Bcl-2-Ome Use Cases
When Bcl-2-Ome is started, the user interface illustrates the Bcl-2 family members as nodes in a graph and experiments defining interactions within the Bcl-2 family as edges connecting the nodes. All integrated data are shown at startup of the application; each shown edge constitutes one experimental outcome (= one database entry).
By clicking on an edge, the edge thickness of this edge is increased and experimental details as well as a link to the primary literature reference are shown in the lower right corner of the user interface.
Example: Quantitative interactions involving Bcl-xL
In case a user is interested in interactions involving Bcl-xL, the user can deselect all other proteins in the right panel. As the option "AND" is still selected, only interactions in between selected proteins are now shown. In this example this means, that only interactions of Bcl-xL with itself are shown.
To show all interactions involving at least the selected protein(s), in this case Bcl-xL with itself or any other protein, change the selection mode to the "OR" option.
If the user is interested only in quantitative data involving Bcl-xL, qualitative interaction data can be hidden by deselecting the "Qualitative" option. As can be seen in the screenshot below, all experiment types for which no experiment is visible anymore in the current selection will appear in gray font in the right panel.
By clicking on individual edges the quantitative interactome of Bcl-xL can now be studied in detail.
Example: Bax activation by BH3-only proteins
For investigating activation studies of the effector Bax, all interactions involving Bax can be selected.
Qualitative studies should be added to the visible selection again to analyze activation of Bax.
Now, only studies describing activation of Bax or Bak can be selected by disabling the "Interaction" option. Edges describing effector activation are indicated by directed edges.
By clicking on individual edges, the activation by different BH3-only proteins can be analyzed in detail. In the example shown below, no Bax activation by Bad was seen in the experiment. This is indicated by the notation "false" in the Experiment Info tab.
For convenient analysis of true / false outcomes, the color mode can be changed to black colored edges in case an effector activation / interaction was observed (true) and gray colored edges in case of negative results.
Example: KD values of BH3-only interactions with prosurvival family members
By using the multiple options for visualizing subsets of the whole database, e.g. all integrated KD values in between BH3-only proteins and pro-survival proteins can be visualized and then analyzed by clicking on individual edges.