Clustering of enhancer sites!!

Question

[asharmatelome]

Hi, I have list of 8 TF's and they bind to various enhancers in the genome.

I have this data in excel and now I want to make a matrix where I want to see

TF A+B= X number of enhancers,

TF A+B+C= X +/- n number of enhancers,

Finally I want to cluster everything

Can anyone help?

Thanks

[asharmatelome]

Thanks,

I tried Cluster3, but I dont I believe I have to download UniConvertor to get the data. I tried downloading this but I couldn't because it require some additional software package sk1.

I am trying with intersectBed but looks like it runs on 'R' and I have to accept that this is the first time I am trying to use this 'code' language. In my PhD I spend 6 yrs on bench and now I need to do these analysis.

[aditi.qamra]

intersectbed will not run on R. it will work on unix command line. (See here)

Cluster 3.0 is easy to download as a GUI application on Windows/Mac. Why do you have to download Uniconvertor ? ( ps. I dont know what Uniconvertor is)

ps. this thread -How To Make Visual Graphs To Represent Common Transcription Factor Binding Sites In Different Enhancers? might help if you can get R working for you.

[PoGibas]

It would be easier if you would show us how your data looks like. Can you update your question?

Answer 1

[Sukhi Singh]

Once you have information in the form of the co-ordinates (which enhancer sites, TF A or B binds), use intersectBed or multiIntersectBed, to get this information in the form of table, then you can make a heatmap after that.

Else use Cluster3 for clustering with the data, where rows contain information for each enhancer and columns are different TF's. The values could me how strongly they bind or how much overlap or how close they are, you can decide that.

Answer 2

[aditi.qamra]

one quick way would be to use intersectBed with your combined list of enhancer file and different combinations of TFs. (eg. A+B, A+B+C..etc)

I'm sure there is a more elegant solution with bedtools though.

For clustering - depends on what your question is. maybe you can explain further.