GenePattern

<h2 id="functionality">Functionality</h2>
<p>GenePattern is a powerful <a href="/facts/Scientific_workflow_system/HkvT6FTF">scientific workflow system</a> that provides access to hundreds of genomic analysis tools. Use these analysis tools as building blocks to design sophisticated analysis pipelines that capture the methods, parameters, and data used to produce analysis results. Pipelines can be used to create, edit and share reproducible in silico results.
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<h2 id="project-objectives">Project Objectives</h2>
<ol><li>Accessibility: Run over 200 regularly updated analysis and visualization tools (that support <a href="/facts/Data_preprocessing/CS2W8m5B">data preprocessing</a>, <a href="/facts/Gene_expression/alCPohLR">gene expression</a> analysis, <a href="/facts/Proteomics/3aqQ1tFh">proteomics</a>, <a href="/facts/Single_nucleotide_polymorphism/Qy5Y2wom">Single nucleotide polymorphism</a> (SNP) analysis, <a href="/facts/Flow_cytometry/M2IvPdL8">flow cytometry</a>, and <a href="/facts/Next-generation_sequencing/FjLl8GGa">next-generation sequencing</a>) and create analytic workflows without any programming through a point and click user interface.</li>
<li>Reproducibility: Automated history and provenance tracking with versioning so that any user can share, repeat and understand a complete computational analysis</li>
<li>Extensibility: Computational users can import their methods and code for sharing using tools that support easy creation and integration</li>
<li>Multiple interfaces: Web browser, application, and programmatic interfaces make analysis modules and pipelines available to a broad range of users; public hosted server</li></ol>
<h2 id="features">Features</h2>
<ul><li>A regularly updated repository of hundreds of computational analysis modules that support data preprocessing, <a href="/facts/Gene_expression/alCPohLR">gene expression</a> analysis, <a href="/facts/Proteomics/3aqQ1tFh">proteomics</a>, <a href="/facts/Single_nucleotide_polymorphism/Qy5Y2wom">single nucleotide polymorphism</a> (SNP) analysis, <a href="/facts/Flow_cytometry/M2IvPdL8">flow cytometry</a>, and short-read sequencing.<a class="footnote-ref" id="fnref:1" href="#fn:1"><sup>1</sup></a></li>
<li>A programmatic interface that makes analysis modules available to computational biologists and developers from Python, Java, MATLAB, and R.</li>
<li>The GenePattern Notebook Environment: Built on the <a href="/facts/IPython/PsAdpgxU">Jupyter Notebook</a> environment, GenePattern Notebook allows researchers to run GenePattern analyses within notebooks that interleave text, graphics, and executable code, creating a single "research narrative."</li>
<li>GParc: Repository and community for GenePattern users to share and discuss their own GenePattern modules</li></ul>
<h2 id="availability">Availability</h2>
<p>GenePattern is available:
</p>
<ol><li>As a free public web application,<a class="footnote-ref" id="fnref:2" href="#fn:2"><sup>2</sup></a> hosted on Amazon Web Services.  Users can create accounts, perform analyses, and create pipelines on the server.</li>
<li>As <a href="/facts/Open-source_software/HzTaB8E9">open-source software</a> that can be downloaded and installed locally.<a class="footnote-ref" id="fnref:3" href="#fn:3"><sup>3</sup></a></li>
<li>Public web servers hosted by other organizations.<a class="footnote-ref" id="fnref:4" href="#fn:4"><sup>4</sup></a></li></ol>
<h2 id="notes">Notes</h2>

