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37 KiB
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37 KiB
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{"url": "http://motifmap.ics.uci.edu/#GeneSearch", "content": "<!DOCTYPE html>\r\n<html>\r\n <head>\r\n <meta http-equiv=\"Content-Type\" content=\"text/html; charset=utf-8\" />\r\n <title>Motifmap</title> \r\n \r\n <!-- Load Style Sheets -->\r\n <!-- \"css/smoothness/jquery.ui.all.css\" -->\r\n <style type=\"text/css\" title=\"currentStyle\"> \r\n @import \"css/jquery.datatable.css\";\r\n @import \"css/jquery.datatable_jui.css\";\r\n @import \"css/jquery.colorbox.css\";\r\n @import \"css/jquery.multiselect.css\";\r\n @import \"css/jquery.autocomplete.css\";\r\n @import \"css/jquery.mediaelementplayer.css\";\r\n @import \"css/flick/jquery-ui-1.8.16.custom.css\"; \r\n @import \"css/ui.spinner.css\"; \r\n @import \"css/motifmap.css\";\r\n @import \"css/TableTools.css\";\r\n @import \"css/TableTools_JUI.css\";\r\n </style>\r\n \r\n <!-- Load JQuery and JQuery UI JavaScript Libraries --> \r\n <script type=\"text/javascript\" src=\"js/jquery/jquery-1.6.2.min.js\"></script>\r\n <script type=\"text/javascript\" src=\"js/jquery/jquery.ui.core.min.js\"></script>\r\n <script type=\"text/javascript\" src=\"js/jquery/jquery.ui.widget.min.js\"></script>\r\n <script type=\"text/javascript\" src=\"js/jquery/jquery.ui.button.min.js\"></script> \r\n <script type=\"text/javascript\" src=\"js/jquery/jquery-ui-1.8.16.custom.min.js\"></script> \r\n <script type=\"text/javascript\" src=\"js/jquery/jquery.colorbox.min.js\"></script>\r\n <script type=\"text/javascript\" src=\"js/jquery/jquery.ui.spinner.min.js\"></script>\r\n <script type=\"text/javascript\" src=\"js/jquery/jquery.multiselect.min.js\"></script>\r\n <script type=\"text/javascript\" src=\"js/jquery/jquery.ui.position.min.js\"></script>\r\n <script type=\"text/javascript\" src=\"js/jquery/jquery.ui.mouse.min.js\"></script>\r\n <script type=\"text/javascript\" src=\"js/jquery/jquery.autocomplete.js\"></script>\r\n <!-- Load dataTables JavaScript Libraries -->\r\n <script type=\"text/javascript\" src=\"js/jquery/jquery.dataTables.min.js\"></script>\r\n <script type=\"text/javascript\" src=\"js/jquery/TableTools.min.js\"></script>\r\n <script type=\"text/javascript\" src=\"js/jquery/ZeroClipboard.js\"></script>\r\n <script type=\"text/javascript\" src=\"js/jquery/mediaelement-and-player.js\"></script>\r\n <!-- Most browsers already have an integrated json lib, however for those that dont... -->\r\n <script type=\"text/javascript\" src=\"js/json2.js\"></script>\r\n <!-- Load Custom MotifMap JavaScript Libraries -->\r\n <script type=\"text/javascript\" src=\"js/motifmap.home.js\"></script>\r\n <script type=\"text/javascript\" src=\"js/motifmap.motif.search.js\"></script>\r\n <script type=\"text/javascript\" src=\"js/motifmap.export.js\"></script>\r\n <script type=\"text/javascript\" src=\"js/motifmap.gene.search.js\"></script>\r\n <script type=\"text/javascript\" src=\"js/motifmap.snper.js\"></script>\r\n <!