Large-scale gene function analysis with the PANTHER classification system

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The system is built with 82 complete genomes organized into gene families and subfamilies, and their evolutionary relationships are captured in phylogenetic trees, multiple sequence alignments and statistical models (hidden Markov models or HMMs). Genes are classified according to their function in several different ways: families and subfamilies are annotated with ontology terms (Gene Ontology (GO) and PANTHER protein class), and sequences are assigned to PANTHER pathways. The PANTHER website includes a suite of tools that enable users to browse and query gene functions, and to analyze large-scale experimental data with a number of statistical tests. It is widely used by bench scientists, bioinformaticians, computer scientists and systems biologists. In the 2013 release of PANTHER (v.8.0), in addition to an update of the data content, we redesigned the website interface to improve both user experience and the system's analytical capability. 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data-test="authors-list" data-component-authors-activator="authors-list"><li class="c-article-author-list__item"><a data-test="author-name" data-track="click" data-track-action="open author" data-track-label="link" href="#auth-Huaiyu-Mi-Aff1" data-author-popup="auth-Huaiyu-Mi-Aff1" data-author-search="Mi, Huaiyu" data-corresp-id="c1">Huaiyu Mi<svg width="16" height="16" focusable="false" role="img" aria-hidden="true" class="u-icon"><use xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="#icon-eds-i-mail-medium"></use></svg></a><sup class="u-js-hide"><a href="#Aff1">1</a></sup>, </li><li class="c-article-author-list__item"><a data-test="author-name" data-track="click" data-track-action="open author" data-track-label="link" href="#auth-Anushya-Muruganujan-Aff1" data-author-popup="auth-Anushya-Muruganujan-Aff1" data-author-search="Muruganujan, Anushya">Anushya Muruganujan</a><sup class="u-js-hide"><a href="#Aff1">1</a></sup>, </li><li class="c-article-author-list__item 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xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="#icon-eds-i-chevron-down-medium"></use></svg><span>Show authors</span></button> <p class="c-article-info-details" data-container-section="info"> <a data-test="journal-link" href="/nprot" data-track="click" data-track-action="journal homepage" data-track-category="article body" data-track-label="link"><i data-test="journal-title">Nature Protocols</i></a> <b data-test="journal-volume"><span class="u-visually-hidden">volume</span> 8</b>, <span class="u-visually-hidden">pages </span>1551–1566 (<span data-test="article-publication-year">2013</span>)<a href="#citeas" class="c-article-info-details__cite-as u-hide-print" data-track="click" data-track-action="cite this article" data-track-label="link">Cite this article</a> </p> <div class="c-article-metrics-bar__wrapper u-clear-both"> <ul class="c-article-metrics-bar u-list-reset"> <li class=" c-article-metrics-bar__item" data-test="access-count"> <p class="c-article-metrics-bar__count">49k <span class="c-article-metrics-bar__label">Accesses</span></p> </li> <li class="c-article-metrics-bar__item" data-test="citation-count"> <p class="c-article-metrics-bar__count">1832 <span class="c-article-metrics-bar__label">Citations</span></p> </li> <li class="c-article-metrics-bar__item" data-test="altmetric-score"> <p class="c-article-metrics-bar__count">29 <span class="c-article-metrics-bar__label">Altmetric</span></p> </li> <li class="c-article-metrics-bar__item"> <p class="c-article-metrics-bar__details"><a href="/articles/nprot.2013.092/metrics" data-track="click" data-track-action="view metrics" data-track-label="link" rel="nofollow">Metrics <span class="u-visually-hidden">details</span></a></p> </li> </ul> </div> </header> <div class="u-js-hide" data-component="article-subject-links"> <h3 class="c-article__sub-heading">Subjects</h3> <ul class="c-article-subject-list"> <li class="c-article-subject-list__subject"><a href="/subjects/computational-platforms-and-environments" data-track="click" data-track-action="view subject" data-track-label="link">Computational platforms and environments</a></li><li class="c-article-subject-list__subject"><a href="/subjects/gene-ontology" data-track="click" data-track-action="view subject" data-track-label="link">Gene ontology</a></li><li class="c-article-subject-list__subject"><a href="/subjects/genomic-analysis" data-track="click" data-track-action="view