THank you!!!
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How to determine genome wide Co-occupancy between two transcription factors?
Hello:
I am currently using Galaxy to analyze several sets of ChIP-Seq datas, including those published and in house generated from my own sample.
When closely looking at two sets of bigWig file of TF binding data in UCSC genome browser, I surprisingly discovered that two of the transcription factors form well overlapped peaks in the promoter region of several genes.
Now I want to do a heat map ploting for genome wide enriched region in one transcription factor and take a look at that generated from another within the same genome X-axis see if it is also enriched. Ho can I do that?
Is there any other bioinformatic assay I could do to determine the extend of co-occupation of two transcription factors?
Thanks in advance for answering those questions!
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Ram
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muhe1985 •
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muhe1985 •
1 answer
If you are a GUI user, you can use SeqMonk to plot the heatmap.
http://www.bioinformatics.babraham.ac.uk/projects/seqmonk/screenshots/#aligned
It is very powerful, you need to take sometime to learn how to use it.
Start here
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Ming Tommy Tang
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Ming Tommy Tang
I just downloaded it and start using it. I opened align prob plot I assume it is what you meant.
Is there any way I could creat such prob according to coordinations provided by a BED file? I am currently generating some random looking probes
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Yes, heatmap is also an option. If you are using galaxy then this site is also an option to make plots
https://code.google.com/p/ngsplot/
you can make venn diagram to show common and unique peaks of two transcription factors and could also make a line plot around TSS showing average occupancy of both
I am a wet lab person mostly I do is using the public server of galaxy(main), do you know a galaxy instance out there that runs NGS.plot? Thanks a lot!
Understandable!
How to run it on galaxy is also given there:
just click this link
Thank you! Is this a public instance? Looks like it is a Mt Sinai instance? Could you share the link to this instance?
I am a wet lab person mostly I do is using the public server of galaxy(main), do you know a galaxy instance out there that runs NGS.plot? Thanks a lot!