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<!DOCTYPE HTML PUBLIC "-//W3C//Dtd HTML 4.01 Transitional//EN"> <html> <head> <!-- Google tag (gtag.js) --> <script async src="https://www.googletagmanager.com/gtag/js?id=G-9H47X4K6P6"></script> <script> window.dataLayer = window.dataLayer || []; function gtag(){dataLayer.push(arguments);} gtag('js', new Date()); gtag('config', 'G-9H47X4K6P6'); </script> <link href="/css/style.css" type="text/css" rel="stylesheet"> <!--Include additional css, etc--> </head> <div id="header"> <body bgcolor="#ffffff" leftmargin=0 topmargin=0 marginwidth="0" marginheight="0" > <!-- Nav Bar --> <table width="915" cellpadding=0 cellspacing=0> <tr><td colspan=8 > <table cellpadding=2 cellspacing=0 width="100%" border=0> <TR> <td rowspan=2 colspan=8 valign=middle align="left"> <DIV style=" padding: 5px 5px 5px 5px;vertical-align: middle;"> <DIV style="float:left; display:table-cell; vertical-align: middle; text-align: center; padding: 10px 20px 5px 5px;"> <a href="/" target="_top"><img src="/images/logos/Panther_logo.jpg" ></a> </DIV> <p style="overflow:hidden;font-size:14px">The mission of the PANTHER knowledgebase is to support biomedical and other research by providing<BR> <b>comprehensive information about the evolution of protein-coding gene families</b>, particularly<BR> protein phylogeny, function and genetic variation impacting that function. <a href="/about.jsp">Learn more</a></p> </DIV> </td> </TR> </table> </td> </tr> <TR> <TD align = "left"><div><b>PANTHER19.0 Released. <a href="/news/news20240620.jsp"> Click</a> for more details.</b></div></TD> </TR> <TR><TD> </TD></TR> <TR> <TD colspan=8 bgcolor="#F0F2F5" valign=middle align="left" > <form name="quicksearch" method=GET onSubmit="javascript:submitQuickSearch();"> <input type="hidden" name="searchType" value="basic"> <input type="hidden" name="fieldName" value="all"> <input type="hidden" name="organism" value="all"> <table align="left" border="0" cellspacing="0" cellpadding="0" height="100%"> <tr> <td 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</TD> <TD bgcolor="#B8C6D8" width=1><img width=1 src="/images/spacer.gif"></TD> <TD nowrap class=headerTabs><a href="/data/" target="_top"> Data Version </A> </TD> <TD bgcolor="#B8C6D8" width=1><img width=1 src="/images/spacer.gif"></TD> <TD nowrap class=headerTabs><a href="/tools/index.jsp" target="_top"> Tools </A> </TD> <TD bgcolor="#B8C6D8" width=1><img width=1 src="/images/spacer.gif"></TD> <TD nowrap class=headerTabs><a href="/services/index.jsp" target="_top"> API/Services </A> </TD> <TD bgcolor="#B8C6D8" width=1><img width=1 src="/images/spacer.gif"></TD> <TD nowrap class=headerTabs><a href="/publications.jsp" target="_top"> Publications </A> </TD> <TD bgcolor="#B8C6D8" width=1><img width=1 src="/images/spacer.gif"></TD> <TD nowrap class=headerTabs><a href="/workspace/" target="_top"> Workspace </A> </TD> <TD bgcolor="#B8C6D8" width=1><img width=1 src="/images/spacer.gif"></TD> <TD nowrap class=headerTabs><a href="/downloads/index.jsp" target="_top"> Downloads </A> </TD> <TD 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width="100%" border=0> <TR> <TD> </TD> <!--<TD><div><b><a href="/data/index.jsp">PANTHER17.0 Released</a>.</b></div></TD>--> <!-- <TD class=listResult valign=top>PANTHER version 17.0 contains <ul> <li>15,619 gene family phylogenetic trees -covering ~2 million genes</li> <li>from different species across the tree of life. <a href="/panther/summaryStats.jsp">more</a></li> </ul> </TD> <TD class=listResult valign=top>Each gene is classified by <ul> <li>protein class</li> <li>protein family and subfamily</li> <li>function (GO terms, pathways)</li> <li><a href="/data/">more</a></li> </TD> --> <TD align = "right" class="formLabel"> Current Release: <a href="/news/news20240620.jsp"><b>PANTHER 19.0</a></b> | <b><a href="/panther/index.jsp">15,683</a></b> family phylogenetic trees | <b><a href="/panther/summaryStats.jsp">144</a></b> species | <a href="/news/news20240620.jsp">News</a> <br><A href="/servlet/GenomeFunctionChartServlet?chartType=1&listType=1&annotType=5&species=Homo sapiens">Whole genome function views</A> </TD> </TR> </table> </div> <!-- end nav bar --> <!-- <table cellpadding=0 cellspacing=0> <tr> <td valign="top"> --!> <!-- </td> <td valign="top">--!><!--Main content page goes here--> <div id="mainBody""> <!