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<title>GoShifter</title>

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    <h1 class="about"><u>G</u>enomic Ann<u>o</u>tation <u>Shifter</u> (GoShifter)</h1>

            <p><B>Overview</B></p>
            <p><u>G</u>enomic Ann<u>o</u>tation <u>Shifter</u> (GoShifter) tests for enrichment
                between trait-associated SNPs and all types of genomic
                annotations, e.g. histone modifications, transcription factor
                binding sites, DNase hypersensitivity sites, gene transcripts etc.
                The significance of an overlap between trait-associated variants
                and genomic annotations is inferred through locally shifting
                annotations within the boundaries of associated loci.</p>
            
                <p>The most powerful feature of GoShifter is its ability to
                distinguish independent causal signals from colocalizing
                annotations. In other words, one can test for the significance of
                an overlap with one type of genomic annotation, stratifying on
                another, possibly colocalizing annotation. For example, if one
                observes a significant enrichment with DHS and H3K4me3 mark (both
                known to colocalize) it is then possible to disentangle this
                signal in more details by testing for enrichment of DHS
                stratifying on H3K4me3, and the other way around. This may, for
                example, unravel that H3K4me3 solely captures the causal signal
                and observed enrichment in DHS is due to strong correlation
                between this two annotations.</p>
            
                <p>Finally, GoShifter highlights specific loci where it can most
                effectively prioritize causal variants.</p>
            
                <p>Here we provide scripts that allow user to:</p>
                <ul>
	                <li>1) Test for significance of an overlap between trait-associated variants and single annotation. </li>
	                <li>2) Test for significance of an overlap between trait-associated variants and two, possibly colocalizing annotations.</li>
                </ul>
                <p>The scripts were written by Gosia Trynka in the lab of
                Soumya Raychaudhuri at the Division of Genetics, Brigham and
                Women's Hospital and Harvard Medical School and the Broad
                Institute.</p>


        <h2>Links</h2>
	    <ul>
		<li>This software has been moved to <a href="https://github.com/immunogenomics/goshifter" target="_blank">GitHub</a>.</li>
            </ul>

        <p>The scripts were written by Gosia Trynka, in the lab of <a              
	    href="/personal/soumya/">Soumya Raychaudhuri</a> at the <a
	    href="http://www.brighamandwomens.org/research/depts/medicine/genetics/default.aspx">Division of Genetics,Brigham and Women’s Hospital</a> and <a
	    href="http://hms.­harvard.­edu">Harvard Medical School</a> and the Broad Institute.</p>




<h2>Reference</h2>

<p>Trynka G, <I>et al., 2015, AJHG</I>  <B><a href="http://www.sciencedirect.com/science/article/pii/S0002929715002025?via%3Dihub">Disentangling effects of colocalizing genomic annotations to functionally prioritize non-coding variants within complex trait loci</a></B> 
</p>


<h2>Questions?</h2>
<p>Please leave a message or issue at our <a href="https://github.com/immunogenomics/goshifter">GitHub repository</a>.</p>

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