-- Do not hot link this, make copy if validation is neccessary -->\r\n <!-- <script type=\"text/javascript\" src=\"http://jzaefferer.github.com/jquery-validation/jquery.validate.js\"></script> ->\r\n \r\n <!-- Currently this is not used, but could be integrated so that each tab is loaded independently -->\r\n <!-- <script type=\"text/javascript\" src=\"js/jquery/jquery-jtemplates.js\"></script> --> \r\n \r\n <script type=\"text/javascript\">\r\n var _gaq = _gaq || [];\r\n _gaq.push(['_setAccount', 'UA-1004168-7']);\r\n _gaq.push(['_trackPageview']);\r\n \r\n (function() {\r\n var ga = document.createElement('script'); ga.type = 'text/javascript'; ga.async = true;\r\n ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-analytics.com/ga.js';\r\n var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);\r\n })();\r\n </script>\r\n </head>\r\n <body>\r\n <!-- Replace with a nice banner, with MotifMap logo -->\r\n <h1>MotifMap: genome-wide maps of regulatory elements.</h1> \r\n <div id=\"content\"> \r\n <!-- Define Tabs --> \r\n <ul> \r\n <li><a href=\"#Home\">Home</a></li>\r\n <li><a href=\"#MotifSearch\">Motif Search</a></li>\r\n <li><a href=\"#GeneSearch\">Gene Search</a></li>\r\n <li><a href=\"#SNPer\">SNPer</a></li> \r\n </ul>\r\n \r\n <!-- Loading swirly GIF -->\r\n <div id=\"loading\"><img src=\"images/loading.gif\"/></div>\r\n \r\n <!-- Home -->\r\n <div id=\"Home\" class=\"tab\">\r\n <div id=\"home-wrapper\" >\r\n <p id=\"intro\">\r\n The <span class=\"bold-small-label\">MotifMap</span> system provides comprehensive maps of candidate regulatory elements encoded in the genomes of model species using databases of transcription factor binding motifs, \r\n refined genome alignments, and a comparative genomic statistical approach- \r\n <span class=\"bold-small-label\">Bayesian Branch Length Score</span> \r\n \r\n </p>\r\n \r\n <div id=\"home-left\"> \r\n <div class=\"home-section-wrapper ui-widget ui-widget-content ui-corner-all\">\r\n <h2 class=\"ui-widget-header\">Getting Started</h2>\r\n \r\n <div class=\"home-subsection-wrapper\"> \r\n <span class=\"video-link-wrapper\">\r\n <img id=\"motif-video-image\" src=\"videos/SNPer.jpg\" style=\"cursor: pointer; box-shadow:10px 10px 20px grey; border: 1px solid grey;\" width=\"116px\" /> \r\n <div class=\"hidden-video\">\r\n <video id=\"motif-video\" width=\"640\" controls=\"controls\" poster=\"videos/SNPer.jpg\" >\r\n <source src=\"videos/MotifSearch.mp4\" type=\"video/mp4\" />\r\n <source src=\"videos/MotifSearch.webm\" type=\"video/webm\" />\r\n <source src=\"videos/MotifSearch.ogv\" type=\"video/ogg\" />\r\n <source src=\"/videos/MotifSearch.mov\" type=\"video/mov\" /> \r\n </video>\r\n </div> \r\n </span> \r\n <p>\r\n <span class=\"bold-small-label\">Motif Search</span> \r\n allows users to select a transcription factor, view its binding sequence logo, \r\n and list its genome-wide putative binding sites.