Flexible expressed region analysis for RNA-seq with derfinder.
Differential expression analysis of RNA sequencing (RNA-seq) data typically relies on reconstructing transcripts or counting reads that overlap known gene structures. We previously introduced an intermediate statistical approach called differentially expressed region (DER) finder that seeks to identify contiguous regions of the genome showing differential expression signal at single base resolution without relying on existing annotation or potentially inaccurate transcript assembly.We present the derfinder software that improves our annotation-agnostic approach to RNA-seq analysis by: (i) implementing a computationally efficient bump-hunting approach to identify DERs that permits genome-scale analyses in a large number of samples, (ii) introducing a flexible statistical modeling framework, including multi-group and time-course analyses and (iii) introducing a new set of data visualizations for expressed region analysis. We apply this approach to public RNA-seq data from the Genotype-Tissue Expression (GTEx) project and BrainSpan project to show that derfinder permits the analysis of hundreds of samples at base resolution in R, identifies expression outside of known gene boundaries and can be used to visualize expressed regions at base-resolution. In simulations, our base resolution approaches enable discovery in the presence of incomplete annotation and is nearly as powerful as feature-level methods when the annotation is complete.derfinder analysis using expressed region-level and single base-level approaches provides a compromise between full transcript reconstruction and feature-level analysis. The package is available from Bioconductor at www.bioconductor.org/packages/derfinder.
Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA.|Center for Computational Biology, Johns Hopkins University, Baltimore, MD 21205, USA.|Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD 21205, USA.
Leonardo
L
Collado-Torres
Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA.|Center for Computational Biology, Johns Hopkins University, Baltimore, MD 21205, USA.|Department of Computer Science, Johns Hopkins University, Baltimore, MD 21218, USA.
Abhinav
A
Nellore
Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA.|Center for Computational Biology, Johns Hopkins University, Baltimore, MD 21205, USA.
Alyssa C
AC
Frazee
Center for Computational Biology, Johns Hopkins University, Baltimore, MD 21205, USA.|Department of Computer Science, Johns Hopkins University, Baltimore, MD 21218, USA.
Christopher
C
Wilks
Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA.|Dana-Farber Cancer Institute, Harvard University, Boston, MA 02215, USA.
Michael I
MI
Love
Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA.|Center for Computational Biology, Johns Hopkins University, Baltimore, MD 21205, USA.|Department of Computer Science, Johns Hopkins University, Baltimore, MD 21218, USA.
Ben
B
Langmead
Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA.|Dana-Farber Cancer Institute, Harvard University, Boston, MA 02215, USA.
Rafael A
RA
Irizarry
Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA jtleek@gmail.com.|Center for Computational Biology, Johns Hopkins University, Baltimore, MD 21205, USA.
Jeffrey T
JT
Leek
Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA andrew.jaffe@libd.org.|Center for Computational Biology, Johns Hopkins University, Baltimore, MD 21205, USA.|Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD 21205, USA.|Department of Mental Health, Johns Hopkins University, Baltimore, MD 21205, USA.
Andrew E
AE
Jaffe
D020869:Gene Expression Profiling / Q000379:methods*; D005786:Gene Expression Regulation; D023281:Genomics / Q000379:methods; D059014:High-Throughput Nucleotide Sequencing; D058977:Molecular Sequence Annotation; D009928:Organ Specificity / Q000235:genetics; D012984:Software; D059467:Transcriptome; D064878:Web Browser
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