Question

motif for TF within CTCF boundary

1

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10.7 years ago

asharmatelome ▴ 60

Hi,

I want to find motif for my TF within the CTCF boundary. I have some 200 genes where I want to do this analysis. I was wondering if there is any tool to identify my TF binding motif within CTCF boundaries for all the genes in one go without doing it manually.

Thanks,

Ankur

ctcf genome R • 2.5k views

ADD COMMENT • link updated 10.7 years ago by Alex Reynolds 36k • written 10.7 years ago by asharmatelome ▴ 60

Ram · Answer 1 · 2014-06-09

1

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10.7 years ago

Alex Reynolds 36k

FIMO will search for TF binding sites within your sequences of interest.

As input, you will need: 1) sequences of interest, and 2) PWMs for your TFs of interest (e.g., JASPAR, TRANSFAC, UniPROBE, etc.).

ADD COMMENT • link updated 5.1 years ago by Ram 44k • written 10.7 years ago by Alex Reynolds 36k

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Hi, How to determine the TAD boundary?

ADD REPLY • link 4.6 years ago by BenHu • 0