\r\n </p>\r\n </div>\r\n \r\n <div class=\"home-subsection-wrapper\"> \r\n <span class=\"video-link-wrapper\">\r\n <img id=\"gene-video-image\" src=\"videos/SNPer.jpg\" style=\"cursor: pointer; box-shadow:10px 10px 20px grey; border: 1px solid grey;\" width=\"116px\" />\r\n <div class=\"hidden-video\">\r\n <video id=\"gene-video\" width=\"640\" controls=\"controls\" poster=\"videos/SNPer.jpg\" >\r\n <source src=\"videos/GeneSearch.mp4\" type=\"video/mp4\" />\r\n <source src=\"videos/GeneSearch.webm\" type=\"video/webm\" />\r\n <source src=\"videos/GeneSearch.ogv\" type=\"video/ogg\" />\r\n <source src=\"/videos/GeneSearch.mov\" type=\"video/mov\" /> \r\n </video>\r\n </div> \r\n </span>\r\n <p>\r\n <span class=\"bold-small-label\">Gene Search</span>\n allows users to select a gene and search for transcription factor\n binding sites in regions upstream and downstream from its transcription start site.\r\n </p> \r\n </div>\r\n \r\n <div class=\"home-subsection-wrapper\"> \r\n <span class=\"video-link-wrapper\">\r\n <img id=\"snper-video-image\" src=\"videos/SNPer.jpg\" style=\"cursor: pointer; box-shadow:10px 10px 20px grey; border: 1px solid grey;\" width=\"116px\" />\r\n <div class=\"hidden-video\">\r\n <video id=\"snper-video\" width=\"640\" controls=\"controls\" poster=\"videos/SNPer.jpg\" >\r\n <source src=\"videos/SNPer.mp4\" type=\"video/mp4\" />\r\n <source src=\"videos/SNPer.webm\" type=\"video/webm\" />\r\n <source src=\"videos/SNPer.ogv\" type=\"video/ogg\" />\r\n <source src=\"/videos/SNPer.mov\" type=\"video/mov\" /> \r\n </video>\r\n </div> \r\n </span>\r\n <p>\r\n <span class=\"bold-small-label\">SNPer</span>\n allows users to select a genomic loci (e.g. a SNP) and search for\n overlapping or neighbouring transcription factor binding sites. \r\n </p>\r\n \r\n <p style=\"padding-top: 15px;\">In all cases, users can filter the results by various criteria and export them to severals file formats or view them directly in the UCSC genome browser.</p>\r\n </div> \n </div>\n\t\t\t<div class=\"home-section-wrapper ui-widget ui-widget-content ui-corner-all\">\n <h2 class=\"ui-widget-header\">New! MotifMap-RNA Portal</h2>\n <div class=\"home-subsection-wrapper\">\nA new portal for all MotifMap functions including the new MotifMap-RNA functions is available at <a\nhref=\"http://motifmap-rna.ics.uci.edu\">MotifMap-RNA web portal</a>. It includes MotifMap-RNA, MotifMap with new genome builds and ChIPSeq\ndatabases with querying functions similar to the Motif Search and Gene Search functions on this site (some results are unpublished). If you use MotifMap-RNA, please cite\nit in addition to MotifMap. Now includes access to hg38 MotifMap results under the MotifMap section (for testing only).\n </div>\n </div>\n\t\t\t<div class=\"home-section-wrapper ui-widget ui-widget-content ui-corner-all\">\n <h2 class=\"ui-widget-header\">BBLS Code</h2>\n <div class=\"home-subsection-wrapper\">\n\t\t\t Documented Python code for computing the Bayesian\nBranch Length Score is available <a\nhref=\"/downloads/BranchLengthScoring.py\">here</a>. The code and\nMotifMap data are freely available for academic use. For commercial\nlicenses, please contact: igb-license [at] ics [.] uci [.] edu</a>.