{"id":11,"date":"2018-01-19T21:31:11","date_gmt":"2018-01-19T21:31:11","guid":{"rendered":"http:\/\/gero.usc.edu\/labs\/benayounlab\/?page_id=11"},"modified":"2024-12-16T22:05:37","modified_gmt":"2024-12-16T22:05:37","slug":"databases-and-other-resources","status":"publish","type":"page","link":"https:\/\/gero.usc.edu\/labs\/benayounlab\/databases-and-other-resources\/","title":{"rendered":"Databases and other resources"},"content":{"rendered":"<div class=\"wpb-content-wrapper\"><p>[vc_row][vc_column][vc_empty_space][\/vc_column][\/vc_row][vc_row][vc_column width=&#8221;1\/2&#8243;][vc_column_text css=&#8221;&#8221;]<\/p>\n<h3>Online Databases<\/h3>\n<p>&nbsp;<\/p>\n<p><strong>Databases on aging:<\/strong><\/p>\n<ul>\n<li><a href=\"http:\/\/genomics.senescence.info\/\" target=\"_blank\" rel=\"noopener\">Human Ageing Genomic Resources<\/a><\/li>\n<li><a href=\"http:\/\/lifespandb.sageweb.org\/\" target=\"_blank\" rel=\"noopener\">Lifespan observation database<\/a><\/li>\n<li><a href=\"http:\/\/info-centre.jenage.de\/ageing\/databases.html\" target=\"_blank\" rel=\"noopener\">Age related databases (JenAge)<\/a><\/li>\n<li><a href=\"http:\/\/ageing-map.org\/\" target=\"_blank\" rel=\"noopener\">Digital Ageing Atlas<\/a>\u200b<\/li>\n<\/ul>\n<p>&nbsp;<\/p>\n<p><strong>Genome browsers:<\/strong><\/p>\n<ul>\n<li><a href=\"https:\/\/genome.ucsc.edu\/\" target=\"_blank\" rel=\"noopener\">UCSC Genome Browser<\/a><\/li>\n<li><a href=\"http:\/\/www.ensembl.org\/index.html\" target=\"_blank\" rel=\"noopener\">ENSEMBL Genome Browser<\/a><\/li>\n<li><a href=\"https:\/\/www.ncbi.nlm.nih.gov\/genome\/\" target=\"_blank\" rel=\"noopener\">NCBI Genome<\/a><\/li>\n<li><a href=\"http:\/\/africanturquoisekillifishbrowser.org\/\" target=\"_blank\" rel=\"noopener\">African Turquoise Killifish Genome Browser<\/a><\/li>\n<li><a href=\"http:\/\/www.informatics.jax.org\/\" target=\"_blank\" rel=\"noopener\">Mouse Genome Informatics at JAX<\/a><\/li>\n<\/ul>\n<p>&nbsp;<\/p>\n<p><strong>Interaction and network databases:<\/strong><\/p>\n<ul>\n<li><a href=\"https:\/\/thebiogrid.org\/\" target=\"_blank\" rel=\"noopener\">BioGriD project<\/a><\/li>\n<li><a href=\"https:\/\/string-db.org\/\" target=\"_blank\" rel=\"noopener\">STRING<\/a><\/li>\n<li><a href=\"http:\/\/www.actrec.gov.in\/histome\/index.php\" target=\"_blank\" rel=\"noopener\">Histome<\/a><\/li>\n<li><a href=\"http:\/\/genemania.org\/\" target=\"_blank\" rel=\"noopener\">GeneMania<\/a><\/li>\n<\/ul>\n<p>&nbsp;<\/p>\n<p><strong>Pathway informations:<\/strong><\/p>\n<ul>\n<li><a href=\"http:\/\/www.geneontology.org\/page\/download-annotations\" target=\"_blank\" rel=\"noopener\">Gene Ontology Consortium<\/a><\/li>\n<li><a href=\"http:\/\/www.genome.jp\/kegg\/pathway.html\" target=\"_blank\" rel=\"noopener\">KEGG<\/a><\/li>\n<li><a href=\"http:\/\/www.wikipathways.org\/index.php\/WikiPathways\" target=\"_blank\" rel=\"noopener\">Wikipathways<\/a><\/li>\n<li><a