Interaction Display in the Gene Page

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There are two types of interaction objects in Wormbase: Interaction and YH. Interaction class holds a number of interaction types (regulation, predicted, etc.). Objects in the YH class are of Y2H and Y1H types, and interactors in these interactions are grouped as target and bait.

The interaction display in the gene page aims to provide a consolidated compact view of the interaction objects in Wormbase. It replaces the previous views.

The interaction display is part of the gene page ($WORMBASE/db/gene/gene). Interactions are displayed from the point of view of the gene of interest. A table contains the interaction types on the x-axis header and genes interacting with the gene of interest on the y-axis. The intersection of the interaction type and the gene has a number that shows the number of interaction objects satisfying this criteria. The headers and the numbers can be clicked to show more information in ballon tips. The table is split into smaller tables to fit to the width of the page.

For each gene that interacts with the gene of interest, GO Terms associated with the gene are compiled. The distribution of GO terms is displayed in pie charts, one pie chart per GO term type. In the pie charts, slices that correspond to less than a threshold (currently 5%) are clustered into the “Other” slice.

The display has the following components:

/cgi-perl/gene/gene script: Contains the display.
 sub interaction_matrix: generates display
 sub go_pie_charts: sub-component that renders GO Term pie charts
/cgi-perl/gene/interaction_details: Side AJAX script that displays details when an item is clicked on the main display
/cgi-perl/lib/WormBase/ module: Generates png or html tables. 
/html/stylesheets/wormbase.css: Styles for tables
 table.interaction_matrix tr td
 table.interaction_matrix td.header
 table.interaction_matrix a


  • add support for directional Interaction object types (currently Enhancement, Regulatory).