chip seq and TRANSFAC

shum1

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Join Date: Apr 2010

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chip seq and TRANSFAC

04-13-2010, 03:22 PM

hi all!

I have done chipseq for finding TF binding sites in the target genes.

Now I want to see which other factors can be near to that factor? I am using TRANSFAC but i dont know how i should proceed using bioinformatics tools?????
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galt

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Join Date: Feb 2010

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04-16-2010, 01:06 AM

sequence analysis, post-ChIPSeq

Originally posted by shum1 View Post

hi all!

I have done chipseq for finding TF binding sites in the target genes.

Now I want to see which other factors can be near to that factor? I am using TRANSFAC but i dont know how i should proceed using bioinformatics tools?????

Dear Shum1,
I suggest you read MDScan documentation: paper and manual, and give it a try. It is a program designed by the same authors of MACS for the very purpose of analyzing sequences after (but not only) ChIPSeq experiments. Good work
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chip seq and TRANSFAC

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