title: Inferring pathway dysregulation in cancers from multiple types of omic data.
abstract: Although in some cases individual genomic aberrations may drive disease development in isolation, a complex interplay among multiple aberrations is common. Accordingly, we developed Gene Set Omic Analysis (GSOA), a bioinformatics tool that can evaluate multiple types and combinations of omic data at the pathway level. GSOA uses machine learning to identify dysregulated pathways and improves upon other methods because of its ability to decipher complex, multigene patterns. We compare GSOA to alternative methods and demonstrate its ability to identify pathways known to play a role in various cancer phenotypes. Software implementing the GSOA method is freely available from https://bitbucket.org/srp33/gsoa.
authors.affiliation: Department of Oncological Sciences, University of Utah, Salt Lake City, UT USA ; Department of Pharmacology and Toxicology, University of Utah, Salt Lake City, UT USA.
authors.forename: Shelley M
authors.initials: SM
authors.lastname: MacNeil
authors.affiliation: Department of Oncological Sciences, University of Utah, Salt Lake City, UT USA ; Division of Computational Biomedicine, Boston University School of Medicine, Boston, MA USA.
authors.forename: William E
authors.initials: WE
authors.lastname: Johnson
authors.affiliation: Department of Oncological Sciences, University of Utah, Salt Lake City, UT USA ; Department of Medicine, University of Utah, Salt Lake City, UT USA ; Department of Human Genetics, University of Utah, Salt Lake City, UT USA.
authors.forename: Dean Y
authors.initials: DY
authors.lastname: Li
authors.affiliation: Department of Pharmacology and Toxicology, University of Utah, Salt Lake City, UT USA ; Division of Computational Biomedicine, Boston University School of Medicine, Boston, MA USA ; Department of Biology, Brigham Young University, Provo, UT USA.
authors.forename: Stephen R
authors.initials: SR
authors.lastname: Piccolo
authors.affiliation: Department of Oncological Sciences, University of Utah, Salt Lake City, UT USA ; Department of Pharmacology and Toxicology, University of Utah, Salt Lake City, UT USA.
authors.forename: Andrea H
authors.initials: AH
authors.lastname: Bild