In this video, we will show how users can search or browse the Cancer Target Discovery
and Development or CTD^2 Network Dashboard.
Any researcher interested in learning about a particular gene, protein, or compound that
has been the subject of an experiment by CTD^2 Network Centers can come to the Dashboard
to quickly and easily find and review Network-generated results, as well as build upon them in their
own work.
CTD^2 Dashboard data are indexed against subject terms and can be queried using the search
box located in the top menu bar.
For instance, when a user searches for genes using synonyms or by Entrez Gene ID, proteins
by UniProt ID, or compounds with PubChem or Chemical Abstract Service numbers, the search
will retrieve a list of all matching genes along with a count of the observations involving
each gene.
Each count is hyperlinked to a detailed list of the relevant observations regardless of
role or Tier.
In addition to search, data can be explored via browsing options from a summary view.
The Dashboard offers three “browse” pages focusing on genes, compounds, and cancer types.
Each page provides a list of biological entities prioritized according to the number, breadth,
and level of validation of the observations involving them.
For example, the "Biomarkers, Targets, Genes & Proteins" browse page provides a tabular
presentation of genes, separated by Dashboard role, and a summary of how many observations
we have at each level, or “tier”, of validation.
Users can download this table as an Excel file using the function called "Export as
Spreadsheet".
The initial ordering of the table rows is determined by a relevance score calculated
as the sum across Centers of the highest Tier evidence provided by each Center contributing
evidence.
Clicking on the button “select roles” will allow the user to change the roles displayed
in the browse page table.
The browse page default is biomarker and target “roles” shown.
For example, the CTNNB1 gene is designated with the role of “biomarker” based on
observations in Tiers 1, 2, and 3.
Depending on the evidence available, subjects may have more than one role.
The browse page is shown here with all possible roles selected.
TP53 gene is designated with the role of “oncogene” and “biomarker” based on observations
in Tiers 1, 2, and 3.
Search and browse operations result in a list of entry points to detailed information about
observations and subjects.
Using the search option will pull-up all the observations regardless of role.
For instance, selecting a specific subject CTNNB1, from a browse page table leads to
a gene-profile page where the top portion contains the basic information about the subject
CTNNB1.
The bottom portion lists the related observations, each with the associated Tier rank and the
Network Center that generated the finding.
As with the browse feature users can download this entire table as an excel file using the
button “Export to Spreadsheet”.
Alternatively, a user can click on the observation number under a specific Tier, to view only
observations in that Tier.
Clicking on the “details” link of any observation navigates to an individual observation
page describing the observation attributes, including: The Tier level, a short summary
of the related investigational finding and the associated Center; the subject table displays
the hyperlinked biological entities like genes, compounds, cell lines, etc., involved in the
study and their specific roles; the submission table has a brief description of the submission,
submission date, and link to download all the data associated with the submission the
evidence table has experimentally and computationally derived evidence supporting the reported finding
along with the data files, links to references, and any associated summary stories.
A user can also explore the data by directly browsing submissions.
The “Centers” link at the site’s top navigation bar leads to a page that lists
all the CTD2 Network Centers.
From that list, users can access all data submissions made by a Center and drill down
to the observation data in each submission.
There is also a link which allows the user to easily and directly download the entire
submission source data package.
Users can also browse for stories.
Research findings that have been explored in detail are featured prominently on the
homepage of the Dashboard in the form of stories.
The aim of these stories is to distill the essential elements of reported results at
a level of detail that is appropriate for a general scientific audience.
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.