title: SigFuge: single gene clustering of RNA-seq reveals differential isoform usage among cancer samples.
abstract: High-throughput sequencing technologies, including RNA-seq, have made it possible to move beyond gene expression analysis to study transcriptional events including alternative splicing and gene fusions. Furthermore, recent studies in cancer have suggested the importance of identifying transcriptionally altered loci as biomarkers for improved prognosis and therapy. While many statistical methods have been proposed for identifying novel transcriptional events with RNA-seq, nearly all rely on contrasting known classes of samples, such as tumor and normal. Few tools exist for the unsupervised discovery of such events without class labels. In this paper, we present SigFuge for identifying genomic loci exhibiting differential transcription patterns across many RNA-seq samples. SigFuge combines clustering with hypothesis testing to identify genes exhibiting alternative splicing, or differences in isoform expression. We apply SigFuge to RNA-seq cohorts of 177 lung and 279 head and neck squamous cell carcinoma samples from the Cancer Genome Atlas, and identify several cases of differential isoform usage including CDKN2A, a tumor suppressor gene known to be inactivated in a majority of lung squamous cell tumors. By not restricting attention to known sample stratifications, SigFuge offers a novel approach to unsupervised screening of genetic loci across RNA-seq cohorts. SigFuge is available as an R package through Bioconductor.
authors.affiliation: Department of Statistics and Operations Research, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
authors.forename: Patrick K
authors.initials: PK
authors.lastname: Kimes
authors.affiliation: Department of Statistics and Operations Research, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA The Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63108, USA.
authors.forename: Christopher R
authors.initials: CR
authors.lastname: Cabanski
authors.affiliation: Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
authors.forename: Matthew D
authors.initials: MD
authors.lastname: Wilkerson
authors.affiliation: Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.
authors.forename: Ni
authors.initials: N
authors.lastname: Zhao
authors.affiliation: Department of Nutrition, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
authors.forename: Amy R
authors.initials: AR
authors.lastname: Johnson
authors.affiliation: Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
authors.forename: Charles M
authors.initials: CM
authors.lastname: Perou
authors.affiliation: Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA Department of Nutrition, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
authors.forename: Liza
authors.initials: L
authors.lastname: Makowski
authors.affiliation: The Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63108, USA.
authors.forename: Christopher A
authors.initials: CA
authors.lastname: Maher
authors.affiliation: Department of Statistics and Operations Research, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
authors.forename: Yufeng
authors.initials: Y
authors.lastname: Liu
authors.affiliation: Department of Statistics and Operations Research, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
authors.forename: J S
authors.initials: JS
authors.lastname: Marron
authors.affiliation: Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA Multidisciplinary Thoracic Oncology Program, Division of Medical Oncology, Department of Internal Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA hayes@med.unc.edu.
authors.forename: D Neil
authors.initials: DN
authors.lastname: Hayes
mesh_terms: D017398:Alternative Splicing; D002294:Carcinoma, Squamous Cell / Q000235:genetics; D002352:Carrier Proteins / Q000235:genetics; D016000:Cluster Analysis; D005091:Exons; D020869:Gene Expression Profiling / Q000379:methods*; D019942:Genes, p16; D056426:Genetic Loci; D006258:Head and Neck Neoplasms / Q000235:genetics; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D047908:Intracellular Signaling Peptides and Proteins; D007610:Kallikreins / Q000235:genetics; D008175:Lung Neoplasms / Q000235:genetics; D009369:Neoplasms / Q000235:genetics*; D009687:Nuclear Proteins; D059368:RNA Isoforms / Q000378:metabolism*; D017423:Sequence Analysis, RNA / Q000379:methods*; D012984:Software; D000077195:Squamous Cell Carcinoma of Head and Neck
chemical_list: D002352:Carrier Proteins; D047908:Intracellular Signaling Peptides and Proteins; D009687:Nuclear Proteins; C512398:PIMREG protein, human; D059368:RNA Isoforms; C497170:KLK12 protein, human; D007610:Kallikreins