Hi Khadijeh,

If you have a crystal structure for your protein in PDB, then most often the DNA binding sites are annotated. You can use PDBSum to analyse the DNA binding regions just by giving the PDB ID (4 alpha numerical ID)

ex: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl?pdbcode=1ic8&template=dna.html

I want study T3 and TSH effects on hepatic gene regulation.

I need to find TRE and TF binding sites in promoter region of target gene

I have worked with thyroid hormone and TRs and I would not recommend to use a bio-informatic / in silico approach to find some TREs, since the consensus site is very short and could be degenerated. On of the moderately trustable online tools is Nubiscan, but you may have to ask for an access. You may rather rely on already published ChIP / ChIP-seq data and try to find if your promoter of interest has been described in the literature as TR binding, better if in the liver. You can probably look for GEO ChIP-seq datasets and try to find if a TRE as been described in the vicinity of you gene of interest, given that you are working with human or mouse. Many people are working with thyroid hormone function in the liver, so you may find relevant information with a quick pubmed search. Good luck!

Hello Khadijeh Mahboobnia,

I think Homer is a quite good tool for what you want to do. Homer is not on-line but the installation is very simple (http://homer.ucsd.edu/homer/download.html).

From the original webpage (http://homer.ucsd.edu/homer/microarray/index.html) I found this:

"findMotifs.pl will analyze the promoters of genes and look for motifs that are enriched in your target gene promoters relative to other promoters.  The idea is to provide a list of genes that you believe should contain the same elements, such as genes that are co-regulated. "

I guess is what you are looking for. Hope it is useful. 

Thanks a lot for your nice guidance

We developed a computational protocol based on molecular and structural criteria to perform biologically meaningful and accurate phylogenetic footprinting analyses. Our protocol considers fundamental aspects of the TF-DNA binding process, such as i) the active homodimeric conformations of TFs that impose symmetric structures on the TFBSs, ii) the cooperative binding of TFs, iii) the effects of the presence or absence of co-inducers, iv) the proximity between two TFBSs or one TFBS and a promoter that leads to very long spurious motifs, v) the presence of AT-rich sequences not recognized by the TF but that are required for DNA flexibility, and vi) the dynamic order in which the different binding events take place to determine a regulatory response (i.e., activation or repression).

With this protocol, you can identify promoter sequences with Transcription factor binding sites (TFBSs) in prokaryotes.

Oliver P, Peralta-Gil M, Tabche ML, Merino E. Molecular and structural considerations of TF-DNA binding for the generation of biologically meaningful and accurate phylogenetic footprinting analysis: the LysR-type transcriptional regulator family as a study model. BMC Genomics. 2016 Aug 27;17:686. doi: 10.1186/s12864-016-3025-3.

Dear Martin

Good day

I really appreciate you for your nice guidance. I want to analyse PCSK9 gene promoter in human. The articles that I have studied, suggested JASPAR or ENCODE for this purpose. Unfortunately I do not know how to work with these tools.

Hi Khadijeh,

This is Aziz from JASPAR database. There are several ways you can use the JASPAR database website and/or it's data for this purpose. We've several tools available, such as "Scan" tool. For example, you can select (or add to cart) the latest vertibrate profiles and scan using the promoter sequence. http://jaspar.genereg.net/search?q=&collection=CORE&tax_group=vertebrates&version=latest

I hope this helps. If you've more questions feel free to contact us here

http://jaspar.genereg.net/contact-us

Regards,

Aziz