Question: How to Find Common Dysregulated Genes in Two or More Sets of Microarray Data
gravatar for pankajnarula84
5.0 years ago by
pankajnarula8410 wrote:

I have two (or more) micro array data of genes of SARS ( and Parkinson disease ( I found the dysregulated genes in these sets by applying criteria that log fold change is greater than 1.5 and p-vlaue < 0.01. My question is how to find the common dysregulated genes in these two sets? Which statistical tests should be applied? Which packages are available in R for this kind analysis? I am new to bioinformatics. Kindly bear with me if question is very basic. Thanks in advance. 

ADD COMMENTlink modified 5.0 years ago by seidel7.0k • written 5.0 years ago by pankajnarula8410
gravatar for seidel
5.0 years ago by
United States
seidel7.0k wrote:

The short answer is that you would use either the hypergeometric distribution (see ?phyper in R), or you could make a contingency table and use a Fisher Exact test. Given a universe of genes in two experiments, if you identify a set of genes in experiment 1, and another set of genes in experiment 2, these can help you evaluate the likelihood of a given degree of overlap. There's also a package in R which does this for you, called GeneOverlap.

ADD COMMENTlink written 5.0 years ago by seidel7.0k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1062 users visited in the last hour