Visualize overlap differentially expressed genes of multiple comparisons.
1
1
Entering edit mode
3.2 years ago

Hello everyone,

I need to represent the overlap of differentially expressed genes across multiple comparisons.

Essentially, I have the log2foldchange of my 4 samples (Control, Treatment 1, 2, 3). Obviously my comparisons are Control vs Treatment 1 Control vs Treatment 2 Control vs Treatment 3 Control vs Treatment 4

Now I want to understand how those 3 comparisons overlap too each other. How many up-regulated genes are commonly up-regulated by every treatment? How many just in the 1st treatment? and so forth.

Now I can see that I can create a sort of monster of Venn diagram by have 8 different "clouds" to intersect (4 comparisons up-regulated and down-regulated).

Is there a better way to represent my data?

RNA-Seq • 2.1k views
ADD COMMENT
0
Entering edit mode

You should check the keyword upset plot.

ADD REPLY
0
Entering edit mode

mmmh that's a good idea, I've already used them.

There is nothing specific for up and down regulated genes though?

ADD REPLY
0
Entering edit mode

I tend to extract the collection of significant genes (either defined by F test or by union over the comparisons), plot the log-fold-changes wrt each contrast on a heatmap and indicate singificance for a given contrast with a black/white row annotation (one row annotation for each contrast). Even with just two contrasts, distinguishing up- and down-regulated genes can lead to overly complicated venn diagrams.

ADD REPLY
0
Entering edit mode

This seems more doable. Would you mind uploading a sample picture to see how it turn out?

ADD REPLY
0
Entering edit mode
2.9 years ago
Liang Sun ▴ 10

you can use this online tool DiVenn which will generate a nice graph https://divenn.noble.org

ADD COMMENT

Login before adding your answer.

Traffic: 1174 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6