Fabregat, A., Sidiropoulos, K., Garapati, P., Gillespie, M., Hausmann, K., Haw, R., Jassal, B., Jupe, S., Korninger, F., McKay, S., Matthews, L., May, B., Milacic, M., Rothfels, K., Shamovsky, V., Webber, M., Weiser, J., Williams, M., Wu, G., Stein, L., Hermjakob, H., D'Eustachio, P. (January 2016) The Reactome pathway Knowledgebase. Nucleic Acids Res, 44 (D1). D481-487. ISSN 1362-4962 (Electronic)0305-1048 (Linking)
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Abstract
The Reactome Knowledgebase (www.reactome.org) provides molecular details of signal transduction, transport, DNA replication, metabolism and other cellular processes as an ordered network of molecular transformations-an extended version of a classic metabolic map, in a single consistent data model. Reactome functions both as an archive of biological processes and as a tool for discovering unexpected functional relationships in data such as gene expression pattern surveys or somatic mutation catalogues from tumour cells. Over the last two years we redeveloped major components of the Reactome web interface to improve usability, responsiveness and data visualization. A new pathway diagram viewer provides a faster, clearer interface and smooth zooming from the entire reaction network to the details of individual reactions. Tool performance for analysis of user datasets has been substantially improved, now generating detailed results for genome-wide expression datasets within seconds. The analysis module can now be accessed through a RESTFul interface, facilitating its inclusion in third party applications. A new overview module allows the visualization of analysis results on a genome-wide Reactome pathway hierarchy using a single screen page. The search interface now provides auto-completion as well as a faceted search to narrow result lists efficiently.
| Item Type: | Paper |
|---|---|
| Subjects: | bioinformatics bioinformatics > genomics and proteomics > databases bioinformatics > genomics and proteomics bioinformatics > genomics and proteomics > datasets |
| CSHL Authors: | |
| Communities: | CSHL labs > Stein lab |
| Depositing User: | Matt Covey |
| Date: | 4 January 2016 |
| Date Deposited: | 25 Mar 2016 15:07 |
| Last Modified: | 25 Mar 2016 15:07 |
| PMCID: | PMC4702931 |
| Related URLs: | |
| URI: | https://repository.cshl.edu/id/eprint/32465 |
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