Reactome knowledgebase of human biological pathways and processes.
作者： H. Hermjakob , B. Jassal , A. Kanapin , S. Lewis , S. Mahajan
DOI: 10.1093/NAR/GKN863
关键词: Biology 、 Computational biology 、 Biological pathway 、 Human proteins 、 Open source 、 Prediction methods 、 Bioinformatics 、 Physiological Phenomenon 、 Data content
摘要: Reactome (http://www.reactome.org) is an expert-authored, peer-reviewed knowledgebase of human reactions and pathways that functions as a data mining resource electronic textbook. Its current release includes 2975 proteins, 2907 4455 literature citations. A new entity-level pathway viewer improved search tools facilitate searching visualizing the analysis user-supplied high-throughput sets. has increased its utility to model organism communities with orthology prediction methods allowing inference for 22 species through collaborations create manually curated datasets including Arabidopsis, Oryza sativa (rice), Drosophila Gallus gallus (chicken). Reactome's content software can all be freely used redistributed under open source terms.
oup.com
core.ac.uk
springer.com
oxfordjournals.org
elsevier.com
cshl.edu
paperity.org参考文章(16)
Gene Ontology Consortium, None, The Gene Ontology in 2010: Extensions and refinements Nucleic Acids Research. ,vol. 38, ,(2010) , 10.1093/NAR/GKP1018
Feng Chen, Aaron J Mackey, Christian J Stoeckert Jr, David S Roos, OrthoMCL-DB: querying a comprehensive multi-species collection of ortholog groups Nucleic Acids Research. ,vol. 34, pp. 363- 368 ,(2006) , 10.1093/NAR/GKJ123
Li Li, Christian J Stoeckert, David S Roos, OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Research. ,vol. 13, pp. 2178- 2189 ,(2003) , 10.1101/GR.1224503
Rasko Leinonen, Ruth Akhtar, Ewan Birney, James Bonfield, Lawrence Bower, Matt Corbett, Ying Cheng, Fehmi Demiralp, Nadeem Faruque, Neil Goodgame, Richard Gibson, Gemma Hoad, Christopher Hunter, Mikyung Jang, Steven Leonard, Quan Lin, Rodrigo Lopez, Michael Maguire, Hamish McWilliam, Sheila Plaister, Rajesh Radhakrishnan, Siamak Sobhany, Guy Slater, Petra Ten Hoopen, Franck Valentin, Robert Vaughan, Vadim Zalunin, Daniel Zerbino, Guy Cochrane, Improvements to services at the European Nucleotide Archive Nucleic Acids Research. ,vol. 38, pp. 39- 45 ,(2010) , 10.1093/NAR/GKP998
S Asburner, CA Ball, JA Blake, D Botstein, H Butler, JM Cherry, AP Davis, K Dolinski, SS Dwight, JT Eppig, MA Harris, DP Hill, L Issel‐Tarver, A Kasarskis, S Lewis, JC Matese, JE Richardson, M Ringwald, GM Rubin, G Sherlock, Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nature Genetics. ,vol. 25, pp. 25- 29 ,(2000) , 10.1038/75556
M. Kanehisa, M. Araki, S. Goto, M. Hattori, M. Hirakawa, M. Itoh, T. Katayama, S. Kawashima, S. Okuda, T. Tokimatsu, Y. Yamanishi, KEGG for linking genomes to life and the environment Nucleic Acids Research. ,vol. 36, pp. 480- 484 ,(2007) , 10.1093/NAR/GKM882
Paula de Matos, Rafael Alcántara, Adriano Dekker, Marcus Ennis, Janna Hastings, Kenneth Haug, Inmaculada Spiteri, Steve Turner, Christoph Steinbeck, Chemical Entities of Biological Interest: an update. Nucleic Acids Research. ,vol. 38, pp. 249- 254 ,(2010) , 10.1093/NAR/GKP886
R. Caspi, H. Foerster, C. A. Fulcher, P. Kaipa, M. Krummenacker, M. Latendresse, S. Paley, S. Y. Rhee, A. G. Shearer, C. Tissier, T. C. Walk, P. Zhang, P. D. Karp, The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases Nucleic Acids Research. ,vol. 36, pp. 459- 471 ,(2007) , 10.1093/NAR/GKM900
Imre Vastrik, Peter D'Eustachio, Esther Schmidt, Geeta Joshi-Tope, Gopal Gopinath, David Croft, Bernard de Bono, Marc Gillespie, Bijay Jassal, Suzanna Lewis, Lisa Matthews, Guanming Wu, Ewan Birney, Lincoln Stein, Reactome: a knowledge base of biologic pathways and processes Genome Biology. ,vol. 8, pp. 1- 13 ,(2007) , 10.1186/GB-2007-8-3-R39
Melissa S Cline, Michael Smoot, Ethan Cerami, Allan Kuchinsky, Nerius Landys, Chris Workman, Rowan Christmas, Iliana Avila-Campilo, Michael Creech, Benjamin Gross, Kristina Hanspers, Ruth Isserlin, Ryan Kelley, Sarah Killcoyne, Samad Lotia, Steven Maere, John Morris, Keiichiro Ono, Vuk Pavlovic, Alexander R Pico, Aditya Vailaya, Peng-Liang Wang, Annette Adler, Bruce R Conklin, Leroy Hood, Martin Kuiper, Chris Sander, Ilya Schmulevich, Benno Schwikowski, Guy J Warner, Trey Ideker, Gary D Bader, Integration of biological networks and gene expression data using Cytoscape. Nature Protocols. ,vol. 2, pp. 2366- 2382 ,(2007) , 10.1038/NPROT.2007.324