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
3 answers
If I'm understanding you correctly, it seems that you have multiple questions.
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.
Does a particular TF have any protein-protein interactions?
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
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.
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Alex Reynolds
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Thanks for your answers. Let me describe my question in another way. In my chip-seq analysis I am looking for binding sites for specific TF. As a part of this approach I performed motif analysis by different web tools, like RSAT, JASPAR and MEME. All analysis confirmed occurrence 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 specific 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 correctly the occurrence of other TFs and their binding site in specific TF motif analysis?
Thanks for your help