Tuesday, 29 October 2013

Vennt : Venn diagrams for lists of Differential Expressed Genes

Recently, I have analysed a number of RNA-seq experiments.  Often these experiments have multiple conditions so it is possible to perform several different pair-wise comparisons.  After doing a number of these pair-wise comparisons, my collaborators invariably ask for the overlap between the gene-lists - or better yet a Venn diagram of them.

So, I wrote a web tool, Vennt, that draws Venn diagrams for gene lists.  Venn diagrams for up to 4 lists are drawn, and we can dynamically adjust the thresholds for significance, and get the explicit gene list for the various overlaps.

It's easy to use for your own from a CSV file of your gene lists.  Just follow the instructions.  Try it out, and let me know what you think!

Try a live demo

Disclaimer: keep in mind that Venn diagrams for gene lists from differential expression experiments is often misleading.  Primarily due to the arbitrary thresholds we use.  I have been known to explain this to collaborators at length, perhaps this tool is my attempt at venting...  However, from using this tool I have actually found that it can be a useful way to explore your gene expression data.

1 comment:

  1. A good chart, thank you for sharing instruction. I can share the good templates for diagrams, very easy to use http://www.pptstar.com/diagrams/. It is very convenient, especially when very little time left.