href=\"http:\/\/software.broadinstitute.org\/gsea\/msigdb\" target=\"_blank\" rel=\"noopener\">GSEA\/MSigDB<\/a><\/li>\n<li><a href=\"http:\/\/www.reactome.org\/\" target=\"_blank\" rel=\"noopener\">REACTOME<\/a><\/li>\n<li><a href=\"https:\/\/cgap.nci.nih.gov\/Pathways\/BioCarta_Pathways\" target=\"_blank\" rel=\"noopener\">Biocarta<\/a><\/li>\n<li><a href=\"http:\/\/www.pantherdb.org\/pathway\/\" target=\"_blank\" rel=\"noopener\">Panther<\/a><\/li>\n<li><a href=\"https:\/\/clue.io\/\" target=\"_blank\" rel=\"noopener\">ConnectivityMap<\/a><\/li>\n<li><a href=\"https:\/\/gtexportal.org\/home\/\" target=\"_blank\" rel=\"noopener\">GTEX<\/a><\/li>\n<li><a href=\"http:\/\/www.omim.org\/downloads\/\" target=\"_blank\" rel=\"noopener\">OMIM\u200b<\/a><\/li>\n<\/ul>\n<p>&nbsp;<\/p>\n<p><strong>Transcription factors, target genes and motifs:<\/strong><\/p>\n<ul>\n<li><a href=\"http:\/\/cisreg.cmmt.ubc.ca\/cgi-bin\/tfe\/home.pl\" target=\"_blank\" rel=\"noopener\">Transcription Factor Encyclopedia<\/a><\/li>\n<li><a href=\"http:\/\/jaspar.genereg.net\/\" target=\"_blank\" rel=\"noopener\">JASPAR<\/a>\u00a0(TF motifs)<\/li>\n<li><a href=\"http:\/\/gene-regulation.com\/index.html\" target=\"_blank\" rel=\"noopener\">TRANSFAC<\/a>\u00a0(TF motifs)<\/li>\n<li><a href=\"http:\/\/www.benoslab.pitt.edu\/stamp\/\" target=\"_blank\" rel=\"noopener\">STAMP<\/a>\u00a0(motif clustering and alignement)<\/li>\n<li><a href=\"http:\/\/amp.pharm.mssm.edu\/lib\/chea.jsp\" target=\"_blank\" rel=\"noopener\">ChEA<\/a>\u00a0(Curated TF binding from ChIP-X experiments)<\/li>\n<li><a href=\"http:\/\/tagc.univ-mrs.fr\/remap\/\" target=\"_blank\" rel=\"noopener\">ReMap2018<\/a>\u00a0(Curated TF binding from ChIP-X experiments)\u200b<\/li>\n<\/ul>\n<p>&nbsp;<\/p>\n<p><strong>Epigenomics resources:<\/strong><\/p>\n<ul>\n<li><a href=\"http:\/\/genome.ucsc.edu\/ENCODE\/downloads.html\" target=\"_blank\" rel=\"noopener\">ENCODE<\/a><\/li>\n<li><a href=\"http:\/\/www.roadmapepigenomics.org\/\" target=\"_blank\" rel=\"noopener\">NIH Roadmap<\/a><\/li>\n<li><a href=\"http:\/\/epigenomegateway.wustl.edu\/\" target=\"_blank\" rel=\"noopener\">WashU Epigenome Browser<\/a><\/li>\n<li><a href=\"http:\/\/www.modencode.org\/\" target=\"_blank\" rel=\"noopener\">ModEncode<\/a><\/li>\n<\/ul>\n<p>&nbsp;<\/p>\n<p><strong>Genomic data repositories:<\/strong><\/p>\n<ul>\n<li><a href=\"https:\/\/www.ncbi.nlm.nih.gov\/geo\/\" target=\"_blank\" rel=\"noopener\">GEO Datasets<\/a><\/li>\n<li><a href=\"https:\/\/www.ebi.ac.uk\/arrayexpress\/\" target=\"_blank\" rel=\"noopener\">ArrayExpress<\/a><\/li>\n<li><a href=\"http:\/\/dc2.cistrome.org\/#\/\" target=\"_blank\" rel=\"noopener\">CistromeMap<\/a><\/li>\n<li><a href=\"https:\/\/www.ncbi.nlm.nih.gov\/sra\" target=\"_blank\" rel=\"noopener\">SRA<\/a><\/li>\n<\/ul>\n<p>[\/vc_column_text][\/vc_column][vc_column width=&#8221;1\/2&#8243;][vc_column_text css=&#8221;&#8221;]<\/p>\n<h3>Other Important