\n </div>\n </div>\n </div>\r\n \r\n <div id=\"home-right\">\r\n <div class=\"home-section-wrapper ui-widget ui-widget-content ui-corner-all\">\r\n <h2 class=\"ui-widget-header\">Available Species</h2>\r\n <div class=\"home-subsection-wrapper\">\n <div style=\"width: 25%;\" class=\"inner-subsection\"><strong>Species</strong><span>Human</span><span>Human</span><span>Mouse</span><span>Fly</span><span>Yeast</span><span>Worm</span></div>\n <div style=\"width: 25%;\" class=\"inner-subsection\"><strong>Build</strong><span>hg18</span><span>hg19</span><span>mm9</span><span>dm3</span><span>sacCer2</span><span>ce6</span></div>\n <div style=\"width: 50%;\" class=\"inner-subsection\"><strong>Alignment</strong><span>multiz28way placental</span><span>multiz46way placental</span><span>multiz30way</span><span>multiz15way flies-only</span><span>multiz7way</span><span>multiz6way</span></div>\n </div>\r\n </div> \r\n\n <div class=\"home-section-wrapper ui-widget ui-widget-content ui-corner-all\">\r\n <h2 class=\"ui-widget-header\">Download data</h2>\r\n <div class=\"home-subsection-wrapper\">\n <div style=\"width: 25%;\" class=\"inner-subsection\"><strong>Species</strong>\n\t\t\t\t\t\t\t\t\t<span>Human</span>\n\t\t\t\t\t\t\t\t\t<span>Mouse</span>\n\t\t\t\t\t\t\t\t</div>\n <div style=\"width: 25%;\" class=\"inner-subsection\"><strong>Build</strong>\n\t\t\t\t\t\t\t\t\t<span>hg19</span>\n\t\t\t\t\t\t\t\t\t<span>mm9</span>\n\t\t\t\t\t\t\t\t\t\n\t\t\t\t\t\t\t\t</div/>\n <div style=\"width: 50%;\" class=\"inner-subsection\"><strong>Alignment</strong>\n\t\t\t\t\t\t\t\t\t<span><a href=\"http://www.igb.uci.edu/~motifmap/motifmap/HUMAN/hg19/multiz46way_placental/HUMAN.hg19_multiz46way.tar.bz2\">multiz46way</a></span>\n\t\t\t\t\t\t\t\t\t<span><a href=\"http://www.igb.uci.edu/~motifmap/motifmap/MOUSE/mm9/multiz30way/MotifMap_MOUSE_mm9.multiz30way.tsv.bz2\">multiz30way</a></span>\n\t\t\t\t\t\t\t\t\t\n\t\t\t\t\t\t\t\t</div>\n </div>\n </div> \n <div class=\"home-section-wrapper ui-widget ui-widget-content ui-corner-all\">\r\n <h2 class=\"ui-widget-header\">Citing MotifMap</h2>\r\n <div class=\"home-subsection-wrapper\">\r\n <p>Kenneth Daily, Vishal R Patel, Paul Rigor, Xiaohui Xie, and Pierre Baldi. \r\n <i>\"MotifMap: integrative genome-wide maps of regulatory motif sites for model species\"</i> \r\n BMC Bioinformatics 2011, 12:495 <a href = \"http://www.biomedcentral.com/1471-2105/12/495/abstract\">(doi:10.1186/1471-2105-12-495)</a></p>\r\n\t\t\t\t<p>Xiaohui Xie, Paul Rigor, and Pierre Baldi. \r\n <i>\"MotifMap: a human genome-wide map of candidate regulatory motif sites.\"</i> \r\n Bioinformatics 2009; 25: 167 - 174. <a href=\"http://bioinformatics.oxfordjournals.org/content/25/2/167.abstract\">(doi:10.1093/bioinformatics/btn605)</a></p>\r\n </div>\r\n <div class=\"home-section-wrapper ui-widget ui-widget-content ui-corner-all\">\r\n <h2 class=\"ui-widget-header\">Acknowledgement</h2>\r\n <div class=\"home-subsection-wrapper\">\n <p>Development of motifmap is made possible by funding from the National Science Foundation and the National Institutes of Health.