The Reactome pathway browser and the molecular overlays. (A) The main features of the pathway browser are the ‘Search’ bar at the top, the ‘Pathways’ panel on the left, the ‘Visualization’ panel on the right and a ‘Details’ panel (hidden by default when the pathway browser first loads). When a pathway is selected from the ‘Pathways’ panel hierarchy, it is highlighted in bright green in the hierarchy and its parent terms are highlighted in yellow–green. A description of any reaction or pathway in the pathway diagrams can be displayed below the diagram in the ‘Details’ panel by selecting the event within the diagram. Right-clicking the mouse while the cursor is over a physical entity displays the context sensitive menus. (B) Selecting ‘Other Pathways’ displays additional Reactome pathways that contain the highlighted physical entity. Navigating to the additional pathway is achieved by clicking the pathway name. (C) Selecting ‘Participating Molecules’ displays additional components of the macromolecular complex. Displaying the component information in the ‘Details’ panel is achieved by clicking the entity name. (D) Protein–protein interactions are displayed in the pathway browser for SHC1 [cytosol] and SHP2 [cytosol] physical entities.

The pathway and expression analysis tools. (A) The results table for the ‘ID mapping and pathway assignment’. The sortable table contains one row for each Reactome pathway and four additional columns: repeats the user-supplied IDs, the corresponding UniProt ID, the species name and names of pathways in which this ID can be found. The names/IDs in the last two columns are clickable links that take the user to a diagram of the named pathway. (B) The results for the ‘overrepresentation analysis’, presented as a list of clickable links of enriched events. The warmer the color, the higher the level of overrepresentation in the given pathway. Clicking on the ‘+’ next to the pathway name gives access to the user-supplied identifiers that are found in the pathway, along with the corresponding UniProt IDs. (C) The results table for the expression analysis. The sortable table contains one row for each Reactome pathway and five additional columns: name of the pathway, Species of presented results, total number of proteins in pathway, number of proteins in the user-supplied data that fall into the pathway, graphical representation of the ratio of these two values and a ‘View’ button that creates a pathway diagram. (D) The pathway browser displaying the colored physical entities that correspond to expression values of the experimental data. The nodes in this diagram have a special color-coding: gray, no match; black, a (multicomponent) complex entity; and other colors represent expression levels. If the numerical data are a time series, the grey bar at the bottom of the colored pathway diagram allows the user to step through time points and visualize changes in expression levels with time of the individual genes involved in the pathway.

Species comparison tool and model organism pathway diagrams. (A) A drop-down menu is used to select the model organism species. (B) Results for the comparison of human and mouse pathways. Each row in the table is a pathway; the columns are pathway name, model organism name, number of proteins in the human pathway, number of orthologous proteins in the inferred model organism pathway, a graphical representation of the ratio of these two values and a ‘View’ button that creates a pathway diagram. ‘Sort’ buttons at the top of each column allow the table to be re-ordered according to cell contents in that column. (C) The pathway browser displaying the comparison of the human and mouse Mitotic M-M/G1 pathways. Physical entities in the pathway diagram are color-coded: gray, no match; black, a complex (multicomponent) entity; and yellow, the protein’s ortholog is present in human. (D) The pathway browser displaying the inferred mouse Mitotic M-M/G1 pathway.