Question: Computing Relative Percentage Of Binding Sites On Each Chromosome
1
gravatar for ChIP
7.3 years ago by
ChIP500
Netherlands
ChIP500 wrote:

Hi!

I have a genome wide binding profile of a transcription factor through ChIP seq expt. The total number of binding sites are 6567 and I also have the chromosomal distribution of these sites. I want to get the relative binding percentage for each chromosome.

The organism is homo sapiens.

formula: (number of binding sites on a chromosome / total number of binding sites) * length of chromosome

Is this formula correct (length of chromosome being in bps).

Or can you suggest something else?

Thank you

seq chip-seq • 1.4k views
ADD COMMENTlink modified 7.3 years ago by Sukhdeep Singh9.8k • written 7.3 years ago by ChIP500
1

Perhaps you want something like:

sites_on_chromosome/length_of_chromosome (in Mb), so you get sites/Mb on each chromosome. You can do the same for sites in the genome and genome length. From there, you can form ratios of interest. Does that get you what you want?

ADD REPLYlink written 7.3 years ago by Sean Davis25k

Hi! What do you mean by relative binding percentage? Just from your formulae, note that you are multiplying with length of chromosome alone (it is not percentage). Can you explain little bit more that what you want to check in the end?

ADD REPLYlink written 7.3 years ago by Vikas Bansal2.3k
1
gravatar for Sukhdeep Singh
7.3 years ago by
Sukhdeep Singh9.8k
Netherlands
Sukhdeep Singh9.8k wrote:

Hi, I agree with Sean, rather then the total length you should calculate per MB. Also, this might be biased as some chromosomes are more densely populated versus other (like chr19) and if you'll compare the bindings later on, you might observe less bindings on small chromosomes comparable to more bindings on big chromosomes.

I think you should also compare the height of the peak or the fold enrichment of the bindings per chromosome or per MB, so that you have a more generalized way. Use the tool pyicos, which gives you the area under the peak, which I think is a better thing to do. Also, check this page for the distribution of genes/exons/introns per chromosome of the human and mouse.

Cheers

ADD COMMENTlink written 7.3 years ago by Sukhdeep Singh9.8k
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