-- Main Content Goes Here --> <div class="header1">PANTHER Publications</div> <BR> <span class="formtitle"><a name="HowToCitePANTHER" id="HowToCitePANTHER">How to cite PANTHER</a></span> <BR> <ul> <li class="orange"><b>Always cite<BR><a href="https://onlinelibrary.wiley.com/doi/epdf/10.1002/pro.4218">PANTHER: Making genome-scale phylogenetics accessible to all</a></b><BR>Paul D. Thomas, Dustin Ebert, Anushya Muruganujan, Tremayne Mushayahama, Laurent-Philippe Albou and Huaiyu Mi<BR><i>Protein Society. 2022;31(1):8-22. doi:10.1002/pro.4218</i><BR> </li> <li class="orange"><b>Enrichment test, over-representation test tools<BR><a href="https://www.nature.com/articles/s41596-019-0128-8">Protocol Update for large-scale genome and gene function analysis with the PANTHER classification system (v.14.0)</a></b><BR> Huaiyu Mi, Anushya Muruganujan, J Xiaosong Huang, Dustin Ebert, Caitlin Mills, Xinyu Guo and Paul D Thomas<BR><i>Nat Protoc. 2019 Mar;14(3):703-721. doi: 10.1038/s41596-019-0128-8</i><BR> </li> <li class="orange"><b> PANTHER pathway<BR><a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6608593/">PANTHER Pathway: An Ontology-Based Pathway Database Coupled with Data Analysis Tools</a></b><BR>Huaiyu Mi and Paul Thomas<BR><i> Protein Networks and Pathway Analysis. Methods in Molecular Biology (Methods and Protocols), vol 563.</i><BR> </li> <li class="orange"><b>GIGA - PANTHER tree building algorithm<BR><a href="http://www.biomedcentral.com/1471-2105/11/312">GIGA: a simple, efficient algorithm for gene tree inference in the genomic age</a></b><BR>Paul D Thomas<BR><i>BMC Bioinformatics 2010, 11:312</i><BR> </li> <li class="orange"><b>Coding SNP analysis tool<BR><a href="http://www.ncbi.nlm.nih.gov/pubmed/27193693">PANTHER-PSEP: predicting disease-causing genetic variants using position-specific evolutionary preservation</a></b><BR>Haiming Tang and Paul D. Thomas<BR><i>Bioinformatics (2016) doi: 10.1093/bioinformatics/btw222</i><BR> </li> <li class="orange"><b>TreeGrafter tool for classifying user-specified sequences<BR><a href="https://pubmed.ncbi.nlm.nih.gov/30032202/">TreeGrafter: phylogenetic tree-based annotation of proteins with Gene Ontology terms and other annotations</a></b><BR>Tang H, Finn RD, Thomas PD.<BR><i>Bioinformatics. 2019 Feb 1;35(3):518-520. doi: 10.1093/bioinformatics/bty625. PMID: 30032202; PMCID: PMC6361231.</i><BR> </li> </ul> <BR> <!-- End Main Content --> </div> <!--</td></tr></table>--> <!-- Page Footer begins here --> <div id="footer"> <table width="915" cellpadding="0" cellspacing="0" border="0" width="100%"> <tr> <td align="center"> <span class="legal"> <DIV style=" padding: 0px 5px 0px 5px;text-align:center;vertical-align:middle;"> <a href="/about.jsp">About</a> | <a href="/releaseInfo.jsp">Release Information</a> | <a href="/feedback.jsp">Contact Us</a> | <a href="/systemRequirements.jsp">System Requirements</a> | <a href="/terms/privacyPolicy.jsp">Privacy Policy</a> | <a href="/terms/disclaimer.jsp">Disclaimer</a> <a href="http://geneontology.org/" target="_top"><img src="/images/logos/go-logo.mini.png" border=0 style="padding: 0px 5px 0px 5px;vertical-align: middle;border:0px"></a> <a href="https://globalbiodata.org/scientific-activities/global-core-biodata-resources" target="_top"><img src="/images/logos/GCBR-Logo-RGB.svg" border=0 width="94px" height="40px" style="vertical-align: middle;border:0px"></a> </DIV> </span> </td> </TR> <TR> <td align="center"> <span class="legal"> © Copyright 2024 Paul Thomas All Rights Reserved.</span> </td> </TR> </table> <br> <!-- Page Footer ends here --> </td></tr></table> <script language="JavaScript" type="text/javascript"> if (null === window.name || undefined === window.name) { window.name="panthermain"; } </script> <script language="JavaScript" type="text/javascript" src="/js/popout_window.js"></script> <script language="JavaScript" type="text/javascript" src="/js/cookie.js"></script> <script language="JavaScript" type="text/javascript" src="/js/pubPantherCommon.js"></script> <script language="JavaScript" type="text/javascript" src="/js/pathway.js"></script> <script language="JavaScript" type="text/javascript" src="/js/quicksearch.js"></script> <script language="JavaScript" type="text/javascript" src="/js/registration.js"></script> <script language="JavaScript" type="text/javascript" src="/js/subscription.js"></script> </div> <!-- footer div--> </body> </html>