How to calculate the distribution of histone modifications on transcription factors

Question

[koyee_d]

Is there a tool to plot distribution of histone modifications on transcription factors?

[seidel]

This question doesn't make sense as written. Can you clarify? Histones can be modified in a number of ways (a distribution of ways perhaps). And then there are transcription factors, which can be covalently modified, but aren't typically thought of in this regard. Histones and Transcription Factors and the modifications each may undergo are separate entities. What are you trying to achieve? What are you trying to figure out? What would your plot consist of? What question would it address?

[koyee_d]

Dear seidel,

Thanks for your reply. I have a bed file of H3K4me1 and a bed file of MCM2, I would like to plot the H3K4me1 enrichment on MCM2 as shown in the image below. The abscissa represents the coordinates of the MCM2. I used a simple Python script to handle it, but the running time was extremely slow because of the huge data, so I wanted to ask if there was a better way to do this thing. Thank you very much. Sincerely.

[lily]

deepTools plotProfile (or plotHeatmap which also adds detailed heatmaps) can be used to plot those enrichment profiles you are referring to. (https://deeptools.readthedocs.io/en/develop/content/tools/plotProfile.html)

However, your bed files won't provide enough information for that, as they only contain the genomic location and average enrichment of (probably) peaks of H3K4me1 and MCM2 and no detailed, binned enrichment values. You would have to run deepTools computeMatrix prior to plotProfile, which requires bigWigs with the signal of your histone modification and transcription factor besides bed files specifying the genomic regions.

[koyee_d]

Hi lily, Thank you so much.

Deeptool is a really powerful tool. I'm going to learn how to use it.

Thanks again.