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    Comparative Genomics with Estrogen

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    Estrogen receptor (ER) is an important transcription factor, which is up-regulated in 70% of all breast cancers. Using the known ER motif to scan the genome yields many thousands matches, although not all of them are functional. Give the following three matches to the motifs, can you use comparative genomics approaches to judge which one is most likely functional (hint, check UCSC genome browser)?

    Chromosome: Start-End (in human genome version Hg17 coordinates)

    a. chr22:41,455,123-41,455,140
    b. chr21:41,974,930-41,974,948
    c. chr21:15,299,684-15,299,702
    d. chr22:45,652,554-45,652,572

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    Solution Preview

    Estrogen receptor is an important transcription factor, which is up-regulated in 70% of all breast cancers. Using the known ER motif to scan the genome yields many thousands of matches, although not all of them are functional. Given the following four matches to the motif, use a comparative genomics approach to judge which one is most likely functional.

    Response: Please see the attached Word document for a complete answer with graphic output from the UCSC Genome Browser.

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    If we go to the UCSC Genome Browser at http://genome.ucsc.edu/cgi-bin/hgGateway, we can plug these coordinates into the genome, extract the data, and analyze ...

    Solution Summary

    This solution takes the student step by step through the graphic output of the data for each genome to help the student understand why (c) is the likely candidate for a true ER motif in a human gene in 251 words with graphics in an attached Word document.

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