This guide will take approximately 5 minutes to complete.
In this guide you will learn how to:
- Explore whether a target is associated with a biological process of interest
- Refine your search results for a specific cell type
- Identify biochemical mediators that are affected by the target of interest which then affect the biological process of interest
Step 0: Login
Refer to https://med.causaly.com
TIP! In case you’ve forgotten your password, you can recover it here.
A. Explore direct interactions between a target and a biological process of interest
Search for the association between target X and process Y
To explore if there is a direct association between target X and biological process Y, use Causaly Discover in the Causaly home page (Figure 1).
Figure 1. Causaly Discover on the Causaly homepage
Begin your search by typing your question into the Causaly Discover search bar in natural language (Figure 2). “Is FOXP3 related to DNA methylation?” will be used as an example (link).
Figure 2: Directly ask a question in natural language in the Causaly Discover search bar
Click "Search" or hit Enter on your keyboard to run the search, which will direct you to the Causaly Discover results page.
Causaly Discover offers an AI-generated summary, complete with in-line citations for transparency into the results, based on the top 20 articles. You can scroll down to view all the documents retrieved in response to your search query.
B. Explore the direct interactions in cell type Z
To narrow down the results to a specific cell type, you can go back to the input box of the Causaly Discover bar and rephrase your question or ask a follow-up question on the Copilot sidebar (Figure 3).
Figure 3: Type your follow up question in natural language in the Copilot side bar on the right
Results now describe the relationship of FOXP3 gene with DNA methylation in leukocytes.
C. How target X affects biological process Y?
The rationale behind this approach is to better understand how and if target X may affect biological process Y. These can also be the cases where the target does not directly induce the biological event but leads to an intermediate effect that begins other processes or interactions and leads to the observed effect.
To do this, you can use the Multi-hop module and look for the potential mediators or pathways by which target X may induce biological process Y.
In this case, enter the target of interest in Concept Box A and the biological or pathologic function of interest in Concept Box C. In Concept Box B, use the Category tab to select the categories of interest - this ensures that you are getting all the potential mediators by which the target may affect the process of interest.
TIP! For more information on how to use the Multi-hop module, please visit this step-by-step guide.
Type “FOXP3 gene” in Concept Box A and “DNA methylation” in Concept Box C. To locate the potential mediators, select the categories “Amino acid, peptide or protein” below the Chemicals and Drugs category, and the “Gene or genome” option below the “Genes and molecular sequences” category in the Concept Box B (link).
The results will include all the genes and proteins that may indirectly relate FOXP3 gene with DNA methylation (Figure 6).
Figure 6: Potential mediators by which FOXP3 gene may affect DNA methylation.
TIP!
- To visualize all the different mediators, move to the network view from the top right corner of your screen (Figure 7).
Figure 7: The network view.
- Based on the type of mediator you are interested in you can select different categories in box B. To search for pathways for example, you can select the “Cell function” and “Molecular function” options below the “Physiology” tab (Figure 8).
Figure 8: The options below the Physiology category, when selecting filters on the Concept Boxes.
Want to learn more about how to find evidence in Causaly?
Find more information and examples on how to search posts by clicking here.