Hi All,
I am going to ask a very basic question about the coexpression of genes. I have a set of few genes for which I have done coexpression analysis using affymetrix data. I am interested in checking which genes in my set are coexpressed. My analysis results are something like this:
geneA coexpressed with mygene1
geneA coexpressed with mygene2
geneA coexpressed with mygene3
geneB coexpressed with mygene1
geneB coexpressed with mygene2
geneB coexpressed with mygene5
mygene1 coexpressed with mygene6
mygene6 coexpressed with mygene1
From the results, it's very clear that mygene1 and mygene6 are coexpressed. Can I also say that mygene 1, 2, 3 are also coexpressed (please note that geneA and geneB are not a part of my set)? Does basic mathematical thing a=b and b=c so c=a will also works in case of coexpression.
Many thanks, R
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written
by
GR
2 answers
Short answer, "No." However, if a=b and b=c, a MIGHT = c.
You should look at bioconductor. It looks like it has some nice tools for testing co-expression: http://www.biomedcentral.com/1471-2105/9/559
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written
by
Zev.Kronenberg
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How are you defining coexpressed? Are you using a correlation metric (which one?) Can you describe your dataset? How many total genes are there (in your set and total on your array data)? More importantly, how many and what type of samples/conditions are you measuring coexpression across?