Resources<\/h3>\n<p>&nbsp;<\/p>\n<p><strong>Transgenic mouse ordering:<\/strong><\/p>\n<ul>\n<li><a href=\"https:\/\/www.jax.org\/mouse-search?p=205:1:10007901312284558903\" target=\"_blank\" rel=\"noopener\">JAX mouse search<\/a><\/li>\n<li><a href=\"https:\/\/www.komp.org\/index.php\" target=\"_blank\" rel=\"noopener\">UC Davis Knock-Out Mouse Project (KOMP)<\/a><\/li>\n<li><a href=\"http:\/\/www.findmice.org\/index\" target=\"_blank\" rel=\"noopener\">International Mouse Strain Resource<\/a><\/li>\n<\/ul>\n<p>&nbsp;<\/p>\n<p><strong>Literature resources:<\/strong><\/p>\n<ul>\n<li><a href=\"http:\/\/nml.usc.edu\/\" target=\"_blank\" rel=\"noopener\">Norris Medical Library<\/a><\/li>\n<li><a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/\" target=\"_blank\" rel=\"noopener\">Pubmed<\/a><\/li>\n<li><a href=\"http:\/\/www.mousemine.org\/mousemine\/begin.do;jsessionid=7BD5ACCCE6BFE41DE9BB900E1B5F248C\" target=\"_blank\" rel=\"noopener\">MouseMine<\/a><\/li>\n<li><a href=\"http:\/\/www.informatics.jax.org\/silver\/contents.shtml\" target=\"_blank\" rel=\"noopener\">Mouse Genetics\u00a0(Lee M. Silver) at MGI<\/a><\/li>\n<li><a href=\"http:\/\/www.nature.com.libproxy1.usc.edu\/collections\/qghhqm\" target=\"_blank\" rel=\"noopener\">Statistics for biologists (Nature Methods)<\/a><\/li>\n<li><a href=\"http:\/\/pubcrawler.gen.tcd.ie\/\" target=\"_blank\" rel=\"noopener\">PubCrawler<\/a>\u00a0(Alert Service for PubMed and GenBank)<\/li>\n<li><a href=\"http:\/\/iclac.org\/databases\/cross-contaminations\/\" target=\"_blank\" rel=\"noopener\">Commonly misidentified cell lines<\/a><\/li>\n<\/ul>\n<p>&nbsp;<\/p>\n<p><strong>Protocol resources:<\/strong><\/p>\n<ul>\n<li><a href=\"http:\/\/www.worthington-biochem.com\/tissuedissociation\/usetested.html\" target=\"_blank\" rel=\"noopener\">Worthington tissue dissociation guide<\/a><\/li>\n<li><a href=\"https:\/\/support.10xgenomics.com\/single-cell-gene-expression\" target=\"_blank\" rel=\"noopener\">10xGenomics protocol resources<\/a><\/li>\n<\/ul>\n<p>&nbsp;<\/p>\n<p><strong>Plasmid databases\/ordering:<\/strong><\/p>\n<ul>\n<li><a href=\"http:\/\/www.addgene.org\/\" target=\"_blank\" rel=\"noopener\">Addgene<\/a><\/li>\n<li><a href=\"http:\/\/www.sigmabioinfo.com\/Informatics_tools\/batch-search.php#shRNA\" target=\"_blank\" rel=\"noopener\">Sigma Mission shRNA search tool<\/a><\/li>\n<\/ul>\n<p>&nbsp;<\/p>\n<p><strong>Antibody validation databases:<\/strong><\/p>\n<ul>\n<li><a href=\"http:\/\/compbio.med.harvard.edu\/antibodies\/\" target=\"_blank\" rel=\"noopener\">The Antibody Validation Database<\/a><\/li>\n<li><a href=\"https:\/\/genome.ucsc.edu\/encode\/antibodies.html\" target=\"_blank\" rel=\"noopener\">ENCODE validated antibodies<\/a><\/li>\n<\/ul>\n<p>&nbsp;<\/p>\n<p><strong>Validated qPCR primer repositories:<\/strong><\/p>\n<ul>\n<li><a href=\"https:\/\/pga.mgh.harvard.edu\/primerbank\/index.html\" target=\"_blank\" rel=\"noopener\">PrimerBank<\/a><\/li>\n<li><a