Views provided by UsageCountsMAAPER: model-based analysis of alternative polyadenylation using 3′ end-linked reads
Copyright policy )NIH| Regulation of Alternatiive Cleavage and Polyadenylation ,
NIH| Regulation and Functions of 3'UTRs in Cellular Stress
Wei Vivian Li; Dinghai Zheng; Ruijia Wang; Bin Tian;
MAAPER: model-based analysis of alternative polyadenylation using 3′ end-linked reads
Abstract Most eukaryotic genes express alternative polyadenylation (APA) isoforms. A growing number of RNA sequencing methods, especially those used for single-cell transcriptome analysis, generate reads close to the polyadenylation site (PAS), termed nearSite reads, hence inherently containing information about APA isoform abundance. Here, we present a probabilistic model-based method named MAAPER to utilize nearSite reads for APA analysis. MAAPER predicts PASs with high accuracy and sensitivity and examines different types of APA events with robust statistics. We show MAAPER’s performance with both bulk and single-cell data and its applicability in unpaired or paired experimental designs.
United States
- Inserm France
- Public Health France
- Center for Systems Biology United States
- Rutgers, The State University of New Jersey United States
- Rutgers New Jersey Medical School United States
Bioinformatics, QH301-705.5, Bioinformatics and Computational Biology, 3′ end reads, Method, Gene Expression, Cellular stress, ' end reads, QH426-470, Polyadenylation, Bioinformatic tool, Mice, Theoretical, Models, Information and Computing Sciences, Genetics, Animals, Humans, Bioinformatics tool, Biology (General), 3' Untranslated Regions, Single cell analysis, Sequence Analysis, RNA, Computational Biology, Alternative polyadenylation, RNA sequencing, Biological Sciences, Models, Theoretical, 004, Trophoblasts, NIH 3T3 Cells, RNA, Generic health relevance, Single-Cell Analysis, RNA-seq, Transcriptome, Sequence Analysis, Environmental Sciences
Bioinformatics, QH301-705.5, Bioinformatics and Computational Biology, 3′ end reads, Method, Gene Expression, Cellular stress, ' end reads, QH426-470, Polyadenylation, Bioinformatic tool, Mice, Theoretical, Models, Information and Computing Sciences, Genetics, Animals, Humans, Bioinformatics tool, Biology (General), 3' Untranslated Regions, Single cell analysis, Sequence Analysis, RNA, Computational Biology, Alternative polyadenylation, RNA sequencing, Biological Sciences, Models, Theoretical, 004, Trophoblasts, NIH 3T3 Cells, RNA, Generic health relevance, Single-Cell Analysis, RNA-seq, Transcriptome, Sequence Analysis, Environmental Sciences
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These citations are derived from selected sources.
This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
Citations provided by BIP!popularityPopularity provided by BIP!
This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
Popularity provided by BIP!influenceInfluence provided by BIP!
This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
Influence provided by BIP!impulseImpulse provided by BIP!
This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
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