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    How to compare promoter structure of several genes

    16th August 2006

    I needed to find out common transcription factor (TF) binding sites (TFBS) in the structure of the promoters of interferon-regulated genes. I tried several different approaches – starting from the simplest sequence-sequence comparisons using BLAST, ClustalW alignments, and searching each of the promoters for transcription factor binding sites – to compare and find common.

    But the easiest way was to use Genomatix’s “Gene2Promoter” tool. With it, the whole procedure is extremely simple:

    1. Login to
    2. Choose “Gene2Promoter” button at the top
    3. Set checkboxes for necessary organisms
    4. Select the method of sequence input:
      • by AffyId, GeneID, gene name
      • choose previously uploaded sequence
      • paste DNA sequence in any of the available formats (plain, EMBL, FASTA, GCG/RSF, GenBank, IG)
      • upload sequence(s) file
      • enter accession numbers
    5. Optionally, somehow name this set of sequences
    6. “Submit” the form
    7. You will get a table with mappings of your sequences to promoters and their transcripts. Here you have to choose which promoters you want to analyze by setting checkboxes. At the end of the list there is an option to hint you on which promoters contain your TFBS of interest.
    8. After all the selections are made, leave the default option “Search for common TF sites in multiple sequences” enabled, and “Start Selected Task”.
    9. Now you will have to select which library of matrices to use (e.g. “Vertebrates”, “Plants” …). You can also filter by tissue specificity, and select the percentage of promoters which have common promoters (e.g., when comparing 5 sequences, you can choose to display TF sites common to from 1 up to 5 sequences, or 20-100%). Here you can also somehow name the result.
    10. When all done – “Submit Query”.
    11. You will get quite a convenient SVG display of you sequences/promoters with overlayed TF binding sites, colour-coded by TF families. From here you can export results to PDF, Excel, and “Show Match Summary Table” of TF-to-promoter hits.

    That is it. Real simple :)


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