chip seq and TRANSFAC

[shum1]

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?????

[galt]

sequence analysis, post-ChIPSeq

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