href=\"https:\/\/pga.mgh.harvard.edu\/primerbank\/index.html\" target=\"_blank\" rel=\"noopener\">RTPrimerDB<\/a><\/li>\n<li><a href=\"https:\/\/mouseprimerdepot.nci.nih.gov\/\" target=\"_blank\" rel=\"noopener\">Mouse qPCR primer depot<\/a>\u00a0(in silico)<\/li>\n<\/ul>\n<p>&nbsp;<\/p>\n<p><strong>Molecular cloning resources:<\/strong><\/p>\n<ul>\n<li><a href=\"http:\/\/nc2.neb.com\/NEBcutter2\/\" target=\"_blank\" rel=\"noopener\">NEBCutter2.0<\/a><\/li>\n<li><a href=\"https:\/\/www.neb.com\/tools-and-resources\/usage-guidelines\/cloning-guide\" target=\"_blank\" rel=\"noopener\">NEB traditional cloning guide<\/a><\/li>\n<li><a href=\"http:\/\/www.snapgene.com\/products\/snapgene_viewer\/\" target=\"_blank\" rel=\"noopener\">SnapGene Viewer<\/a>\u00a0(Plasmid map annotation)<\/li>\n<\/ul>\n<p>&nbsp;<\/p>\n<p><strong>Online Protocol resources:<\/strong><\/p>\n<ul>\n<li><a href=\"http:\/\/groups.molbiosci.northwestern.edu\/morimoto\/research\/protocols.html\">Morimoto Lab protocols<\/a><\/li>\n<\/ul>\n<p>[\/vc_column_text][\/vc_column][\/vc_row]<\/p>\n<\/div>","protected":false},"excerpt":{"rendered":"<p>[vc_row][vc_column][vc_empty_space][\/vc_column][\/vc_row][vc_row][vc_column width=&#8221;1\/2&#8243;][vc_column_text css=&#8221;&#8221;] Online Databases &nbsp; Databases on aging: Human Ageing Genomic Resources Lifespan observation database Age related databases (JenAge) Digital Ageing Atlas\u200b &nbsp; Genome browsers: UCSC Genome Browser ENSEMBL Genome Browser NCBI Genome African Turquoise Killifish Genome Browser Mouse Genome Informatics at JAX &nbsp; Interaction and network databases: BioGriD project STRING Histome GeneMania &nbsp; [&hellip;]<\/p>\n","protected":false},"author":1,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"page-full.php","meta":{"_acf_changed":false,"footnotes":""},"class_list":["post-11","page","type-page","status-publish","hentry"],"acf":[],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v27.3 - https:\/\/yoast.com\/product\/yoast-seo-wordpress\/ -->\n<title>Databases and other resources - The Benayoun Lab<\/title>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" href=\"https:\/\/gero.usc.edu\/labs\/benayounlab\/databases-and-other-resources\/\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Databases and other resources - The Benayoun Lab\" \/>\n<meta property=\"og:description\" content=\"[vc_row][vc_column][vc_empty_space][\/vc_column][\/vc_row][vc_row][vc_column width=&#8221;1\/2&#8243;][vc_column_text css=&#8221;&#8221;] Online Databases &nbsp; Databases on aging: Human Ageing Genomic Resources Lifespan observation database Age related databases (JenAge) Digital Ageing Atlas\u200b &nbsp; Genome browsers: UCSC Genome Browser ENSEMBL Genome Browser NCBI Genome African Turquoise Killifish Genome Browser Mouse Genome Informatics at JAX &nbsp; Interaction and network databases: BioGriD project STRING