subject" data-track-label="link">Genomic analysis</a></li><li class="c-article-subject-list__subject"><a href="/subjects/software" data-track="click" data-track-action="view subject" data-track-label="link">Software</a></li> </ul> </div> </div> <div class="c-article-body"> <section aria-labelledby="Abs1" data-title="Abstract" lang="en"><div class="c-article-section" id="Abs1-section"><h2 class="c-article-section__title js-section-title js-c-reading-companion-sections-item" id="Abs1">Abstract</h2><div class="c-article-section__content" id="Abs1-content"><p>The PANTHER (protein annotation through evolutionary relationship) classification system (<a href="http://www.pantherdb.org/">http://www.pantherdb.org/</a>) is a comprehensive system that combines gene function, ontology, pathways and statistical analysis tools that enable biologists to analyze large-scale, genome-wide data from sequencing, proteomics or gene expression experiments. The system is built with 82 complete genomes organized into gene families and subfamilies, and their evolutionary relationships are captured in phylogenetic trees, multiple sequence alignments and statistical models (hidden Markov models or HMMs). Genes are classified according to their function in several different ways: families and subfamilies are annotated with ontology terms (Gene Ontology (GO) and PANTHER protein class), and sequences are assigned to PANTHER pathways. The PANTHER website includes a suite of tools that enable users to browse and query gene functions, and to analyze large-scale experimental data with a number of statistical tests. It is widely used by bench scientists, bioinformaticians, computer scientists and systems biologists. In the 2013 release of PANTHER (v.8.0), in addition to an update of the data content, we redesigned the website interface to improve both user experience and the system's analytical capability. This protocol provides a detailed description of how to analyze genome-wide experimental data with the PANTHER classification system.</p></div></div></section> <noscript> <div class="c-nature-box c-nature-box--side " data-component="entitlement-box"> <div class="js-access-button"> <a href="https://wayf.springernature.com?redirect_uri=https%3A%2F%2Fwww.nature.com%2Farticles%2Fnprot.2013.092" class="c-article__button" data-test="ra21"> <svg class="u-icon" width="18" height="18" aria-hidden="true" focusable="false"><use href="#icon-institution"></use></svg> <span class="c-article__button-text">Access through your institution</span> </a> </div> <div class="js-buy-button"> <a href="#access-options" class="c-article__button c-article__button--inverted" data-test="ra21"> <span>Buy or subscribe</span> </a> </div> </div> </noscript> <div class="js-context-bar-sticky-point-mobile" data-track-context="article body"> </div> <div class="c-article-access-provider u-mb-32 u-mt-0"> <p 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body" data-track-label="link">Contact customer support</a> </li> </ul> </nav> <div class="u-display-none"> <div class="c-article-section__figure js-c-reading-companion-figures-item" data-test="figure" data-container-section="figure" id="figure-1"><figure><figcaption><b id="Fig1" class="c-article-section__figure-caption" data-test="figure-caption-text">Figure 1: Overview of PANTHER infrastructure.</b></figcaption><div class="c-article-section__figure-content"><div class="c-article-section__figure-item"><picture><source type="image/webp" srcset="//media.springernature.com/m312/springer-static/image/art%3A10.1038%2Fnprot.2013.092/MediaObjects/41596_2013_Article_BFnprot2013092_Fig1_HTML.jpg?as=webp"><img src="//media.springernature.com/m312/springer-static/image/art%3A10.1038%2Fnprot.2013.092/MediaObjects/41596_2013_Article_BFnprot2013092_Fig1_HTML.jpg" alt="" loading="lazy" width="312" height="189"></picture></div></div></figure></div><div class="c-article-section__figure js-c-reading-companion-figures-item" data-test="figure" data-container-section="figure" id="figure-2"><figure><figcaption><b id="Fig2" class="c-article-section__figure-caption" data-test="figure-caption-text">Figure 2: Sample phylogenetic tree from PANTHER.