In this video, we will show users how to use Gene Cart on the CTD^2 Dashboard to predict
or verify molecular interactions like DNA-DNA, DNA-protein, and protein-protein within a
variety of tissue- and disease-specific interactomes.
This tool can be accessed through the “Gene Cart” link available in CTD^2 Dashboard’s
navigation menu.
The Gene Cart allows users to build a list of genes and query the Cellular Networks Knowledge
Base (or CNKB) for molecular interactions involving the selected genes.
The CNKB is a database of gene interaction networks maintained at Columbia University.
To learn more about how it was developed and how the data can be interpreted, visit the
GeWorkbench.
The Gene Cart allows users to build different types of interactomes directly from the Dashboard
platform that also has general and experimental details for each gene of interest.The genes
of interest can be added directly into the Gene Cart by clicking on the green “+”
icon, adjacent to gene symbols.
Users can also add genes manually by typing in the gene names using the option “Add
Gene”.
The Gene Cart is editable, meaning one can add genes, delete genes, or clear the list.
In addition, users can load a list of genes from a file directly into the cart.
After genes are placed into the Gene Cart, users can query databases of molecular interactions.
Users can choose different interactomes and when selected the basis behind each interactome
will appear.
For example, select interactome BCi, a database of protein-protein, protein-DNA and modulatory
interactions in human B cells and select version and then click the submit button.
Results of the query are summarized in a tabular view, with one row per query gene.
Each row shows the number of interactions involving the corresponding gene, categorized
according to interaction type, like protein-protein or protein-DNA.
Users can select one, more than one or select all of the query genes.
Results can be exported as a SIF-format file for display in third-party software such as
Cytoscape.
Or click on the “Create Network” link to generate a graph view of the interactions.
The yellow nodes represent query genes.
Edges represent interactions and are colored according to the type of interaction.
As the Dashboard continues to be updated with new Network-generated data, its importance
as a resource for the research community will be enhanced in keeping with the FAIR principles.
For more information on the Dashboard organization, including additional term definitions, please
click text “CTD2 Dashboard: A Platform to Explore Evidence-based Observations” ” or
read our manuscript “CTD2 Dashboard: A searchable web interface to connect validated results
from the Cancer Target Discovery and Development Network” in the journal Database.
We appreciate your valuable feedback, please send your questions/comments to ocg@mail.nih.gov.