Histome GeneMania &nbsp; [&hellip;]\" \/>\n<meta property=\"og:url\" content=\"https:\/\/gero.usc.edu\/labs\/benayounlab\/databases-and-other-resources\/\" \/>\n<meta property=\"og:site_name\" content=\"The Benayoun Lab\" \/>\n<meta property=\"article:modified_time\" content=\"2024-12-16T22:05:37+00:00\" \/>\n<meta name=\"twitter:card\" content=\"summary_large_image\" \/>\n<meta name=\"twitter:label1\" content=\"Est. reading time\" \/>\n\t<meta name=\"twitter:data1\" content=\"1 minute\" \/>\n<script type=\"application\/ld+json\" class=\"yoast-schema-graph\">{\"@context\":\"https:\\\/\\\/schema.org\",\"@graph\":[{\"@type\":\"WebPage\",\"@id\":\"https:\\\/\\\/gero.usc.edu\\\/labs\\\/benayounlab\\\/databases-and-other-resources\\\/\",\"url\":\"https:\\\/\\\/gero.usc.edu\\\/labs\\\/benayounlab\\\/databases-and-other-resources\\\/\",\"name\":\"Databases and other resources - The Benayoun Lab\",\"isPartOf\":{\"@id\":\"https:\\\/\\\/gero.usc.edu\\\/labs\\\/benayounlab\\\/#website\"},\"datePublished\":\"2018-01-19T21:31:11+00:00\",\"dateModified\":\"2024-12-16T22:05:37+00:00\",\"breadcrumb\":{\"@id\":\"https:\\\/\\\/gero.usc.edu\\\/labs\\\/benayounlab\\\/databases-and-other-resources\\\/#breadcrumb\"},\"inLanguage\":\"en-US\",\"potentialAction\":[{\"@type\":\"ReadAction\",\"target\":[\"https:\\\/\\\/gero.usc.edu\\\/labs\\\/benayounlab\\\/databases-and-other-resources\\\/\"]}]},{\"@type\":\"BreadcrumbList\",\"@id\":\"https:\\\/\\\/gero.usc.edu\\\/labs\\\/benayounlab\\\/databases-and-other-resources\\\/#breadcrumb\",\"itemListElement\":[{\"@type\":\"ListItem\",\"position\":1,\"name\":\"Home\",\"item\":\"https:\\\/\\\/gero.usc.edu\\\/labs\\\/benayounlab\\\/\"},{\"@type\":\"ListItem\",\"position\":2,\"name\":\"Databases and other resources\"}]},{\"@type\":\"WebSite\",\"@id\":\"https:\\\/\\\/gero.usc.edu\\\/labs\\\/benayounlab\\\/#website\",\"url\":\"https:\\\/\\\/gero.usc.edu\\\/labs\\\/benayounlab\\\/\",\"name\":\"The Benayoun Lab\",\"description\":\"\",\"potentialAction\":[{\"@type\":\"SearchAction\",\"target\":{\"@type\":\"EntryPoint\",\"urlTemplate\":\"https:\\\/\\\/gero.usc.edu\\\/labs\\\/benayounlab\\\/?s={search_term_string}\"},\"query-input\":{\"@type\":\"PropertyValueSpecification\",\"valueRequired\":true,\"valueName\":\"search_term_string\"}}],\"inLanguage\":\"en-US\"}]}<\/script>\n<!-- \/ Yoast SEO plugin. -->","yoast_head_json":{"title":"Databases and other resources - The Benayoun Lab","robots":{"index":"index","follow":"follow","max-snippet":"max-snippet:-1","max-image-preview":"max-image-preview:large","max-video-preview":"max-video-preview:-1"},"canonical":"https:\/\/gero.usc.edu\/labs\/benayounlab\/databases-and-other-resources\/","og_locale":"en_US","og_type":"article","og_title":"Databases and other resources - The Benayoun Lab","og_description":"[vc_row][vc_column][vc_empty_space][\/vc_column][\/vc_row][vc_row][vc_column width=&#8221;1\/2&#8243;][vc_column_text css=&#8221;&#8221;] Online