ArticlePacific Symposium on Biocomputing. Pacific Symposium on Biocomputing2015
Kleat: cleavage site analysis of transcriptomes.
Article in Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- Challenges in identifying mRNA transcript starts and ends from long-read sequencing data.Genome research · 2024Review
- PolyAMiner-Bulk is a deep learning-based algorithm that decodes alternative polyadenylation dynamics from bulk RNA-seq data.Cell reports methods · 2024Article
- Transcriptome sequencing suggests that pre-mRNA splicing counteracts widespread intronic cleavage and polyadenylation.NAR genomics and bioinformatics · 2023Article
- A Survey on Methods for Predicting Polyadenylation Sites from DNA Sequences, Bulk RNA-seq, and Single-cell RNA-seq.Genomics, proteomics & bioinformatics · 2023Review
- Aptardi predicts polyadenylation sites in sample-specific transcriptomes using high-throughput RNA sequencing and DNA sequence.Nature communications · 2021Article
- Profiling Alternative 3' Untranslated Regions in Sorghum using RNA-seq Data.Frontiers in genetics · 2020Article
- Detection of Differentially Expressed Cleavage Site Intervals Within 3' Untranslated Regions Using CSI-UTR Reveals Regulated Interaction Motifs.Frontiers in genetics · 2019Article
- Recurrent tumor-specific regulation of alternative polyadenylation of cancer-related genes.BMC genomics · 2018Article
- An integrative model for alternative polyadenylation, IntMAP, delineates mTOR-modulated endoplasmic reticulum stress response.Nucleic acids research · 2018Article
- DE-kupl: exhaustive capture of biological variation in RNA-seq data through k-mer decomposition.Genome biology · 2017Article
- Analyses of alternative polyadenylation: from old school biochemistry to high-throughput technologies.BMB reports · 2017Review
- Prediction of Poly(A) Sites by Poly(A) Read Mapping.PloS one · 2017Article
- Roar: detecting alternative polyadenylation with standard mRNA sequencing libraries.BMC bioinformatics · 2016Article
- Article
Corrections and comments
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Authors and funding
10 authors.
Funding
Abstract
In eukaryotic cells, alternative cleavage of 3' untranslated regions (UTRs) can affect transcript stability, transport and translation. For polyadenylated (poly(A)) transcripts, cleavage sites can be characterized with short-read sequencing using specialized library construction methods. However, for large-scale cohort studies as well as for clinical sequencing applications, it is desirable to characterize such events using RNA-seq data, as the latter are already widely applied to identify other relevant information, such as mutations, alternative splicing and chimeric transcripts. Here we describe KLEAT, an analysis tool that uses de novo assembly of RNA-seq data to characterize cleavage sites on 3' UTRs. We demonstrate the performance of KLEAT on three cell line RNA-seq libraries constructed and sequenced by the ENCODE project, and assembled using Trans-ABySS. Validating the KLEAT predictions with matched ENCODE RNA-seq and RNA-PET libraries, we show that the tool has over 90% positive predictive value when there are at least three RNA-seq reads supporting a poly(A) tail and requiring at least three RNA-PET reads mapping within 100 nucleotides as validation. We also compare the performance of KLEAT with other popular RNA-seq analysis pipelines that reconstruct 3' UTR ends, and show that it performs favourably, based on an ROC-like curve.
Indexed as
Identifiers
25592595PMC4350765What 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.