title: f-divergence cutoff index to simultaneously identify differential expression in the integrated transcriptome and proteome.
abstract: The ability to integrate 'omics' (i.e. transcriptomics and proteomics) is becoming increasingly important to the understanding of regulatory mechanisms. There are currently no tools available to identify differentially expressed genes (DEGs) across different 'omics' data types or multi-dimensional data including time courses. We present fCI (f-divergence Cut-out Index), a model capable of simultaneously identifying DEGs from continuous and discrete transcriptomic, proteomic and integrated proteogenomic data. We show that fCI can be used across multiple diverse sets of data and can unambiguously find genes that show functional modulation, developmental changes or misregulation. Applying fCI to several proteogenomics datasets, we identified a number of important genes that showed distinctive regulation patterns. The package fCI is available at R Bioconductor and http://software.steenlab.org/fCI/.
authors.affiliation: Departments of Pathology, Boston Children's Hospital and Harvard Medical School, Boston, MA 02115, USA.
authors.forename: Shaojun
authors.initials: S
authors.lastname: Tang
authors.affiliation: Department of Ophthalmology, Boston Children's Hospital, Boston, MA 02115, USA.
authors.forename: Martin
authors.initials: M
authors.lastname: Hemberg
authors.affiliation: F.M. Kirby Neurobiology Center, Boston Children's Hospital, and Department of Neurology, Harvard Medical School, Boston, MA 02115, USA.
authors.forename: Ertugrul
authors.initials: E
authors.lastname: Cansizoglu
authors.affiliation: F.M. Kirby Neurobiology Center, Boston Children's Hospital, and Department of Neurology, Harvard Medical School, Boston, MA 02115, USA.
authors.forename: Stephane
authors.initials: S
authors.lastname: Belin
authors.affiliation: Neuroscience Research Institute, University of California at Santa Barbara, Santa Barbara, CA 93106, USA.
authors.forename: Kenneth
authors.initials: K
authors.lastname: Kosik
authors.affiliation: Department of Ophthalmology, Boston Children's Hospital, Boston, MA 02115, USA.
authors.forename: Gabriel
authors.initials: G
authors.lastname: Kreiman
authors.affiliation: Departments of Pathology, Boston Children's Hospital and Harvard Medical School, Boston, MA 02115, USA Hanno.Steen@Childrens.Harvard.edu.
authors.forename: Hanno
authors.initials: H
authors.lastname: Steen
authors.affiliation: F.M. Kirby Neurobiology Center, Boston Children's Hospital, and Department of Neurology, Harvard Medical School, Boston, MA 02115, USA Judith.Steen@Childrens.Harvard.edu.
authors.forename: Judith
authors.initials: J
authors.lastname: Steen
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D015870:Gene Expression; D020869:Gene Expression Profiling / Q000379:methods*; D040901:Proteomics / Q000379:methods*; D017423:Sequence Analysis, RNA; D053719:Tandem Mass Spectrometry