</b></figcaption><div class="c-article-section__figure-content"><div class="c-article-section__figure-item"><picture><source type="image/webp" srcset="//media.springernature.com/m312/springer-static/image/art%3A10.1038%2Fnprot.2013.092/MediaObjects/41596_2013_Article_BFnprot2013092_Fig2_HTML.jpg?as=webp"><img src="//media.springernature.com/m312/springer-static/image/art%3A10.1038%2Fnprot.2013.092/MediaObjects/41596_2013_Article_BFnprot2013092_Fig2_HTML.jpg" alt="" loading="lazy" width="312" height="172"></picture></div></div></figure></div><div class="c-article-section__figure js-c-reading-companion-figures-item" data-test="figure" data-container-section="figure" id="figure-3"><figure><figcaption><b id="Fig3" class="c-article-section__figure-caption" data-test="figure-caption-text">Figure 3: Example of a PANTHER pathway diagram.</b></figcaption><div class="c-article-section__figure-content"><div class="c-article-section__figure-item"><picture><source type="image/webp" srcset="//media.springernature.com/m312/springer-static/image/art%3A10.1038%2Fnprot.2013.092/MediaObjects/41596_2013_Article_BFnprot2013092_Fig3_HTML.jpg?as=webp"><img src="//media.springernature.com/m312/springer-static/image/art%3A10.1038%2Fnprot.2013.092/MediaObjects/41596_2013_Article_BFnprot2013092_Fig3_HTML.jpg" alt="" loading="lazy" width="312" height="230"></picture></div></div></figure></div><div class="c-article-section__figure js-c-reading-companion-figures-item" data-test="figure" data-container-section="figure" id="figure-4"><figure><figcaption><b id="Fig4" class="c-article-section__figure-caption" data-test="figure-caption-text">Figure 4</b></figcaption><div class="c-article-section__figure-content"><div class="c-article-section__figure-item"><picture><source type="image/webp" srcset="//media.springernature.com/m312/springer-static/image/art%3A10.1038%2Fnprot.2013.092/MediaObjects/41596_2013_Article_BFnprot2013092_Fig4_HTML.jpg?as=webp"><img src="//media.springernature.com/m312/springer-static/image/art%3A10.1038%2Fnprot.2013.092/MediaObjects/41596_2013_Article_BFnprot2013092_Fig4_HTML.jpg" alt="" loading="lazy" width="312" height="237"></picture></div></div></figure></div><div class="c-article-section__figure js-c-reading-companion-figures-item" data-test="figure" data-container-section="figure" id="figure-7"><figure><figcaption><b id="Fig7" class="c-article-section__figure-caption" data-test="figure-caption-text">Figure 7</b></figcaption><div class="c-article-section__figure-content"><div class="c-article-section__figure-item"><picture><source type="image/webp" srcset="//media.springernature.com/m312/springer-static/image/art%3A10.1038%2Fnprot.2013.092/MediaObjects/41596_2013_Article_BFnprot2013092_Fig7_HTML.jpg?as=webp"><img src="//media.springernature.com/m312/springer-static/image/art%3A10.1038%2Fnprot.2013.092/MediaObjects/41596_2013_Article_BFnprot2013092_Fig7_HTML.jpg" alt="" loading="lazy" width="312" height="137"></picture></div></div></figure></div><div class="c-article-section__figure js-c-reading-companion-figures-item" data-test="figure" data-container-section="figure" id="figure-8"><figure><figcaption><b id="Fig8" class="c-article-section__figure-caption" data-test="figure-caption-text">Figure 8: Summary of the results from the statistical overrepresentation test displayed in a table.</b></figcaption><div class="c-article-section__figure-content"><div class="c-article-section__figure-item"><picture><source type="image/webp" srcset="//media.springernature.com/m312/springer-static/image/art%3A10.1038%2Fnprot.2013.092/MediaObjects/41596_2013_Article_BFnprot2013092_Fig8_HTML.jpg?as=webp"><img src="//media.springernature.com/m312/springer-static/image/art%3A10.1038%2Fnprot.2013.092/MediaObjects/41596_2013_Article_BFnprot2013092_Fig8_HTML.jpg" alt="" loading="lazy" width="312" height="217"></picture></div></div></figure></div><div class="c-article-section__figure js-c-reading-companion-figures-item" data-test="figure" data-container-section="figure" id="figure-9"><figure><figcaption><b id="Fig9" class="c-article-section__figure-caption" data-test="figure-caption-text">Figure 9: Results from the statistical enrichment test.</b></figcaption><div class="c-article-section__figure-content"><div class="c-article-section__figure-item"><picture><source type="image/webp" srcset="//media.springernature.com/m312/springer-static/image/art%3A10.1038%2Fnprot.2013.092/MediaObjects/41596_2013_Article_BFnprot2013092_Fig9_HTML.jpg?as=webp"><img src="//media.springernature.com/m312/springer-static/image/art%3A10.1038%2Fnprot.2013.092/MediaObjects/41596_2013_Article_BFnprot2013092_Fig9_HTML.jpg" alt="" loading="lazy" width="312" height="226"></picture></div></div></figure></div><div class="c-article-section__figure js-c-reading-companion-figures-item" data-test="figure" data-container-section="figure" id="figure-10"><figure><figcaption><b id="Fig10" class="c-article-section__figure-caption" data-test="figure-caption-text">Figure 10: Graph view of results from the statistical enrichment test.