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Differential analysis of gene regulation at transcript resolution with RNA-seq

Trapnell, Cole and Hendrickson, David G. and Sauvageau, Martin and Goff, Loyal and Rinn, John L. and Pachter, Lior (2013) Differential analysis of gene regulation at transcript resolution with RNA-seq. Nature Biotechnology, 31 (1). pp. 46-53. ISSN 1087-0156. PMCID PMC3869392. doi:10.1038/nbt.2450.

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Differential analysis of gene and transcript expression using high-throughput RNA sequencing (RNA-seq) is complicated by several sources of measurement variability and poses numerous statistical challenges. We present Cuffdiff 2, an algorithm that estimates expression at transcript-level resolution and controls for variability evident across replicate libraries. Cuffdiff 2 robustly identifies differentially expressed transcripts and genes and reveals differential splicing and promoter-preference changes. We demonstrate the accuracy of our approach through differential analysis of lung fibroblasts in response to loss of the developmental transcription factor HOXA1, which we show is required for lung fibroblast and HeLa cell cycle progression. Loss of HOXA1 results in significant expression level changes in thousands of individual transcripts, along with isoform switching events in key regulators of the cell cycle. Cuffdiff 2 performs robust differential analysis in RNA-seq experiments at transcript resolution, revealing a layer of regulation not readily observable with other high-throughput technologies.

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Pachter, Lior0000-0002-9164-6231
Additional Information:© 2012 Macmillan Publishers Limited. Received 04 May 2012. Accepted 09 November 2012. Published online 09 December 2012. We are grateful to D. Kelley for a careful reading of the manuscript, and B. Wold for sharing the hESC RNA-seq data. We are also thankful for the ongoing development efforts of A. Roberts, B. Langmead, D. Kim, G. Pertea, H. Pimentel and S. Salzberg. C.T. and D.G.H. are Damon Runyon Postdoctoral Fellows. J.L.R. is a Damon Runyon-Rachleff Inovator fellow. This work was supported by US National Institutes of Health grants DP2OD006670, P01GM099117, P50HG006193 and RO1ES020260 (to J.L.R.) and R01 HG006129 and R01 DK094699 (to L.P.). These authors contributed equally to this work. Cole Trapnell & David G Hendrickson These authors contributed equally to this work. John L Rinn & Lior Pachter Author Contributions: C.T. and L.P. developed the mathematics and statistics. D.G.H. and M.S. performed the experiments. D.G.H. and C.T. designed the experiments and performed the analysis. C.T. and L.G. implemented the software. L.P., J.L.R., D.G.H. and C.T. conceived the research. All authors wrote and approved the manuscript. The authors declare no competing financial interests.
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Damon Runyon Cancer Research FoundationUNSPECIFIED
NIHR01 HG006129
NIHR01 DK094699
Issue or Number:1
PubMed Central ID:PMC3869392
Record Number:CaltechAUTHORS:20170303-161532491
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Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:74743
Deposited By: George Porter
Deposited On:06 Mar 2017 16:26
Last Modified:11 Nov 2021 05:29

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