Reactome knowledgebase of human biological pathways and processes - PubMed (original) (raw)

. 2009 Jan;37(Database issue):D619-22.

doi: 10.1093/nar/gkn863. Epub 2008 Nov 3.

Gopal Gopinath, Marc Gillespie, Michael Caudy, David Croft, Bernard de Bono, Phani Garapati, Jill Hemish, Henning Hermjakob, Bijay Jassal, Alex Kanapin, Suzanna Lewis, Shahana Mahajan, Bruce May, Esther Schmidt, Imre Vastrik, Guanming Wu, Ewan Birney, Lincoln Stein, Peter D'Eustachio

Affiliations

Reactome knowledgebase of human biological pathways and processes

Lisa Matthews et al. Nucleic Acids Res. 2009 Jan.

Abstract

Reactome (http://www.reactome.org) is an expert-authored, peer-reviewed knowledgebase of human reactions and pathways that functions as a data mining resource and electronic textbook. Its current release includes 2975 human proteins, 2907 reactions and 4455 literature citations. A new entity-level pathway viewer and improved search and data mining tools facilitate searching and visualizing pathway data and the analysis of user-supplied high-throughput data sets. Reactome has increased its utility to the model organism communities with improved orthology prediction methods allowing pathway inference for 22 species and through collaborations to create manually curated Reactome pathway datasets for species including Arabidopsis, Oryza sativa (rice), Drosophila and Gallus gallus (chicken). Reactome's data content and software can all be freely used and redistributed under open source terms.

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Figures

Figure 1.

Figure 1.

Practical applications of Reactome tools in data analysis. Gene sets derived from large-scale experiments such as microarray analyses (A) can be analyzed using the SkyPainter (B). The reaction arrows in the reaction map are colored according to the number of genes in the user-supplied data set whose products participate in the reaction. Statistically over-represented events (ones with significantly more user-specified participants than would be expected if the user-specified genes were randomly distributed over events) are highlighted in color and can be viewed as an ordered list. A mapping of submitted identifiers to reactions is provided. These colored reaction maps can be downloaded in publication quality PNG, SVG or PDF formats. Here, Apoptosis is the overrepresented pathway. (C) BioMart can be used to learn more about genes in a data set. To identify the complexes that contain a protein/proteins of interest, the ‘complexes’ data set is selected, the protein Uniprot identifier(s) are entered as a filter and complex names/identifiers are selected as attributes to be displayed. By selecting the ‘Dataset’ button (bottom left), users can combine searches across additional databases such as UniProt to retrieve additional data, e.g. the amino-acid sequences of the individual proteins making up the complexes annotated in Reactome. In this example, numerous FASL:FAS receptor complexes have been identified. (D) The entity-level pathway visualization tool can be used to identify events involving FASL:FAS receptor complexes. Searching on FASL produces a hit list presented in the hierarchy panel. The selected event/entity, Fasl/CD95L signaling is displayed on the map highlighted in green. Reactions are represented as arrows. Reaction names are displayed by clicking on the ‘nodes’. Molecules are represented as boxes and their names are displayed upon scroll over. Selecting an event in the event hierarchy centers the map on that event and highlights it. Selecting a reaction on the map highlights that reaction in the event hierarchy. A zoom/scroll box is available in the upper left. A ‘birds-eye view’ of a pathway is provided in a box at the lower left. Dragging the box in this view repositions the focal point of the zoomed view. The entire pathway can be moved within the window by clicking/dragging it. A collapsible details section at the bottom of the page provides the option to view the event page description of the selected reaction or pathway. (E) A part of the FASL/CD95L signaling pathway drawn using the new author tool. Diagrams include a graphical representation of the subcellular localization of the reactions and their constituent molecules as well as the stoichiometry, states and post-translational modifications and binding features of these molecules.

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