</b></figcaption><div class="c-article-section__figure-content"><div class="c-article-section__figure-item"><picture><source type="image/webp" srcset="//media.springernature.com/m312/springer-static/image/art%3A10.1038%2Fnprot.2013.092/MediaObjects/41596_2013_Article_BFnprot2013092_Fig10_HTML.jpg?as=webp"><img src="//media.springernature.com/m312/springer-static/image/art%3A10.1038%2Fnprot.2013.092/MediaObjects/41596_2013_Article_BFnprot2013092_Fig10_HTML.jpg" alt="" loading="lazy" width="312" height="210"></picture></div></div></figure></div><div class="c-article-section__figure js-c-reading-companion-figures-item" data-test="figure" data-container-section="figure" id="figure-11"><figure><figcaption><b id="Fig11" class="c-article-section__figure-caption" data-test="figure-caption-text">Figure 11: Results from the statistical enrichment test as visualized in the pathway diagram.</b></figcaption><div class="c-article-section__figure-content"><div class="c-article-section__figure-item"><picture><source type="image/webp" srcset="//media.springernature.com/m312/springer-static/image/art%3A10.1038%2Fnprot.2013.092/MediaObjects/41596_2013_Article_BFnprot2013092_Fig11_HTML.jpg?as=webp"><img src="//media.springernature.com/m312/springer-static/image/art%3A10.1038%2Fnprot.2013.092/MediaObjects/41596_2013_Article_BFnprot2013092_Fig11_HTML.jpg" alt="" loading="lazy" width="312" height="282"></picture></div></div></figure></div><div class="c-article-section__figure js-c-reading-companion-figures-item" data-test="figure" data-container-section="figure" id="figure-5"><figure><figcaption><b id="Fig5" class="c-article-section__figure-caption" data-test="figure-caption-text">Figure 5: Results of functional classification displayed as a gene list page.</b></figcaption><div class="c-article-section__figure-content"><div class="c-article-section__figure-item"><picture><source type="image/webp" srcset="//media.springernature.com/m312/springer-static/image/art%3A10.1038%2Fnprot.2013.092/MediaObjects/41596_2013_Article_BFnprot2013092_Fig5_HTML.jpg?as=webp"><img src="//media.springernature.com/m312/springer-static/image/art%3A10.1038%2Fnprot.2013.092/MediaObjects/41596_2013_Article_BFnprot2013092_Fig5_HTML.jpg" alt="" loading="lazy" width="312" height="168"></picture></div></div></figure></div><div class="c-article-section__figure js-c-reading-companion-figures-item" data-test="figure" data-container-section="figure" id="figure-6"><figure><figcaption><b id="Fig6" class="c-article-section__figure-caption" data-test="figure-caption-text">Figure 6: PANTHER pie chart results using <a data-track="click" data-track-label="link" data-track-action="supplementary material anchor" href="/articles/nprot.2013.092#MOESM459">Supplementary Data 1</a> as the input gene list file.</b></figcaption><div class="c-article-section__figure-content"><div class="c-article-section__figure-item"><picture><source type="image/webp" srcset="//media.springernature.com/m312/springer-static/image/art%3A10.1038%2Fnprot.2013.092/MediaObjects/41596_2013_Article_BFnprot2013092_Fig6_HTML.jpg?as=webp"><img src="//media.springernature.com/m312/springer-static/image/art%3A10.1038%2Fnprot.2013.092/MediaObjects/41596_2013_Article_BFnprot2013092_Fig6_HTML.jpg" alt="" loading="lazy" width="312" height="178"></picture></div></div></figure></div><div class="c-article-section__figure js-c-reading-companion-figures-item" data-test="figure" data-container-section="figure" id="figure-12"><figure><figcaption><b id="Fig12" class="c-article-section__figure-caption" data-test="figure-caption-text">Figure 12: Results of the statistical overrepresentation test viewed in the PANTHER pathway, 'Heterotrimeric G protein signaling pathway – G<sub>i</sub>-α and G<sub>s</sub>-α–mediated pathway (PANTHER accession code <a href="http://www.pantherdb.org/pathway/pathwayDiagram.jsp?catAccession=P00026">P00026</a>)'.