title: Differential analysis of gene regulation at transcript resolution with RNA-seq.
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.
authors.affiliation: Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts, USA.
authors.forename: Cole
authors.initials: C
authors.lastname: Trapnell
authors.forename: David G
authors.initials: DG
authors.lastname: Hendrickson
authors.forename: Martin
authors.initials: M
authors.lastname: Sauvageau
authors.forename: Loyal
authors.initials: L
authors.lastname: Goff
authors.forename: John L
authors.initials: JL
authors.lastname: Rinn
authors.forename: Lior
authors.initials: L
authors.lastname: Pachter
mesh_terms: D005347:Fibroblasts / Q000166:cytology; D005786:Gene Expression Regulation; D006367:HeLa Cells; D018398:Homeodomain Proteins / Q000235:genetics; D006801:Humans; D008168:Lung / Q000166:cytology / Q000378:metabolism; D012333:RNA, Messenger / Q000235:genetics*; D017423:Sequence Analysis, RNA / Q000379:methods*; D014157:Transcription Factors / Q000235:genetics; D000099261:Homeobox A1 Protein
chemical_list: D018398:Homeodomain Proteins; D012333:RNA, Messenger; D014157:Transcription Factors; D000099261:Homeobox A1 Protein