequencing data.Genome biology · 2023Article
- A Survey on Methods for Predicting Polyadenylation Sites from DNA Sequences, Bulk RNA-seq, and Single-cell RNA-seq.Genomics, proteomics & bioinformatics · 2023Review
- Review
- Pseudouridine synthases modify human pre-mRNA co-transcriptionally and affect pre-mRNA processing.Molecular cell · 2022Article
- MAAPER: model-based analysis of alternative polyadenylation using 3' end-linked reads.Genome biology · 2021Article
- LABRAT reveals association of alternative polyadenylation with transcript localization, RNA binding protein expression, transcription speed, and cancer survival.BMC genomics · 2021Article
- flexiMAP: a regression-based method for discovering differential alternative polyadenylation events in standard RNA-seq data.Bioinformatics (Oxford, England) · 2021Article
- The Detection and Bioinformatic Analysis of Alternative 3International journal of molecular sciences · 2021Review
- Alternative polyadenylation: methods, mechanism, function, and role in cancer.Journal of experimental & clinical cancer research : CR · 2021Review
- Animal-APAdb: a comprehensive animal alternative polyadenylation database.Nucleic acids research · 2021Article
- Quantifying alternative polyadenylation in RNAseq data with LABRAT.Methods in enzymology · 2021Article
- Alternative polyadenylation drives oncogenic gene expression in pancreatic ductal adenocarcinoma.Genome research · 2020Article
Corrections and comments
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundPost-transcriptional regulation is a complex mechanism that plays a central role in defining multiple cellular identities starting from a common genome. Modifications in the length of 3'UTRs have been found to play an important role in this context, since alternative 3' UTRs could lead to differences for example in regulation by microRNAs and cellular localization of the transcripts thus altering their fate.
resultsWe propose a strategy to identify the genes undergoing regulation of 3' UTR length using RNA sequencing data obtained from standard libraries, thus widely applicable to data originally obtained to perform classical differential expression analyses. We decided to exploit previously annotated APA sites from public databases, in contrast with other approaches recently proposed in which the location of the APA site is inferred from the data together with the relative abundance of the isoforms. We demonstrate the reliability of our method by comparing it to the results of other microarray based or specific RNA-seq libraries methods and show that using APA sites databases results in higher sensitivity compared to de novo site prediction approach.
conclusionsWe implemented the algorithm in a Bioconductor package to facilitate its broad usage in the scientific community. The ability of this approach to detect shortening from libraries with a number of reads comparable to that needed for differential expression analyses makes it useful for investigating if alternative polyadenylation is relevant in a certain biological process without requiring specific experimental assays.
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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.