</b></figcaption><div class="c-article-section__figure-content"><div class="c-article-section__figure-item"><picture><source type="image/webp" srcset="//media.springernature.com/m312/springer-static/image/art%3A10.1038%2Fnprot.2013.092/MediaObjects/41596_2013_Article_BFnprot2013092_Fig12_HTML.jpg?as=webp"><img src="//media.springernature.com/m312/springer-static/image/art%3A10.1038%2Fnprot.2013.092/MediaObjects/41596_2013_Article_BFnprot2013092_Fig12_HTML.jpg" alt="" loading="lazy" width="312" height="172"></picture></div></div></figure></div> </div> <section aria-labelledby="inline-recommendations" data-title="Inline Recommendations" class="c-article-recommendations" data-track-component="inline-recommendations"> <h3 class="c-article-recommendations-title" id="inline-recommendations">Similar content being viewed by others</h3> <div class="c-article-recommendations-list"> <div 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McAnulla and M. Martin, for their support in providing up-to-date Reference Proteome data set, and we thank Y. Matsuoka and K. Manami from the Systems Biology Institute Japan for their support on CellDesigner and pathway file update. This work is supported by the US National Institutes of Health (NIH)/National Institute of General Medical Sciences (NIGMS) grant no. GM081084 to P.D.T. Funding for open access was provided by the University of Southern California.</p></div></div></section><section aria-labelledby="author-information" data-title="Author information"><div class="c-article-section" id="author-information-section"><h2 class="c-article-section__title js-section-title js-c-reading-companion-sections-item" id="author-information">Author information</h2><div class="c-article-section__content" id="author-information-content"><h3 class="c-article__sub-heading" id="affiliations">Authors and Affiliations</h3><ol class="c-article-author-affiliation__list"><li id="Aff1"><p class="c-article-author-affiliation__address">Department of Preventive Medicine, Division of Bioinformatics, Keck School of Medicine, University of Southern California, Los Angeles, California, USA</p><p class="c-article-author-affiliation__authors-list">Huaiyu Mi, Anushya Muruganujan, John T Casagrande & Paul D Thomas</p></li></ol><div class="u-js-hide u-hide-print" data-test="author-info"><span class="c-article__sub-heading">Authors</span><ol class="c-article-authors-search u-list-reset"><li id="auth-Huaiyu-Mi-Aff1"><span class="c-article-authors-search__title u-h3 js-search-name">Huaiyu Mi</span><div class="c-article-authors-search__list"><div class="c-article-authors-search__item c-article-authors-search__list-item--left"><a href="/search?author=Huaiyu%20Mi" class="c-article-button" data-track="click" data-track-action="author link - publication" data-track-label="link" rel="nofollow">View author publications</a></div><div class="c-article-authors-search__item c-article-authors-search__list-item--right"><p class="search-in-title-js c-article-authors-search__text">You can also search for this author in <span class="c-article-identifiers"><a class="c-article-identifiers__item" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=search&term=Huaiyu%20Mi" data-track="click" data-track-action="author link - pubmed" data-track-label="link" rel="nofollow">PubMed</a><span class="u-hide"> </span><a class="c-article-identifiers__item" href="http://scholar.google.co.uk/scholar?as_q=&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_sauthors=%22Huaiyu%20Mi%22&as_publication=&as_ylo=&as_yhi=&as_allsubj=all&hl=en" data-track="click" data-track-action="author link - scholar" data-track-label="link" rel="nofollow">Google Scholar</a></span></p></div></div></li><li id="auth-Anushya-Muruganujan-Aff1"><span class="c-article-authors-search__title u-h3 js-search-name">Anushya Muruganujan</span><div class="c-article-authors-search__list"><div class="c-article-authors-search__item c-article-authors-search__list-item--left"><a href="/search?author=Anushya%20Muruganujan" class="c-article-button" data-track="click" data-track-action="author link - publication" data-track-label="link" rel="nofollow">View author publications</a></div><div class="c-article-authors-search__item c-article-authors-search__list-item--right"><p class="search-in-title-js c-article-authors-search__text">You can also search for this author in <span class="c-article-identifiers"><a class="c-article-identifiers__item" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=search&term=Anushya%20Muruganujan" data-track="click" data-track-action="author link - pubmed" data-track-label="link" rel="nofollow">PubMed</a><span class="u-hide"> </span><a class="c-article-identifiers__item" href="http://scholar.google.co.uk/scholar?as_q=&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_sauthors=%22Anushya%20Muruganujan%22&as_publication=&as_ylo=&as_yhi=&as_allsubj=all&hl=en" data-track="click" data-track-action="author link - scholar" data-track-label="link" rel="nofollow">Google Scholar</a></span></p></div></div></li><li id="auth-John_T-Casagrande-Aff1"><span class="c-article-authors-search__title u-h3 js-search-name">John T Casagrande</span><div