Interactions Tab, Feature-Level¶
The Interactions Tab provides experimentally and computationally derived host-pathogen protein-protein interaction data and visualizations from more than 15 public repositories, including STRINGDB, with a total of 55 million protein-protein interactions. Interactions are available at both the genome and feature levels, and are presented in tabular and graph format.
Accessing the Feature-Level Interactions Table on the PATRIC Website¶
Clicking the Interactions Tab in a Feature View displays the Interactions Table, listing of all of the interactions in PATRIC associated with that feature.
Interactions Table, Feature-Level
The tables include the following columns (fields) for each interaction, and are based on PSI-MITAB format:
- Interactor A: PATRIC ID (unique primary identifier) for one of the two interacting features (protein-coding genes).
- Gene A: Gene name for the feature, if available.
- Desc A: Protein product (functional annotation) associated with the feature.
- Interactor B: PATRIC ID for the other of the two interacting features.
- Gene B: Gene name for the feature, if available.
- Desc B: Protein product associated with the feature.
- Category: Category of interaction:
- PPI = protein-protein interaction
- HPI = host-pathogen interaction
- Interaction Type: Interaction types, taken from the corresponding PSI-MI controlled vocabulary.
- Detection Method: Interaction detection method, taken from the corresponding PSI-MI controlled vocabulary.
- Evidence: Evidence of the interaction:
- Experimental = identified by laboratory method
- Computational = predicted by computational method
Clicking the Graph option at the top left of the table displays the Cytoscape-based Interactions Viewer.
In the graph, proteins (interactors) are displayed as nodes and the interactions between the nodes are displayed as lines. Scrolling with the mouse zooms in/out in the graph. Clicking and dragging with the mouse moves the graph in the display. Gene names, where available, are displayed on the nodes. Mousing over a node or line displays detailed information about that interactor/interaction. Clicking and dragging on a node moves it in the graph, allowing rearrangement for better visualization.
Additional options are available from the upper right area of the graph. These include the following:
- Export: Creates a png image file of the graph and makes it available for saving to disk.
- Subgraph: Auto-selects subgraphs with more than 5, 10, or 20 nodes, or auto-selection of the largest subgraph.
- Hub Protein: Auto-selects hub proteins with more than 5, 10, or 20 nodes, or auto-selection of the most connected hub
- Layout: Changes the layout of the display, with several options available
After selecting one or more of the nodes by clicking it (ctrl-clicking to select multiple nodes), a set of options becomes available in the vertical green Action Bar on the right side of the table. These include
- Hide/Show: Toggles (hides) the right-hand side Details Pane.
- Download: Downloads the selected items (rows).
- Copy: Copies the selected items to the clipboard.
- Feature: Loads the Feature Page for the selected feature. Available only if a single feature is selected.
- Features: Loads the Features Table for the selected features. Available only if multiple features are selected.
- FASTA: Provides the FASTA DNA or protein sequence for the selected feature(s).
- MSA: Launches the PATRIC Multiple Sequence Alignment (MSA) tool and aligns the selected features by DNA or protein sequence in an interactive viewer.
- Group: Opens a pop-up window to enable adding the selected sequences to an existing or new group in the private workspace.
More details are available in the Action Buttons user guide.