Comparing ChIP-seq regions between species

Question

[neumann.sylvia]

Hi, I have ChIP-seq data for different TFs and histone marks from rat cells and I would like to compare them to published data sets from mouse cells. Are there any tools to do this? Thank you. Sylvia

Just to clarify, by comparing I mean to obtain the homolgous regions within the two genomes. Thank you. Sylvia

[ATpoint]

I doubt that something like this will ever produce meaningful results. In order to make statements you would need to ensure that differences are not of technical nature, so the exact same library preparation and ChIP method would need to be used in the same lab for all samples, prepared in the exact same way. There are so many confounders and technical biases in ChIP even when comparing in the same species, but different species, from different experiments...maybe others will prove me wrong but I do not see how you could ever distinguish technical from biological differences. This is just something that cannot be done with data you did not produce yourself in the aforementioned fashion.

[neumann.sylvia]

Thank you for your opinion. I agree that the results have to be interpreted with care, as with any type of ChIP-seq analyses. I think that there is value in doing these type of analyses, focusing on the common findings instead of the differences.