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.