Find out common genes in our dataset

Question

[aranyak111]

I have gene names for 10 differentially expressed genes (DEG) datasets. I want to find out a good visual representation of the datasets finding out unique, common genesets in the dataset. Venn diagram is not a very good way of representing the datasets. Can you provide some suggestions on how to go about it?

The first few lines of the datasets look like this.

KDR-mir24   KDR-mir128  KDR-let7    KDR-150 KDR-mir99   KDR-125a    KDR-125b    KDR-mir187  KDR_Notch
tox2    he1a    cryba2a zgc:113413  tfa uba1    dao.1   nsa2    hspa8
ndufb2  epcam   capn3a  ctsla   ccdc85b grinab  mt-atp8 CR735126.1  igfbp5a
nme2b.2 dap1b   cryba4  ywhabb  sptbn2  col4a1  znf292b ENSDARG00000042961  fabp1b.1
maptb   hsp90aa1.2  crygm2d19   zgc:162356  baz2ba  zgc:86609   pygma   prrg1   pfkfb4b

Answer 1

[seidel]

UpSet plots are a way to illustrate intersections among multiple data sets. Have you considered these? They can take getting used to, which is maybe not what you want.

[ATpoint]

+1 for Upsets. There is also a ggplot-based implementation available: https://github.com/const-ae/ggupset