ArticleGene2013
Dynamic expression of 3' UTRs revealed by Poisson hidden Markov modeling of RNA-Seq: implications in gene expression profiling.
Article in Gene, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 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
14 citing papers in PubMed, 23 citations in OpenAlex.
- A fuzzy based chicken swarm optimization algorithm for efficient fault node detection in Wireless Sensor Networks.Scientific reports · 2024Article
- A Survey on Methods for Predicting Polyadenylation Sites from DNA Sequences, Bulk RNA-seq, and Single-cell RNA-seq.Genomics, proteomics & bioinformatics · 2023Review
- The microRNA target site landscape is a novel molecular feature associating alternative polyadenylation with immune evasion activity in breast cancer.Briefings in bioinformatics · 2021Article
- Maximizing the Utility of Transcriptomics Data in Inflammatory Skin Diseases.Frontiers in immunology · 2021Review
- Profiling Alternative 3' Untranslated Regions in Sorghum using RNA-seq Data.Frontiers in genetics · 2020Article
- mountainClimber Identifies Alternative Transcription Start and Polyadenylation Sites in RNA-Seq.Cell systems · 2019Article
- Alternative polyadenylation produces multiple 3' untranslated regions of odorant receptor mRNAs in mouse olfactory sensory neurons.BMC genomics · 2019Article
- Detection of Differentially Expressed Cleavage Site Intervals Within 3' Untranslated Regions Using CSI-UTR Reveals Regulated Interaction Motifs.Frontiers in genetics · 2019Article
- TAPAS: tool for alternative polyadenylation site analysis.Bioinformatics (Oxford, England) · 2018Article
- Roar: detecting alternative polyadenylation with standard mRNA sequencing libraries.BMC bioinformatics · 2016Article
- High-throughput and quantitative genome-wide messenger RNA sequencing for molecular phenotyping.BMC genomics · 2015Article
- 3USS: a web server for detecting alternative 3'UTRs from RNA-seq experiments.Bioinformatics (Oxford, England) · 2015Article
- MicroRNA-27a directly targetsOncology letters · 2015Article
- The concordance between RNA-seq and microarray data depends on chemical treatment and transcript abundance.Nature biotechnology · 2014Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors at 2 institutions in 1 country.
Funding
Abstract
RNA sequencing (RNA-Seq) allows for the identification of novel exon-exon junctions and quantification of gene expression levels. We show that from RNA-Seq data one may also detect utilization of alternative polyadenylation (APA) in 3' untranslated regions (3' UTRs) known to play a critical role in the regulation of mRNA stability, cellular localization and translation efficiency. Given the dynamic nature of APA, it is desirable to examine the APA on a sample by sample basis. We used a Poisson hidden Markov model (PHMM) of RNA-Seq data to identify potential APA in human liver and brain cortex tissues leading to shortened 3' UTRs. Over three hundred transcripts with shortened 3' UTRs were detected with sensitivity >75% and specificity >60%. Tissue-specific 3' UTR shortening was observed for 32 genes with a q-value ≤ 0.1. When compared to alternative isoforms detected by Cufflinks or MISO, our PHMM method agreed on over 100 transcripts with shortened 3' UTRs. Given the increasing usage of RNA-Seq for gene expression profiling, using PHMM to investigate sample-specific 3' UTR shortening could be an added benefit from this emerging technology.
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.