Question: How to determine genome wide Co-occupancy between two transcription factors?
0
gravatar for muhe1985
4.7 years ago by
muhe198510
United States
muhe198510 wrote:

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!

 

 

 

chip-seq • 2.8k views
ADD COMMENTlink modified 4.7 years ago by Ming Tang2.5k • written 4.7 years ago by muhe198510

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

ADD REPLYlink written 4.7 years ago by Manvendra Singh2.1k

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 alot!

ADD REPLYlink modified 4.7 years ago • written 4.7 years ago by muhe198510

Understandable!

How to run it on galaxy is also given there:

just click this link

https://code.google.com/p/ngsplot/wiki/webngsplot

 

ADD REPLYlink written 4.7 years ago by Manvendra Singh2.1k

Thank you! Is this a public instance? Looks like it is a Mt Sinai instance? Could you share the link to this instance?

ADD REPLYlink written 4.7 years ago by muhe198510

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 alot!

ADD REPLYlink modified 4.7 years ago • written 4.7 years ago by muhe198510
0
gravatar for Ming Tang
4.7 years ago by
Ming Tang2.5k
Houston/MD Anderson Cancer Center
Ming Tang2.5k wrote:

If you are a GUI user, you can use SeqMonk to plot the heatmap.

http://www.bioinformatics.babraham.ac.uk/projects/seqmonk/screenshots/#aligned

http://www.bioinformatics.babraham.ac.uk/projects/seqmonk/

It is very powerful, you need to take sometime to learn how to use it.

start from here https://www.youtube.com/user/BabrahamBioinf

 

ADD COMMENTlink modified 4.7 years ago • written 4.7 years ago by Ming Tang2.5k

THank you!!!

ADD REPLYlink written 4.7 years ago by muhe198510

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

ADD REPLYlink written 4.7 years ago by muhe198510
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