title: ReactomePA: an R/Bioconductor package for reactome pathway analysis and visualization.
abstract: Reactome is a manually curated pathway annotation database for unveiling high-order biological pathways from high-throughput data. ReactomePA is an R/Bioconductor package providing enrichment analyses, including hypergeometric test and gene set enrichment analyses. A functional analysis can be applied to the genomic coordination obtained from a sequencing experiment to analyze the functional significance of genomic loci including cis-regulatory elements and non-coding regions. Comparison among different experiments is also supported. Moreover, ReactomePA provides several visualization functions to produce highly customizable, publication-quality figures. The source code and documents of ReactomePA are freely available through Bioconductor (http://www.bioconductor.org/packages/ReactomePA).
authors.affiliation: Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou, 510632, China. tqyhe@jnu.edu.cn and State Key Laboratory of Emerging Infectious Disease, School of Public Health, The University of Hong Kong, Hong Kong SAR, China.
authors.forename: Guangchuang
authors.initials: G
authors.lastname: Yu
authors.affiliation: Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou, 510632, China. tqyhe@jnu.edu.cn.
authors.forename: Qing-Yu
authors.initials: QY
authors.lastname: He
mesh_terms: D000818:Animals; D047369:Chromatin Immunoprecipitation; D016208:Databases, Factual; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D053858:Metabolic Networks and Pathways; D060066:Protein Interaction Maps; D040901:Proteomics; D015398:Signal Transduction