class="c-article-authors-search__list"><div class="c-article-authors-search__item c-article-authors-search__list-item--left"><a href="/search?author=John%20T%20Casagrande" class="c-article-button" data-track="click" data-track-action="author link - publication" data-track-label="link" rel="nofollow">View author publications</a></div><div class="c-article-authors-search__item c-article-authors-search__list-item--right"><p class="search-in-title-js c-article-authors-search__text">You can also search for this author in <span class="c-article-identifiers"><a class="c-article-identifiers__item" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=search&term=John%20T%20Casagrande" data-track="click" data-track-action="author link - pubmed" data-track-label="link" rel="nofollow">PubMed</a><span class="u-hide"> </span><a class="c-article-identifiers__item" href="http://scholar.google.co.uk/scholar?as_q=&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_sauthors=%22John%20T%20Casagrande%22&as_publication=&as_ylo=&as_yhi=&as_allsubj=all&hl=en" data-track="click" data-track-action="author link - scholar" data-track-label="link" rel="nofollow">Google Scholar</a></span></p></div></div></li><li id="auth-Paul_D-Thomas-Aff1"><span class="c-article-authors-search__title u-h3 js-search-name">Paul D Thomas</span><div class="c-article-authors-search__list"><div class="c-article-authors-search__item c-article-authors-search__list-item--left"><a href="/search?author=Paul%20D%20Thomas" class="c-article-button" data-track="click" data-track-action="author link - 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J.T.C. maintained the database and web servers. H.M. generated the content of the system and supervised the project. P.D.T. provided the funding and supervised the project. H.M. wrote the manuscript with contributions from all the authors.</p><h3 class="c-article__sub-heading" id="corresponding-author">Corresponding author</h3><p id="corresponding-author-list">Correspondence to <a id="corresp-c1" href="mailto:huaiyumi@usc.edu">Huaiyu Mi</a>.</p></div></div></section><section data-title="Ethics declarations"><div class="c-article-section" id="ethics-section"><h2 class="c-article-section__title js-section-title js-c-reading-companion-sections-item" id="ethics">Ethics declarations</h2><div class="c-article-section__content" id="ethics-content"> <h3 class="c-article__sub-heading">Competing interests</h3> <p>The authors declare no competing financial interests.</p> </div></div></section><section data-title="Supplementary information"><div class="c-article-section" id="Sec25-section"><h2 class="c-article-section__title js-section-title js-c-reading-companion-sections-item" id="Sec25">Supplementary information</h2><div class="c-article-section__content" id="Sec25-content"><div data-test="supplementary-info"><div id="figshareContainer" class="c-article-figshare-container" data-test="figshare-container"></div><div class="c-article-supplementary__item" data-test="supp-item" id="MOESM459"><h3 class="c-article-supplementary__title u-h3"><a class="print-link" data-track="click" data-track-action="view supplementary info" data-test="supp-info-link" data-track-label="supplementary data 1" href="https://static-content.springer.com/esm/art%3A10.1038%2Fnprot.2013.092/MediaObjects/41596_2013_BFnprot2013092_MOESM459_ESM.txt" data-supp-info-image="">Supplementary Data 1</a></h3><div class="c-article-supplementary__description" data-component="thumbnail-container"><p>File containing 555 gene IDs, 500 of which can be classified in PANTHER. It can be used as a sample upload file to test the functional classification tools and the overrepresentation tool. (TXT 10 kb)</p></div></div><div class="c-article-supplementary__item" data-test="supp-item" id="MOESM460"><h3 class="c-article-supplementary__title u-h3"><a class="print-link" data-track="click" data-track-action="view supplementary info" data-test="supp-info-link" data-track-label="supplementary data 2" href="https://static-content.springer.com/esm/art%3A10.1038%2Fnprot.2013.092/MediaObjects/41596_2013_BFnprot2013092_MOESM460_ESM.txt" data-supp-info-image="">Supplementary Data 2</a></h3><div class="c-article-supplementary__description" data-component="thumbnail-container"><p>File containing 19,911 genes, with IDs in the first column and numeric experimental values in the second column. This file can be used as a sample upload file for all tools. 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Large-scale gene function analysis with the PANTHER classification system | Nature Protocols