title: Characterizing transcriptional heterogeneity through pathway and gene set overdispersion analysis.
abstract: The transcriptional state of a cell reflects a variety of biological factors, from cell-type-specific features to transient processes such as the cell cycle, all of which may be of interest. However, identifying such aspects from noisy single-cell RNA-seq data remains challenging. We developed pathway and gene set overdispersion analysis (PAGODA) to resolve multiple, potentially overlapping aspects of transcriptional heterogeneity by testing gene sets for coordinated variability among measured cells.
authors.affiliation: Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, USA.
authors.forename: Jean
authors.identifier: http://orcid.org/0000-0002-0212-5451
authors.initials: J
authors.lastname: Fan
authors.affiliation: Illumina Inc., San Diego, California, USA.
authors.forename: Neeraj
authors.initials: N
authors.lastname: Salathia
authors.affiliation: Department of Bioengineering, University of California, San Diego, California, USA.
authors.forename: Rui
authors.initials: R
authors.lastname: Liu
authors.affiliation: Department of Molecular and Cellular Neuroscience, Dorris Neuroscience Center, The Scripps Research Institute, La Jolla, California, USA.
authors.forename: Gwendolyn E
authors.initials: GE
authors.lastname: Kaeser
authors.affiliation: Department of Molecular and Cellular Neuroscience, Dorris Neuroscience Center, The Scripps Research Institute, La Jolla, California, USA.
authors.forename: Yun C
authors.initials: YC
authors.lastname: Yung
authors.affiliation: Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, USA.
authors.forename: Joseph L
authors.initials: JL
authors.lastname: Herman
authors.affiliation: Illumina Inc., San Diego, California, USA.
authors.forename: Fiona
authors.initials: F
authors.lastname: Kaper
authors.affiliation: Illumina Inc., San Diego, California, USA.|Present address: AnchorDx Corporation, International Biotech Island, Guangzhou, Guangdong, China.
authors.forename: Jian-Bing
authors.initials: JB
authors.lastname: Fan
authors.affiliation: Department of Bioengineering, University of California, San Diego, California, USA.
authors.forename: Kun
authors.identifier: http://orcid.org/0000-0002-7596-5224
authors.initials: K
authors.lastname: Zhang
authors.affiliation: Department of Molecular and Cellular Neuroscience, Dorris Neuroscience Center, The Scripps Research Institute, La Jolla, California, USA.
authors.forename: Jerold
authors.initials: J
authors.lastname: Chun
authors.affiliation: Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, USA.
authors.forename: Peter V
authors.identifier: http://orcid.org/0000-0002-6036-5875
authors.initials: PV
authors.lastname: Kharchenko
mesh_terms: D000818:Animals; D002478:Cells, Cultured; D003198:Computer Simulation; D020869:Gene Expression Profiling / Q000379:methods*; D051379:Mice; D008954:Models, Biological; D015233:Models, Statistical; D009474:Neurons / Q000502:physiology; D020543:Proteome / Q000737:chemistry / Q000378:metabolism*; D017423:Sequence Analysis, RNA / Q000379:methods*; D015398:Signal Transduction / Q000502:physiology*; D014158:Transcription, Genetic / Q000502:physiology*; D059467:Transcriptome / Q000502:physiology*
chemical_list: D020543:Proteome