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
Step 1. Use the Intelligent Search to look 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 the Intelligent Search on the Causaly home page (Figure 1).
Figure 1. The Intelligent Search on the Causaly homepage
Example: The relationship between FOXP3 gene and DNA methylation (link) (Figure 2)
Figure 2: Fill in the input box when looking for a relationship of interest
TIP! You can consider this input box as a regular keyword search box in a typical research engine. For more information on how to properly use it, you can visit this guide.
After selecting the “Relationship between FOXP3 gene and DNA methylation” option, as illustrated in Figure 2, the appropriate concepts will be added in the respective concept boxes, so as to locate all the associated biomedical literature.
TIP! When you perform a direct search, Causaly will look for associations not only between the target and the process of interest but also for the narrower and related concepts, such as the alleles, variants, mutations, etc. or the associated dysfunctions of biological process Y, respectively (Figure 3).
Figure 3: The causal relationships found between FOXP3 gene and DNA methylation.
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 Intelligent Search bar and add the cell type of interest (Figure 4).
Example: The relationship between FOXP3 gene and DNA methylation in leukocytes (link) (Figure 4)
Figure 5: Narrow down your results to leukocytes by using the text box to enter the cell type of interest.
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.