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Get the functional enrichment analysis?

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Get the functional enrichment analysis?
Answer
11/3/11 9:41 PM
Hi,

I have a list of genes that I want to know is there any function enrichment of this gene group. I am curious about whether what I did making sense?

1. I create the log value of 3 (and also 1 for significance (the derived column) ) for the genes on the list
2. I create the log value of 0.1 (and also 0 for significance (the derived column) ) for other genes of the genome
3. I choose the corresponding mapping file
4. I run the PageMan analysis for Fisher test with correction for multiple testing.

However, I ended of getting nothing. Does that mean there is no function enrichment of this gene group?

Thanks for your help.

RE: Get the functional enrichment analysis?
Answer
11/3/11 9:51 PM as a reply to Joseph Laird.
Hi,

unfortunately pageman doesn't use the derived column yet.

But in any case it tries to your "gene universe" so try supplying a gene list of all genes that could have been chosen and mark the significant ones e.g. with one and negattive one.

Let's assume you at1g53500 and at3g23820 were significant and you looked at these 5 genes
at1g53500
at3g23820
at1g53510
at1g53560
at1g53570

then try it like this
ID value
at1g53500 1
at3g23820 1
at1g53510 0
at1g53560 0
at1g53570 0


Cheers,
Björn