In this tutorial, we will be exploring the regulatory pathways of the tp53 gene using Consensus Path DB Human. Before we dive into the tutorial, let's first understand what we are working on.
The Guardians of the Genome: TP53
Our investigation focuses on TP53, often referred to as the guardians of the genome. TP53 is a gene that codes for a protein called tumor protein p53. The "TP" stands for tumor protein, and the "53" refers to the molecular weight of the protein, which is approximately 53 kilo daltons. The p53 protein is a critical regulator of cell division and acts as a tumor suppressor.
It plays a crucial role in monitoring the integrity of the genome by regulating cell cycle progression, DNA repair, apoptosis, and cellular aging. When cells experience stress or damage, such as DNA damage or oncogene activation, TP53 is activated and orchestrates appropriate cellular responses to maintain genomic stability and prevent the development of cancer.
Why Consensus Path DB?
Now, let's discuss why we are using Consensus Path DB for our investigation. Consensus Path DB is used to integrate and analyze various biological pathways and interactions from multiple sources. It eliminates redundancy in pathway data, facilitates exploration and analysis of biological pathways, and assists in making informed decisions for experimental design and target identification. Additionally, it supports research in bioinformatics, systems biology, and drug discovery.
Having a basic understanding of the concepts we are working with, let's dive into the tutorial.
Getting Started
To begin, open an appropriate browser and enter "pathDB" in the search bar. Click on "ConsensusPathDB" from the search results.
On the ConsensusPathDB website, you will see three databases: Human, Yeast, and Mouse. For our tutorial, we will be working with the Human gene. It is always recommended to use a database mentioned in the literature paper you are referring to.
Once you've selected the Human database, click on "Search" in the sidebar. Add the interested gene you want to explore the pathways for. In this case, we will type "TP53" and then click on "Search".
You will now see an array of pathway names related to TP53. We are interested in the regulation and expression of TP53, so let's make an interaction between the regulation of TP53 activity and expression. Select the pathway and click on "Show Interaction".
Now, you will see a list of pathways involved in the regulation and expression of TP53, such as silation, methylation, and degradation. Select any two pathways you want to explore further. For this tutorial, we will click on the first pathway, which is "Association with co-actors and regulation of TP53 through methylation".
Next, click on the button "Map and Visualize the Interaction". Here, you will see a visual representation of the interaction between the selected pathways. The graph may appear complex, but we can simplify it for better understanding.
Interpreting the Graph
To understand the graph, we can click on the "Graph Legend". This will provide information about the shapes and colors used to represent different physical entities. The graph is movable, allowing you to rearrange the elements and create a more understandable pathway.
As you navigate through the graph, you can point your cursor on a specific compound, protein, or gene to view more information about it. The description below the graph provides additional details about the selected entity.
Integrated databases are also accessible within the graph. By clicking on a specific entity, you can view its properties and related information from various integrated databases. Certain compounds may even have additional dialogue boxes with more information.
If you find the pathway too complex, you can edit it according to your preferences. By clicking on the interaction information, you can access details about the selected interaction, including citations and backlinks to related interactions and processes.
If you are interested in targeting a particular interaction, you can make connections between them by selecting the entities and creating a graph focused on the desired interaction.
By exploring the graph, you can gain insights into the various interactions taking place behind the TP53 gene. Additionally, by clicking on "Miscellaneous Function", you can see the types of physical entities involved in the pathway and their quantities.
Unfortunately, there is no option to export the pathway as an image file. However, you can still take a screenshot and save it for your research paper or personal interest.
Conclusion
In conclusion, using Consensus Path DB Human, we can explore the regulatory pathways of the tp53 gene. TP53 plays a crucial role as the guardians of the genome, regulating cell division, DNA repair, apoptosis, and cellular aging. Consensus Path DB allows us to integrate and analyze biological pathways, making it a valuable tool for researchers in bioinformatics, systems biology, and drug discovery.
By following this tutorial, you can learn how to search for and visualize pathways related to TP53. Remember to refer to the literature paper to ensure you are using the appropriate database for your research.
Happy exploring!
