ArticleNucleic acids research2009
A hierarchical Bayesian model for comparing transcriptomes at the individual transcript isoform level.
Article in Nucleic acids research, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed.
- Alternative splicing programming of axon formation.Wiley interdisciplinary reviews. RNA · 2020Review
- Developmental Xist induction is mediated by enhanced splicing.Nucleic acids research · 2019Article
- When one becomes many-Alternative splicing in β-cell function and failure.Diabetes, obesity & metabolism · 2018Review
- A survey of best practices for RNA-seq data analysis.Genome biology · 2016Review
- WemIQ: an accurate and robust isoform quantification method for RNA-seq data.Bioinformatics (Oxford, England) · 2015Article
- BADGE: a novel Bayesian model for accurate abundance quantification and differential analysis of RNA-Seq data.BMC bioinformatics · 2014Article
- NPEBseq: nonparametric empirical bayesian-based procedure for differential expression analysis of RNA-seq data.BMC bioinformatics · 2013Article
- A broadly applicable high-throughput screening strategy identifies new regulators of Dlg4 (Psd-95) alternative splicing.Genome research · 2013Article
- Statistical and Computational Methods for High-Throughput Sequencing Data Analysis of Alternative Splicing.Statistics in biosciences · 2013Article
- eQTL Mapping Using RNA-seq Data.Statistics in biosciences · 2013Article
- Estimation of alternative splicing variability in human populations.Genome research · 2012Article
- Estimation of Gene Expression at Isoform Level from mRNA-Seq Data by Bayesian Hierarchical Modeling.Frontiers in genetics · 2012Article
- Efficiently identifying genome-wide changes with next-generation sequencing data.Nucleic acids research · 2011Article
- IsoformEx: isoform level gene expression estimation using weighted non-negative least squares from mRNA-Seq data.BMC bioinformatics · 2011Article
- Article
- SAMMate: a GUI tool for processing short read alignments in SAM/BAM format.Source code for biology and medicine · 2011Article
- Article
- MapSplice: accurate mapping of RNA-seq reads for splice junction discovery.Nucleic acids research · 2010Article
- Article
- A global comparison between nuclear and cytosolic transcriptomes reveals differential compartmentalization of alternative transcript isoforms.Nucleic acids research · 2010Article
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2 authors.
Funding
Abstract
The complexity of mammalian transcriptomes is compounded by alternative splicing which allows one gene to produce multiple transcript isoforms. However, transcriptome comparison has been limited to differential analysis at the gene level instead of the individual transcript isoform level. High-throughput sequencing technologies and high-resolution tiling arrays provide an unprecedented opportunity to compare transcriptomes at the level of individual splice variants. However, sequence read coverage or probe intensity at each position may represent a family of splice variants instead of one single isoform. Here we propose a hierarchical Bayesian model, BASIS (Bayesian Analysis of Splicing IsoformS), to infer the differential expression level of each transcript isoform in response to two conditions. A latent variable was introduced to perform direct statistical selection of differentially expressed isoforms. Model parameters were inferred based on an ergodic Markov chain generated by our Gibbs sampler. BASIS has the ability to borrow information across different probes (or positions) from the same genes and different genes. BASIS can handle the heteroskedasticity of probe intensity or sequence read coverage. We applied BASIS to a human tiling-array data set and a mouse RNA-seq data set. Some of the predictions were validated by quantitative real-time RT-PCR experiments.
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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.