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?
•
written
by
lucatucciarone
1 answer
you can use this online tool DiVenn which will generate a nice graph https://divenn.noble.org
Log in to answer this question.
-
How to perfrom a statistical test on a 3-way Venn Diagram
written by ivingan •
-
Any tools for systematic downstream enrichment analysis/comparison
written by alwayshope •
-
Extract Genes from ggvenn
written by axe880 •
-
Venn Diagram and Heatmap with RNA seq Data
written by MR A •
-
Statistical test for overlap
written by pixie@bioinfo
-
vennDigram for multiple RNA-seq data
written by ta_awwad
-
How to perform edgeR based on serial paired samples? (model.matrix design)
written by CandiceChuDVM
-
Venn Diagram Help
written by kevluv93
-
Two questions about plotting a venn diagram!
written by Parham
-
How to draw venn diagram for two CNV lists?
written by lyz10302012
You should check the keyword
upset plot.mmmh that's a good idea, I've already used them.
There is nothing specific for up and down regulated genes though?
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.
This seems more doable. Would you mind uploading a sample picture to see how it turn out?