Question: Is there a tool to retrive transcription factors (Tfs) which have the common binding site?or a tool that takes a sequence as input and suggest possible coresponding Tfs?
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gravatar for mary99
3.6 years ago by
mary9980
European Union
mary9980 wrote:

Hello ,

I am doing chip-seq down stream analysis.After motif discovery I found several transcription factors and their motifs plus my Tf of my interest.In my analysis also it is so important to figure out the Tfs which have interaction with my main Tf.So my question is beside finding from papers is there a tool that can help me in this field?

Thanks in advance,

Maryam

chip-seq next-gen sequence • 1.8k views
ADD COMMENTlink modified 3.6 years ago by Alex Reynolds27k • written 3.6 years ago by mary9980
1
gravatar for Kamil
3.6 years ago by
Kamil1.9k
Boston
Kamil1.9k wrote:

If I'm understanding you correctly, it seems that you have multiple questions. 

  1. Which TFs might bind to a particular sequence?
    • Try the MEME suite: website and paper.
    • Look at real data. For example, download ChIP-seq data from ENCODE for the transcription factor of interest, or else search GEO for data that might be suitable for your particular scientific question.
       
  2. Does a particular TF have any protein-protein interactions?
ADD COMMENTlink modified 3.6 years ago • written 3.6 years ago by Kamil1.9k
1
gravatar for TriS
3.6 years ago by
TriS3.6k
United States, Buffalo
TriS3.6k wrote:

for TF binding you can use: MAPPER 

for building an interactome you can use the supplementary table offered in the Science paper "Uncovering disease-disease relationships through the incomplete interactome", Science 20 February 2015: Vol. 347 no. 6224

ADD COMMENTlink written 3.6 years ago by TriS3.6k
1
gravatar for Alex Reynolds
3.6 years ago by
Alex Reynolds27k
Seattle, WA USA
Alex Reynolds27k wrote:

Say you know the genomic regions of your main TF.

Say these and your regions of found TFs are in BED format. If you don't have found TFs, you could use a tool like FIMO (part of the MEME suite) to discover them with some statistical likelihood.

You can then use a tool like BEDOPS bedops --range to define a range upstream of the main TF, like a promoter region, where regulatory interactions are likely to occur.

You can use bedops --element-of (or BEDOPS bedmap --echo --echo-map) to map other TFs of interest to this upstream regulatory region of the main TF.

ADD COMMENTlink modified 3.6 years ago • written 3.6 years ago by Alex Reynolds27k

Thanks Alex for introducing BEDOPS,it sounds so intresting.

ADD REPLYlink modified 3.6 years ago • written 3.6 years ago by mary9980
0
gravatar for mary99
3.6 years ago by
mary9980
European Union
mary9980 wrote:

Thanks for your answers.Let me describe my question in another way.In my chip-seq analysis I am looking for binding sites for spesific TF.As a part of this approach I performed motif analysis by different web tools,like RSAT,JASPAR and MEME.All analysis confirmed occurnce of the TF of my interest.But RSAT also report another TFs in motif discovery.My question is how I can find the binding site that is just spesific to my TF not the other that probably are so close to this TF or  those which have synergy with my TF?or much ideal how I can reasoning corectly the occurnce of other TFs and their binding site in  specific TF motif analysis?

Thanks for your helps        

ADD COMMENTlink modified 3.6 years ago • written 3.6 years ago by mary9980
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