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

Nat Biotechnol
Authors
Keywords
Abstract

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.

Year of Publication
2013
Journal
Nat Biotechnol
Volume
31
Issue
1
Pages
46-53
Date Published
2013 Jan
ISSN
1546-1696
URL
DOI
10.1038/nbt.2450
PubMed ID
23222703
PubMed Central ID
PMC3869392
Links
Grant list
DP2 OD006670 / OD / NIH HHS / United States
P01 GM099117 / GM / NIGMS NIH HHS / United States
R01 HG006129 / HG / NHGRI NIH HHS / United States
P01GM099117 / GM / NIGMS NIH HHS / United States
P50 HG006193 / HG / NHGRI NIH HHS / United States
R01 ES020260 / ES / NIEHS NIH HHS / United States
DP2OD006670 / OD / NIH HHS / United States
P50HG006193 / HG / NHGRI NIH HHS / United States
R01 DK094699 / DK / NIDDK NIH HHS / United States
R01ES020260 / ES / NIEHS NIH HHS / United States