Question: Displaying overlap in 5-6 list transcriptome data
2
gravatar for kevluv93
5.5 years ago by
kevluv93150
United States
kevluv93150 wrote:

So I have a 6 lists of differentially expressed genes taken at different periods of time. I need a way to show overlap in the genes that recur between lists. Naturally I tried to make a venn diagram, but 5-6 list venn diagrams are hard to follow. Is anyone aware of other methods of presenting data like this? I've been going through google scholars to find papers that present data like this, but I can't find anything.

Thanks, any help is appreciated!

rna-seq venn diagram • 1.7k views
ADD COMMENTlink modified 5.5 years ago by mehran.karimzade180 • written 5.5 years ago by kevluv93150
1

just a table with y=genes and x=list-id ?

ADD REPLYlink written 5.5 years ago by Pierre Lindenbaum133k

If I were to do that, I'd basically just be presenting the raw data though. This is more of a method to present data for a figure than anything else. Like I mentioned, I have lists of differentially expressed genes taken at different time points. I want to find overlaps between these data sets.

ADD REPLYlink written 5.5 years ago by kevluv93150
2
gravatar for mehran.karimzade
5.5 years ago by
Canada
mehran.karimzade180 wrote:

UpSetR is a recently released R package with powerful graphics for visualizing intersections in complicated cases such as yours.

https://cran.r-project.org/web/packages/UpSetR/index.html

ADD COMMENTlink written 5.5 years ago by mehran.karimzade180

I'll definitely check this out, I'll come back with results as to how I did. Thanks for the help

ADD REPLYlink written 5.5 years ago by kevluv93150
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