Identifying differentially expressed transcripts from RNA-seq data with biological variation.

Bioinformatics
Peter GlausMagnus Rattray

Abstract

High-throughput sequencing enables expression analysis at the level of individual transcripts. The analysis of transcriptome expression levels and differential expression (DE) estimation requires a probabilistic approach to properly account for ambiguity caused by shared exons and finite read sampling as well as the intrinsic biological variance of transcript expression. We present Bayesian inference of transcripts from sequencing data (BitSeq), a Bayesian approach for estimation of transcript expression level from RNA-seq experiments. Inferred relative expression is represented by Markov chain Monte Carlo samples from the posterior probability distribution of a generative model of the read data. We propose a novel method for DE analysis across replicates which propagates uncertainty from the sample-level model while modelling biological variance using an expression-level-dependent prior. We demonstrate the advantages of our method using simulated data as well as an RNA-seq dataset with technical and biological replication for both studied conditions. The implementation of the transcriptome expression estimation and differential expression analysis, BitSeq, has been written in C++ and Python. The software is available online fr...Continue Reading

References

Feb 12, 2004·Proceedings of the National Academy of Sciences of the United States of America·Thomas L Griffiths, Mark Steyvers
Jun 10, 2006·Briefings in Bioinformatics·Magnus RattrayNeil D Lawrence
Sep 21, 2007·Bioinformatics·Mark D Robinson, Gordon K Smyth
Jun 3, 2008·Nature Methods·Ali MortazaviBarbara Wold
Jun 3, 2008·Nature Methods·Nicole CloonanSean M Grimmond
Jul 29, 2008·Nucleic Acids Research·Juliane C DohmHeinz Himmelbauer
Nov 19, 2008·Nature Reviews. Genetics·Zhong WangMichael Snyder
Mar 6, 2009·Genome Biology·Ben LangmeadSteven L Salzberg
Dec 22, 2009·Bioinformatics·Bo LiColin N Dewey
Mar 4, 2010·Genome Biology·Mark D Robinson, Alicia Oshlack
Aug 12, 2010·BMC Bioinformatics·Thomas J Hardcastle, Krystyna A Kelly
Oct 29, 2010·Genome Biology·Simon Anders, Wolfgang Huber
Nov 9, 2010·Nature Methods·Yarden KatzChristopher B Burge
Dec 15, 2010·Journal of Bioinformatics and Computational Biology·Xi WangXuegong Zhang
Dec 24, 2010·Genome Biology·Alicia OshlackMatthew D Young
Dec 24, 2010·Nature·Brenton R GraveleySusan E Celniker
Mar 18, 2011·Genome Biology·Adam RobertsLior Pachter

❮ Previous
Next ❯

Citations

Dec 12, 2012·Nature Biotechnology·Cole TrapnellLior Pachter
Feb 23, 2013·Bioinformatics·Ning LengChristina Kendziorski
Sep 21, 2013·Bioinformatics·Lauren A SugdenCharles E Lawrence
Jul 12, 2013·Database : the Journal of Biological Databases and Curation·Valerio BianchiManuela Helmer-Citterich
Apr 16, 2013·Nucleic Acids Research·Philipp DreweGunnar Rätsch
Jun 23, 2012·Genome Research·Simon AndersWolfgang Huber
Jul 11, 2013·BMC Bioinformatics·Jianqiang SunKoji Kadota
Dec 7, 2013·BMC Bioinformatics·Ximeng Zheng, Etsuko N Moriyama
Nov 28, 2013·Bioinformatics·Ernest TurroSimon Tavaré
Oct 7, 2015·Proceedings of the National Academy of Sciences of the United States of America·Antti HonkelaMagnus Rattray
Sep 22, 2015·Journal of Bioinformatics and Computational Biology·Zengmiao WangMinghua Deng
Mar 2, 2016·Statistical Applications in Genetics and Molecular Biology·Zhixiang LinHongyu Zhao
Dec 18, 2014·Genome Biology·Michael I LoveSimon Anders
Sep 1, 2015·Bioinformatics·James HensmanMagnus Rattray
Dec 15, 2015·Genome Biology·Laura-Jayne GardinerAnthony Hall
Dec 1, 2015·Journal of the American Statistical Association·Wei SunFernando Pardo-Manuel de Villena
Sep 5, 2015·BioMed Research International·Yongchao DouChi Zhang
Aug 5, 2015·BMC Genomics·John E CollinsElisabeth M Busch-Nentwich
Feb 25, 2015·BMC Bioinformatics·Hong SunYixue Li
Apr 12, 2014·Frontiers in Cellular Neuroscience·Alessandro GuffantiHermona Soreq
Jun 19, 2016·Bioinformatics·Yuanhua Huang, Guido Sanguinetti
Aug 6, 2016·Science·Elvira MassFrederic Geissmann
Nov 6, 2015·PeerJ·Tsung Fei Khang, Ching Yee Lau
Jan 19, 2017·Nature Methods·Paul DatlingerChristoph Bock

❮ Previous
Next ❯

Datasets Mentioned

BETA
SRA012427

Methods Mentioned

BETA
RNA-seq
BitSeq

Software Mentioned

BitSeq
baySeq
R package
Cuffdiff
edgeR
mseq
Bowtie
Cufflinks
Fastq
DESeq

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.