Mastering Venn Diagram Interpretation for RNA-seq

Table of Contents

1. Introduction
2. Understanding Veni 2.1 web tool
3. Uploading gene lists
4. Comparing control with treatment one
5. Comparing control with treatment two
6. Comparing treatment one with treatment two
7. Finding common genes between all treatments
8. Finding different genes between treatment one and control
9. Finding different genes between treatment two and control
10. Making the Venn diagram suitable for export

Article

Introduction

Welcome to another video tutorial where I will guide you through the process of creating and interpreting Venn diagrams for RNA-seq data using the web tool Veni 2.1. Venn diagrams are a powerful visualization tool that allows us to compare the gene expression patterns between different treatments and identify common and unique genes.

Understanding Veni 2.1 web tool

Veni 2.1 is an online web tool that makes it easy to create and interpret Venn diagrams for RNA-seq data. To access the tool, simply open your preferred web browser and search for "Veni 2.1". Click on the first link that appears and it will take you to the interface of Veni 2.1.

Uploading gene lists

To use Veni 2.1, you need to upload the lists of genes for the different treatments you want to compare. Let's say we have a control group (CK) and two treatment groups (Treatment 1 and Treatment 2). In the web tool, you will find fields where you can enter the names of these treatments.

Comparing control with treatment one

Once you have entered the names of the treatments, you can copy and paste the corresponding gene lists for each treatment. Veni 2.1 will automatically calculate the number of genes in each list. In our example, the control group has 50 genes and treatment one has 56 genes. Veni 2.1 will also show you the number of genes that are common between the two treatments. In this case, there are 40 common genes.

Comparing control with treatment two

Next, we can compare the control group with treatment two. Paste the gene list for treatment two and Veni 2.1 will calculate the number of genes in each group. In our example, the control group has 50 genes and treatment two has 55 genes. Veni 2.1 will also show you the number of common genes between the two treatments.

Comparing treatment one with treatment two

Now, let's compare treatment one with treatment two. Paste the gene list for treatment two and Veni 2.1 will calculate the number of genes in each group. In our example, treatment one has 56 genes and treatment two has 55 genes. Veni 2.1 will also show you the number of common genes between the two treatments.

Finding common genes between all treatments

If you want to identify the genes that are common between all three treatments, Veni 2.1 can help you with that as well. In our example, there are 35 genes that are common between the control, treatment one, and treatment two. Clicking on this number will display the list of those 35 genes.

Finding different genes between treatment one and control

To find the genes that are differentially expressed between treatment one and the control group, click on the number that represents the difference. In our example, there are 5 genes that are different between treatment one and the control group. Clicking on this number will display the list of those 5 genes.

Finding different genes between treatment two and control

Similarly, to find the genes that are differentially expressed between treatment two and the control group, click on the number that represents the difference. In our example, there are 16 genes that are different between treatment two and the control group. Clicking on this number will display the list of those 16 genes.

Making the Venn diagram suitable for export

Once you have explored the different gene sets and identified the genes of interest, you may want to customize the Venn diagram for use in your research article. In Veni 2.1, you can change the style, color, and font size of the diagram according to your preferences. When you are satisfied with the appearance of the diagram, you can export it as a high-quality PNG image.

By utilizing the power of Venn diagrams and the Veni 2.1 web tool, you can effectively visualize and analyze your RNA-seq data, uncovering insights into gene expression patterns and identifying potential candidate genes for further investigation.

Highlights

• Veni 2.1 is an online web tool for creating and interpreting Venn diagrams for RNA-seq data.
• It allows you to compare gene expression patterns between different treatments and identify common and unique genes.
• You can easily upload gene lists for the treatments you want to compare and Veni 2.1 will calculate the number of genes in each group.
• The tool provides a visual representation of the overlapping and differentially expressed genes between treatments.
• You can customize the style, color, and font of the Venn diagram before exporting it as a high-quality image.

FAQ

Q: What is the purpose of using Venn diagrams in RNA-seq data analysis? A: Venn diagrams help visualize the overlap and differences between gene sets from different treatments, allowing researchers to identify common genes and unique genes associated with each treatment.

Q: How can I upload gene lists in Veni 2.1? A: In Veni 2.1, you can simply copy and paste the gene lists for each treatment in the respective fields. The tool will automatically calculate the number of genes in each group.

Q: Can I customize the appearance of the Venn diagram in Veni 2.1? A: Yes, Veni 2.1 allows you to change the style, color, and font size of the Venn diagram to suit your preferences. You can adjust these settings before exporting the diagram as an image.

Q: How can I use the Venn diagram in my research article? A: Once you are satisfied with the appearance of the Venn diagram, you can export it as a high-quality PNG image. You can then include this image in your research article to visually represent the gene expression patterns and differences between treatments.