[BioC] package or code to quantify the significance of the venn overlap between 2 or 3 lists of genes

Karl Brand k.brand at erasmusmc.nl
Wed Mar 17 12:26:13 CET 2010

Dear BioCers,

I've got six lists of gene's which i'm focused on the overlaps between.

What i'm searching for is a package or code to quantify the significance 
of the overlap between both a pair of gene lists, and also between three 
gene-lists. Six might be interesting, but not necessary.

Specifically, what would the overlap be expected by chance, and how many 
standard deviations my actual overlap is from the estimated chance overlap?

Whilst some of my lists are independent, others are not in being derived 
from tissues of the same origin. I understand this would exclude such 
tests like Fishers Rxact test which assume independence.

By using the same numbers of chip-background probes and short-listed 
probes of interest, randomly selected and checking the overlap, 
performed say 10,000 times, i think i could obtain the estimates i'm 
looking for in a 'statistically acceptable' manner.

Does anyone know of a package or code written for this purpose? I failed 
to find anything in BioConductor or in the BioC lists. As simple as 
coding it no doubt is, my lack of R knowledge would make doing it with a 
calculator the faster option :)

Look forward to any recommendations or suggestions with appreciation,


Karl Brand k.brand-asperand-erasmusmc.nl
Department of Genetics
Erasmus MC
Dr Molewaterplein 50
3015 GE Rotterdam
lab +31 (0)10 704 3409 fax +31 (0)10 704 4743 mob +31 (0)642 777 268

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