Databases &nbsp; Databases on aging: Human Ageing Genomic Resources Lifespan observation database Age related databases (JenAge) Digital Ageing Atlas\u200b &nbsp; Genome browsers: UCSC Genome Browser ENSEMBL Genome Browser NCBI Genome African Turquoise Killifish Genome Browser Mouse Genome Informatics at JAX &nbsp; Interaction and network databases: BioGriD project STRING Histome GeneMania &nbsp; [&hellip;]","og_url":"https:\/\/gero.usc.edu\/labs\/benayounlab\/databases-and-other-resources\/","og_site_name":"The Benayoun Lab","article_modified_time":"2024-12-16T22:05:37+00:00","twitter_card":"summary_large_image","twitter_misc":{"Est. reading time":"1 minute"},"schema":{"@context":"https:\/\/schema.org","@graph":[{"@type":"WebPage","@id":"https:\/\/gero.usc.edu\/labs\/benayounlab\/databases-and-other-resources\/","url":"https:\/\/gero.usc.edu\/labs\/benayounlab\/databases-and-other-resources\/","name":"Databases and other resources - The Benayoun Lab","isPartOf":{"@id":"https:\/\/gero.usc.edu\/labs\/benayounlab\/#website"},"datePublished":"2018-01-19T21:31:11+00:00","dateModified":"2024-12-16T22:05:37+00:00","breadcrumb":{"@id":"https:\/\/gero.usc.edu\/labs\/benayounlab\/databases-and-other-resources\/#breadcrumb"},"inLanguage":"en-US","potentialAction":[{"@type":"ReadAction","target":["https:\/\/gero.usc.edu\/labs\/benayounlab\/databases-and-other-resources\/"]}]},{"@type":"BreadcrumbList","@id":"https:\/\/gero.usc.edu\/labs\/benayounlab\/databases-and-other-resources\/#breadcrumb","itemListElement":[{"@type":"ListItem","position":1,"name":"Home","item":"https:\/\/gero.usc.edu\/labs\/benayounlab\/"},{"@type":"ListItem","position":2,"name":"Databases and other resources"}]},{"@type":"WebSite","@id":"https:\/\/gero.usc.edu\/labs\/benayounlab\/#website","url":"https:\/\/gero.usc.edu\/labs\/benayounlab\/","name":"The Benayoun Lab","description":"","potentialAction":[{"@type":"SearchAction","target":{"@type":"EntryPoint","urlTemplate":"https:\/\/gero.usc.edu\/labs\/benayounlab\/?s={search_term_string}"},"query-input":{"@type":"PropertyValueSpecification","valueRequired":true,"valueName":"search_term_string"}}],"inLanguage":"en-US"}]}},"_links":{"self":[{"href":"https:\/\/gero.usc.edu\/labs\/benayounlab\/wp-json\/wp\/v2\/pages\/11","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/gero.usc.edu\/labs\/benayounlab\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/gero.usc.edu\/labs\/benayounlab\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/gero.usc.edu\/labs\/benayounlab\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/gero.usc.edu\/labs\/benayounlab\/wp-json\/wp\/v2\/comments?post=11"}],"version-history":[{"count":0,"href":"https:\/\/gero.usc.edu\/labs\/benayounlab\/wp-json\/wp\/v2\/pages\/11\/revisions"}],"wp:attachment":[{"href":"https:\/\/gero.usc.edu\/labs\/benayounlab\/wp-json\/wp\/v2\/media?parent=11"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}