BioPlex sub-networks are displayed using Cytoscape.js.
Within each display there are multiple options for exploring the BioPlex interactions with your protein interest. Nodes can be selected using CTRL+click-and-drag.
- Core Network Display
- Network Search
- Context Menu
- GO Annotation Enrichment
- GO Annotation Coloring
- Node and Edge Info.
- Export Data
- Interaction Table
Core Network Display
For display purposes the "core network" or "core sub-network"
refer to the protein-of-interest (selected on the home page search) and any other protein observed in a direct interaction with said protein-of-interest.
The below network shows the EGFR Core Network
This dropdown menu allows users to add, select and remove nodes
according to several criteria.
First Neighbor Interactions
Users can use this feature to select all first neighbor nodes for a protein of interest. This feature can help to identify proteins interactions of interest in large networks (e.g. secondary networks or community networks).
For each core sub-network
, users can add secondary interactions. These secondary proteins do no directly interact with the original protein of interest, but interact with the original protein's interactors.
Additionally, adding Secondary Interactions will update the Gene Ontoogy Enrichment table
Users can add a subset of AP-MS identified interactions that fall below the threshold (probability of interaction = 0.75)
necessary to be considered an true interaction in the BioPlex dataset.
Important these interactions are NOT part of the final, statistically-filtered BioPlex interactome and should not be viewed or used as such.
Within either the core or secondary networks
individual proteins can be highlighted in the "Search in Network"
This search bar will accept and try to match protein symbols, gene ID numbers, and Uniprot Accession numbers. If the requisite node exists in the network it will be highlighted.
Each network can be recolored based on protein attributes. Currently, this includes coloring nodes by their abundance in HEK293 cells, Gene Age and by their GO/PFAM annotations.
To color by HEK293 abundance, click the "Theme"
dropdown menu above the network and select "HEK293 Coloring".
GO Annotation Enrichment
Each sub-network within the Bioplex network is automatically tested for Gene Ontology (GO) enrichment based on the Fisher's Exact Test
, adjusted based on the Benjamini-Hochberg FDR.
Annotations with an FDR less than 0.001 are highlighted in the GO Annotation Table and the top 4 GO annotations from each network that pass the 0.001 FDR threshold are displayed next to each graph.
We note that all GO Enrichments (both primary and secondary networks) are calculated based on the proteins in a network with a probability of interaction greater than or equal to 0.75.
GO Annotation Coloring
By clicking on enriched GO annotation, the proteins associated with the GO term will be highlighted
and the highlighed annotation name will be overlaid on the network.
Node and Edge Information
More information for both the nodes and the edges can be obtained by clicking on either the node or edge. This includes links to Uniprot references for each protein and the probability of interaction for each edge.
Node information from the core network
can be found in the node table at the bottom of each page. Clicking the protein symbol
will highlight the protein within the network. Clicking the Uniprot Accessions
links out the Uniprot
Networks can be exported as either a flat text
file containing all interaction information for the sub-network, a PNG
displaying the network (either the original image or the current one), or as a JSON
file that can be directly imported into Cytoscape to further explore the data.
Very large networks can cause the PNG image export to fail. If your download does not succeed at first, please try to reduce the size of the network canvas (bottom left corner).