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<title>GRAIL: Gene Relationhips Across Implicated Loci</title>

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<h1 class="about">GRAIL: Gene Relationships Across Implicated Loci</h1>

            <p>GRAIL is a tool to examine relationships between genes
	    in different disease associated loci. Given several
	    genomic regions or SNPs associated with a particular
	    phenotype or disease, GRAIL looks for similarities in the
	    published scientific text among the associated genes.
            <p>As input, users can upload either (1) <B>SNPs</B> that have
	      emerged from a genome-wide association study or (2)
	      <B>genomic regions</B> that have emerged from a linkage scan or
	    are associated common or rare copy number variants. SNPs
	      should be listed according to their rs#'s and must be
	      listed in HapMap. Genomic Regions are specified by a
	      user-defined identifier, the chromosome that it is
	      located on, and the start and end base-pair positions
	      for the region. </p>
	    <p>Grail can take two sets of inputs - <B>Query</B> regions and
	      <B>Seed</B> regions. Seed regions are definitely associated
	      SNPs or genomic regions, and Query regions are those
	      regions that the user is attempting to evaluate agains
	      them. In many applications the two sets are identical.
	      </p>
	    <p>Based on textual relationships between genes, GRAIL
	      assigns a <I>p</I>-value to each region suggesting its degree
	      of functional connectivity, and picks the best candidate
	    gene.</p>
            <p>GRAIL is developed by <a
		href="/personal/soumya/">Soumya Raychaudhuri</a> in
	      the labs of David Altshuler and Mark Daly at the <a
		href="http://chgr.mgh.harvard.edu/">Center for Human
		Genetic Research</a> of <a
		href="http://www.mgh.harvard.edu">Massachusetts
		General Hospital</a> and <a
		href="http://hms.harvard.edu">Harvard Medical
		School</a>, and the Broad Institute.  GRAIL is
	      described in manuscript, currently in preparation.

<h2>Links</h2>
	    <ul>
              <li><a href="/mpg/grail/grail.php">SUBMIT Disease
	    Associated (HapMap) SNPs or Genomic Regions to GRAIL</a></li>
              <li><a href="/mpg/grail/vizgrail.html">Download software
	    to visualize grail results</a></li>
              <li><a href="/mpg/grail/faq.html">Frequently asked
	    questions</a></li>
              <li><a href="/mpg/grail/gene_word_matrix.gz">Download
	    gene-text vectors (December 2006)</a></li>
              <li><a href="/mpg/grail/gene_word_matrix_2009.gz">Download
	    gene-text vectors (March 2009)</a></li>
              <li><a href="/mpg/grail/gene_word_matrix_2010.gz">Download
	    gene-text vectors (May 2010)</a></li>
              <li><a href="/mpg/grail/gene_word_matrix_2011.gz">Download
	    gene-text vectors (April 2011)</a></li>
            </ul>
            <ul>

<h2>Reference</h2>

<p><a href="http://www.plosgenetics.org/doi/pgen.1000534">Raychaudhuri, S., Plenge, R.M., Rossin, E.J., Ng, A.C.Y., International Schizophrenia Consortium, Purcell, S.M., Sklar, P., Scolnick, E.M., Xavier, R.J., Altshuler, D., and Daly, M.J.</a> Identifying Relationships Among Genomic Disease Regions: Predicting Genes at Pathogenic SNP Associations and Rare Deletions. PLOS Genetics, 2009. 5(6):e1000534.
</p>
<p>

</p>


<h2>Any questions?</h2>
<p>You can contact us at G R A I L at broad . mit . edu.</p>

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