<ul><li>The GenePattern Notebook Environment] Reich M, Tabor T, Liefeld T, Thorvaldsdóttir H, Hill B, Tamayo P, Mesirov JP. <i>Cell Syst</i>. 2017 Aug 23;5(2):149-151.e1. <a href="/facts/Doi_(identifier)/muM9Etpq">doi</a>:<a href="https://doi.org/10.1016%2Fj.cels.2017.07.003">10.1016/j.cels.2017.07.003</a>. Epub 2017 Aug 16. <a href="/facts/PMID_(identifier)/JlHAvMHt">PMID</a> <a href="https://pubmed.ncbi.nlm.nih.gov/28822753">28822753</a>; <a href="/facts/PMC_(identifier)/dX1zMt71">PMC</a> <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5572818/">5572818</a>.</li>
<li>Integrative genomic analysis by interoperation of bioinformatics tools in GenomeSpace Qu K, Garamszegi S, Wu F, Thorvaldsdottir H, Liefeld T, Ocana M, Borges-Rivera D, Pochet N, Robinson JT, Demchak B, Hull T, Ben-Artzi G, Blankenberg D, Barber GP, Lee BT, Kuhn RM, Nekrutenko A, Segal E, Ideker T, Reich M, Regev A, <a href="/facts/Howard_Y._Chang/Cs3zhBG1">Chang HY</a>, Mesirov JP. <i>Nat Methods</i>. 2016 Mar;13(3):245-247. <a href="/facts/Doi_(identifier)/muM9Etpq">doi</a>:<a href="https://doi.org/10.1038%2Fnmeth.3732">10.1038/nmeth.3732</a>. Epub 2016 Jan 18. <a href="/facts/PMID_(identifier)/JlHAvMHt">PMID</a> <a href="https://pubmed.ncbi.nlm.nih.gov/26780094">26780094</a>; <a href="/facts/PMC_(identifier)/dX1zMt71">PMC</a> <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4767623/">4767623</a>.</li>
<li>Using GenePattern for Gene Expression Analysis]  Kuehn, H., Liberzon, A., Reich, M. and Mesirov, J. P.  <i>Current Protocols in Bioinformatics</i>. 2008. 22:7.12:7.12.1–7.12.39. <a href="/facts/Doi_(identifier)/muM9Etpq">doi</a>:<a href="https://doi.org/10.1002%2F0471250953.bi0712s22">10.1002/0471250953.bi0712s22</a></li>
<li>GenePattern 2.0  Michael Reich, Ted Liefeld, Joshua Gould, Jim Lerner, Pablo Tamayo & <a href="/facts/Jill_P._Mesirov/UqCuUxd1">Jill P. Mesirov</a>.  <i>Nature Genetics</i> - 38, 500 - 501 (2006) <a href="/facts/Doi_(identifier)/muM9Etpq">doi</a>:<a href="https://doi.org/10.1038%2Fng0506-500">10.1038/ng0506-500</a></li></ul>
<h2 id="external-links">External links</h2>
<ul><li><a href="http://www.broadinstitute.org/cancer/software/genepattern/">Official GenePattern website</a></li>
<li><a href="http://genepattern-notebook.org/">Official GenePattern Notebook website</a></li>
<li><a href="http://gparc.org/">GParc</a></li>
<li><a href="https://github.com/genepattern/genepattern-server">GenePattern</a> on GitHub</li></ul>
<p>Related software:
</p>
<ul><li><a href="http://genomespace.org/">GenomeSpace</a></li>
<li><a href="http://www.broadinstitute.org/igv/">Integrative Genomics Viewer</a></li></ul>

<h2 id="references">References</h2>

<ol>
<li id="fn:1"><p>Kuehn, Heidi; Liberzon, Arthur; Reich, Michael; Mesirov, Jill P. (June 2008). "Using GenePattern for Gene Expression Analysis". Current Protocols in Bioinformatics. 22 (1): 7.12.1–7.12.39. doi:10.1002/0471250953.bi0712s22. ISSN 1934-3396. PMC 3893799. PMID 18551415. <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3893799" target="_blank">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3893799</a> <a href="#fnref:1" class="footnote-back-ref">↩</a></p></li>
<li id="fn:2"><p>"GenePattern". cloud.genepattern.org. Retrieved 2012-05-07. <a href="http://cloud.genepattern.org" target="_blank">http://cloud.genepattern.org</a> <a href="#fnref:2" class="footnote-back-ref">↩</a></p></li>
<li id="fn:3"><p>"GenePattern: Download GenePattern". Broadinstitute.org. Archived from the original on 2012-05-09. Retrieved 2012-05-07. <a href="https://web.archive.org/web/20120509201241/http://www.broadinstitute.org/cancer/software/genepattern/download/index" target="_blank">https://web.archive.org/web/20120509201241/http://www.broadinstitute.org/cancer/software/genepattern/download/index</a> <a href="#fnref:3" class="footnote-back-ref">↩</a></p></li>
<li id="fn:4"><p>"Use GenePattern". genepattern.org. 2006-10-07. Archived from the original on 2012-06-07. Retrieved 2012-05-07. <a href="https://web.archive.org/web/20120607234324/http://www.broadinstitute.org/cancer/software/genepattern/desc/collaborations" target="_blank">https://web.archive.org/web/20120607234324/http://www.broadinstitute.org/cancer/software/genepattern/desc/collaborations</a> <a href="#fnref:4" class="footnote-back-ref">↩</a></p></li>
</ol>

GenePattern open-in-new

GenePattern