Simple text search

The simple text search tool is located top right of the Home page. To search type a word, phrase or identifier in the search box. The search has an auto- complete function; if the text you wanted to use appears in the drop-down list, select it and results will be displayed. For other text click Search.

search box

Search results are presented in categories with grey headers, representing molecular entity or event types.

Below the header is a list of items from the named type that match your search terms. Matching words are highlighted in grey. Click on the name of an item to go to a page of details.

On the left side of the search results page are groups of check boxes. These can be used to change defaults and add filters. Check or uncheck boxes for types that you do/don’t want to see, e.g. if you want to see results for Mus musculus, under Species uncheck Homo sapiens and check Mus musculus. In the Type, Compartment and Reaction Type filter groups, select to only see results that fall into the selected category, e.g. to see only reactions, select Reaction in the Types filter group. To see only Reactions that occur in the cytosol, also select Cytosol in Compartments.

protein kinase results

Click on any of the results to go to a page of information about it. The contents of these Results Detail pages will depend on the type, but all have a section named ‘Locations in the PathwayBrowser’.

calmodulin details

This contains an expandable hierarchy that identifies the locations of the item in Reactome pathway diagrams. Click the plus symbol to open the hierarchy.

This hierarchy reflects the organisation of events in Reactome. ‘Top-level’ pathways representing a broad area of biology typically contain one or more levels of subpathways, becoming more specific with each level. The levels of the hierarchy are represented here by indentation; the most general pathways are closest to the left-hand edge of the screen, the most specific subpathways have the greatest indentation to the right. Note that some search result items (e.g. proteins) can be in more than one pathway, which may be in different broad areas of biology, resulting in representation in multiple hierarchies. Note that you can open all the hierarchy levels with a single click on the Expand all link, on the right side. Select any event name to open the corresponding Pathway Diagram. The diagram will open with an animation that shows you where the pathway is located in the Pathway Overview. If the selected item was an event it will be highlighted in blue in the Pathway Diagram. If it was a protein, all instances of it will be highlighted in pink.

Diagram Search (Searching in the Pathway Browser)

Searches can be performed within the Pathway Browser by selecting the Search Button (magnifying glass icon) on the top left corner of the Pathway Panel. This opens the search panel. Note: When the Pathway Overview is displayed, all of Reactome is searched, but if a Pathway Diagram is displayed, only the objects represented in the diagram are searched. The format of results also differs.

Searching the Pathway Overview

In the example below, the search term ‘IL6’ has been entered. The search tool has predicted results that match this search term and and displays a dropdown list of these matches. Notice the blue bar, which indicates that there are 70 results shown in 18 pages. The forward button (white triangle on blue circle) can be used to move to the next page of results. The first page lists 4 results. The first 2 results, with a blue circle icon to the left of the name, represent matches to single molecules, in both cases to IL6. There are 2 matches because IL6 is found in two cellular compartments and consequently represented as 2 peptides in Reactome, each with its own identifier. In this initial search result, the cellular compartment is not shown, to see the associated compartment term select the result. The third result is the IL6 gene, with double-helix icon to the left. The fourth result is a complex, with icon showing a brown circle above a blue oval. Other types of matching object include sets (square in square icon) and reaction (icon showing above/below boxes on left connected by right-pointing arrow to box on right).

Notice that below the blue bar is a set of filtering buttons. in the view below, the browser window is too small to show all the available buttons so a horizontal scrollbar is present. Selecting a button will filter the results. Click the button again to deselect it. Select any of the matches to see more information.

In the following image, the first match in the Search Results Panel has been selected and is highlighted in blue. Selecting an item in the initial Search Results Panel causes the Overview to zoom and recentre, focusing on the region that represents pathways containing the selected item. Selecting an item in the Search Results Panel also causes a second dropdown panel of details to appear. This identifies the selected item and lists the pathways that contain the selected item. Note that in the image below, the Search Results Detail Panel extends beyond the limits of the Pathway Diagram Panel, consequently some results are hidden. This explains why the results details title says Present in 6 pathways but only 2 are visible. To see all the matching pathways, click in the list and use the mouse scroll wheel to scroll. Note: Resizing the Pathway Diagram panel cannot be used to reveal all pathway matches if there are more than 4, scrolling is the only way to see the entire list.

Selecting a pathway name (single-click) in the Search Results Detail Panel will select the corresponding object in the Overview. If it is not visible, the Pathway Diagram will re-centre to show it. Double-click a pathway name in the Search Results Detail Panel to open the corresponding Pathway Diagram. If you need to return to the Overview, you can use the browser back button.

Searching a Pathway Diagram

In the example below, the search has identified LYN and produced a dropdown list of matches. The first match is to a reaction, as indicated by the icon on the left. The second and third matches with the icon showing a brown circle above a blue oval are to complexes. The fourth match, with blue circle icon, is to LYN as a protein, in the cytosol. Note that if LYN was represented in two cellular compartments in this diagram it would appear twice in this initial search result.

Select any of the matches to see more information. in the image below, the match for LYN as a protein was selected, producing a second drop-down panel. Note: in this example, the panel extends beyond the limits of the Pathway Diagram panel and consequently some results are hidden. To see all the matches, it is necessary to resize the Pathway Diagram panel. To do this click and drag on the boundary between the Pathway Diagram panel and the Description Panel.

The image below shows the effect of resizing the Pathway Diagram panel, revealing the hidden lower section of the Search Result Detail Panel.

The search results details are presented in sections representing the type of the match. Directly in the diagram indicates that the search term matches a single molecule present in the Pathway Diagram, LYN in the example above. The second section shows that LYN is part of 2 complexes visible in the Pathway Diagram. The third section shows that LYN participates in 2 reactions in the Pathway Diagram. The fourth section is a scrollable list of LYN interactors, obtained from the IntAct database, showing the name of the Interactor, which is a link to UniProt, and the word ‘Evidence’ followed by a number and score. The word Evidence links to details of experimental interaction observations in the IntAct database. The number to the right of Evidence is a count of the number of experimental records of the interaction. The score is an indicator of interaction confidence.   

Selecting names in the Search Results Detail Panel will select the corresponding object in the Pathway Diagram, if it is not visible, the Pathway Diagram will re-centre to show it.

Getting Started

Search Exercises

This exercise encourages you to find information via the menu bar and Search

  1. What’s the latest news item on the Reactome Home page?
  2. How many human proteins are represented in Reactome?
  3. What’s the first item listed that will be included in the next release?
  4. Is VAV2 in Reactome?
  5. How many reactions involve VAV2?
  6. Are there any complexes that include VAV2?
  7. Is CRB2 in Reactome?