Question: enrichment of transcription factors
0
gravatar for rotemkat
2.5 years ago by
rotemkat0
rotemkat0 wrote:

hi there, I have a list of genes, and i want to check if this group is enriched with TF (or maybe i should say TFs that bind to these genes) compared to all human genes.

any idea how i do it? i checked enrichr but seems like it doesn't answer my question... Thanks

gene • 1.1k views
ADD COMMENTlink modified 24 months ago by Biostar ♦♦ 20 • written 2.5 years ago by rotemkat0
7
gravatar for Alex Reynolds
2.5 years ago by
Alex Reynolds30k
Seattle, WA USA
Alex Reynolds30k wrote:

Do some counting:

  1. Count the number of TF binding sites in genes-of-interest (or their promoters, etc.).
  2. Count the number of genes-of-interest.
  3. Count the number of TF binding sites in all genes (or, again, their promoters, etc.).
  4. Count the number of total genes.

Look up the hypergeometric test in R via ?phyper.

The phyper() function takes at least four arguments:

  1. q: The number of white balls drawn without replacement from an urn which contains both black and white balls.
  2. m: The number of white balls in the urn.
  3. n: The number of black balls in the urn.
  4. k: The number of balls drawn from the urn.

In this case, q is the number of TF binding sites in the genes-of-interest. The m is the number of TF binding sites in all genes. The n is the number of TF binding sites in genes that are not TF binding sites in genes-of-interest (subtract the count of sites in genes-of-interest from the count of sites in genes). The k is the count of genes-of-interest.

The resulting p-value should indicate the likelihood of observing q or fewer TF sites in genes-of-interest by chance, relative to TF sites over all genes. If that value is less than a pre-decided threshold (say 0.01) then you could argue this suggests enrichment for those particular TF sites.

ADD COMMENTlink modified 2.5 years ago • written 2.5 years ago by Alex Reynolds30k
0
gravatar for russhh
2.5 years ago by
russhh5.4k
UK, U. Glasgow
russhh5.4k wrote:

If it's human or mouse, you could try using this

ADD COMMENTlink written 2.5 years ago by russhh5.4k
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