</p>\r\n </div>\r\n </div>\r\n </div>\r\n </div>\r\n </div>\r\n </div> \r\n \r\n <!-- Search Motif -->\r\n <div id=\"MotifSearch\" class=\"tab\"> \r\n <div class=\"sub-header\"><button id=\"mymotifs\"><span>My Motifs (<span id=\"motifNum\">0</span>)</span></button></div>\r\n <div id=\"track-wrapper\">\r\n <p><strong>Select species track and click next</strong></p>\r\n <select id=\"supportedTracks\"></select> \r\n </div> \r\n \r\n <div id=\"motif-wrapper\">\r\n <h2 class=\"selectedTrack\"></h2>\r\n <p><strong>Select motif and click next</strong></p>\r\n <div id=\"motif-table-wrapper\">\r\n <table id=\"motifs\" class=\"display\">\r\n <thead>\r\n <th>Motif ID</th> <th>TF Name</th> <th>Consensus</th> <th>Length</th> \r\n </thead>\r\n <tbody></tbody>\r\n </table> \r\n </div>\r\n \r\n <div id=\"img-motif-seq\">Click on a Motif to view sequence logo</div> \r\n </div> \r\n \r\n <div id=\"motif-details-wrapper\">\r\n <h2 id=\"selectedMotif\"><span class=\"selectedTrack\"></span> -> <span class=\"selectedMotif\"></span></h2>\r\n <p><strong>Set filters and click search to list binding sites</strong></p>\r\n <div id=\"motif-filters-wrapper\" class=\"ui-widget ui-widget-content ui-corner-all\">\r\n <h4 class=\"ui-widget-header small-label\">Filters</h4> \r\n \r\n <div id=\"motif-filters\">\r\n <div class=\"inner-filter\">\r\n <label class=\"label\">Conservation Scores</label>\r\n <div style=\"float:left;\">\r\n <span style=\"display:block;\">BBLS</span>\r\n <span style=\"display:block;\">BLS</span>\r\n </div>\r\n <div style=\"float:left; text-align: right;\">\r\n <input style=\"display:block;\" id=\"bbls\" name=\"bbls\" type=\"number\" value=\"0.00\" />\r\n <input style=\"display:block;\" id=\"bls\" name=\"bls\" type=\"number\" value=\"0.00\" />\r\n </div>\r\n </div> \r\n <div class=\"inner-filter\">\r\n <label class=\"label\">False Discovery Rate</label> \r\n <div style=\"float:left;\">\r\n <span style=\"display:block;\" class=\"spinner-label\">FDR </span>\r\n </div>\r\n <div style=\"float:left; text-align: right;\">\r\n <input style=\"display:block;\" id=\"fdr\" name=\"fdr\" type=\"number\" value=\"0.50\" />\r\n </div>\r\n </div> \r\n <div class=\"inner-filter\">\r\n <label class=\"label\">Motif Scores</label>\r\n <div style=\"float:left;\">\r\n <span style=\"display:block;\" class=\"spinner-label\">NLOD </span>\r\n <span style=\"display:block;\" class=\"spinner-label\">Z-Score </span>\r\n </div>\r\n <div style=\"float:left; text-align: right;\">\r\n <input style=\"display:block;\" id=\"nlod\" name=\"nlod\" type=\"number\" value=\"0.65\" /> \r\n <input style=\"display:block;\" id=\"zscore\" name=\"zscore\" type=\"number\" value=\"1\" />\r\n </div> \r\n </div> \r\n <div class=\"inner-filter\">\r\n <label class=\"label\">Distance To Closest Gene</label>\r\n <div style=\"float:left;\">\r\n <span style=\"display:block;\" class=\"spinner-label\">Distance (bp)</span> \r\n </div>\r\n <div style=\"float:left; text-align: right;\">\r\n <input style=\"display:block;\" id=\"distance\" name=\"distance\" type=\"number\" value=\"1000\" /> \r\n </div>\r\n </div>\r\n </div>\r\n <button id=\"search\">Search</button> \r\n </div>\r\n \r\n <table id=\"genes\" class=\"display\">\r\n <thead>\r\n <th></th> <th>cid</th> <th>Location</th> <th>+/-</th> <th>BBLS</th> <th>BLS</th> <th>NLOD</th> <th>Z-Score</th> <th>FDR</th> <th>Closest Gene</th> <th>Distance (bp)</th> <th>Description</th>\r\n </thead>\r\n <tbody></tbody>\r\n </table> \r\n </div>\r\n \r\n <div class=\"button-wrapper\"><button id=\"back\">Back</button> <button id=\"next\">Next</button> <button id=\"save\">Save</button></div> \r\n </div> \r\n \r\n <!-- Gene Search -->\r\n <div id=\"GeneSearch\" class=\"tab\">\r\n <div id=\"gsearch-tracks-wrapper\"> \r\n <p><strong>Select species (alignment) and click next</strong></p>\r\n <select id=\"gSearchSupportedTracks\"></select>\r\n </div> \r\n \r\n <div id=\"gsearch-genes-wrapper\">\r\n <h2 class=\"gSelectedTrack\"></h2> \r\n <p><strong>Enter a gene name (official gene symbol or refSeq transcript id) and click next</strong></p> \r\n <input id=\"gene\" placeholder=\"\" value=\"\" />\r\n <div id=\"selectedGenes\"></div>\r\n </div>\r\n \r\n <div id=\"gsearch-motifs-wrapper\">\r\n <h2 id=\"gSelectedMotif\"><span class=\"gSelectedTrack\"></span> -> <span class=\"gSelectedMotif\"></span></h2>\r\n <p><strong>Set filters and click search to list binding sites</strong></p>\r\n <div id=\"gmotif-filters-wrapper\" class=\"ui-widget ui-widget-content ui-corner-all\">\r\n <h4 class=\"ui-widget-header small-label\">Filters:</h4> \r\n \r\n <div id=\"gmotif-filters\">\r\n <div class=\"inner-filter\">\r\n <label class=\"label\">Conservation Scores</label>\r\n <div style=\"float:left;\">\r\n <span style=\"display:block;\">BBLS</span>\r\n <span style=\"display:block;\">BLS</span>\r\n </div>\r\n <div style=\"float:left; text-align: right;\">\r\n <input style=\"display:block;\" id=\"gbbls\" name=\"gbbls\" type=\"number\" value=\"0.00\" />\r\n <input style=\"display:block;\" id=\"gbls\" name=\"gbls\" type=\"number\" value=\"0.00\" />\r\n </div>\r\n </div> \r\n <div class=\"inner-filter\">\r\n <label class=\"label\">False Discovery Rate</label> \r\n <div style=\"float:left;\">\r\n <span style=\"display:block;\" class=\"spinner-label\">FDR </span>\r\n </div>\r\n <div style=\"float:left; text-align: right;\">\r\n <input style=\"display:block;\" id=\"gfdr\" name=\"gfdr\" type=\"number\" value=\"0.50\" />\r\n </div>\r\n </div> \r\n <div class=\"inner-filter\">\r\n <label class=\"label\">Motif Scores</label>\r\n <div style=\"float:left;\">\r\n <span style=\"display:block;\" class=\"spinner-label\">NLOD </span>\r\n <span style=\"display:block;\" class=\"spinner-label\">Z-Score </span>\r\n </div>\r\n <div style=\"float:left; text-align: right;\">\r\n <input style=\"display:block;\" id=\"gnlod\" name=\"gnlod\" type=\"number\" value=\"0.65\" /> \r\n <input style=\"display:block;\" id=\"gzscore\" name=\"gzscore\" type=\"number\" value=\"1\" />\r\n </div> \r\n </div> \r\n <div class=\"inner-filter\">\r\n <label class=\"label\">Distance From TSS</label>\r\n <div style=\"float:left;\">\r\n <span style=\"display:block;\" class=\"spinner-label\">Upstream</span>\r\n <span style=\"display:block;\" class=\"spinner-label\">Downstream</span>\r\n </div>\r\n <div style=\"float:left; text-align: right;\">\r\n <input style=\"display:block;\" id=\"gupstream\" name=\"gupstream\" type=\"number\" value=\"1000\" />\r\n <input style=\"display:block;\" id=\"gdownstream\" name=\"gdownstream\" type=\"number\" value=\"1000\" />\r\n </div>\r\n </div>\r\n </div>\r\n <button id=\"geneSearch\">Search</button> \r\n </div>\r\n \r\n <div id=\"geneExport\"> \r\n <button class=\"export\">Other</button>\r\n <ul id=\"gene-export-menu\">\r\n <li><a href=\"#\">BED</a></li>\r\n <li><a href=\"#\">CSV</a></li>\r\n <li><a href=\"#\">GFF3</a></li>\r\n <li><a href=\"#\">TXT</a></li>\r\n <li><a href=\"#\">UCSC Browser</a></li>\r\n </ul>\r\n </div>\r\n <div id=\"gSearchMotifsTableTools\"></div> \r\n <label class=\"export-label\">Export:</label>\r\n <table id=\"gSearchMotifs\" class=\"display\">\r\n <thead>\r\n <th></th> <th>cid</th> <th>Location</th> <th>+/-</th> <th>BBLS</th> <th>BLS</th> <th>NLOD</th> <th>Z-Score</th> <th>FDR</th> <th>Motif ID</th> <th>TF Name</th> <th>Gene</th> <th>Distance (bp)</th> <th>Region</th>\r\n </thead>\r\n <tbody></tbody>\r\n </table>\r\n </div>\r\n \r\n <div class=\"button-wrapper\"><button id=\"geneBack\">Back</button> <button id=\"geneNext\">Next</button></div>\r\n </div>\r\n \r\n <!-- My Motifs-->\r\n <div id=\"mymotifs-hidden-wrapper\">\r\n <div id=\"mymotifs-wrapper\">\r\n <iframe id=\"downloadIFrame\" src=\"\" style=\"display:none; visibility:hidden;\"></iframe>\r\n \r\n <label class=\"label\">My Motifs</label>\r\n \r\n <div id=\"motifExport\" class=\"top-button-wrapper\">\r\n <button class=\"export\">Export</button>\r\n <ul id=\"motif-export-menu\">\r\n <li><a href=\"#\">BED</a></li>\r\n <li><a href=\"#\">CSV</a></li>\r\n <li><a href=\"#\">GFF3</a></li>\r\n <li><a href=\"#\">TXT</a></li>\r\n <li><a href=\"#\">UCSC Browser</a></li>\r\n </ul>\r\n </div>\r\n \r\n <div id=\"mymotif-table-wrapper\">\r\n <table id=\"myMotifs\" class=\"display\">\r\n <thead>\r\n <th></th> <th>Motif ID</th> <th>Name</th> <th>BBLS</th> <th>BLS</th> <th>NLOD</th> <th>ZScore</th> <th>FDR</th> <th>Distance (bp)</th> <th>Species</th>\r\n </thead>\r\n <tbody></tbody>\r\n </table>\r\n </div> \r\n </div>\r\n </div>\r\n \r\n <!-- SNPer -->\r\n <div id=\"SNPer\" class=\"tab\">\r\n <div id=\"snper-tracks-wrapper\">\r\n <p><strong>Select species (alignment) and click next</strong></p>\r\n\r\n <select id=\"snperSupportedTracks\"></select> \r\n </div>\r\n \r\n <div id=\"snper-motifs-wrapper\">\r\n <h2 id=\"snperSelected\"><span class=\"sSelectedTrack\"></span></h2>\r\n <p><strong>Select genome location and click search</strong></p> \r\n \r\n <div id=\"chromosomes-wrapper\"> \r\n <div class=\"snper-input-wrapper\"> \r\n <span class=\"snper-label\">Chromosome</span>\r\n <select id=\"chromosomes\"></select>\r\n </div> \r\n <div class=\"snper-input-wrapper\">\r\n <span class=\"snper-label\">Location</span>\r\n <input id=\"slocation\" name=\"slocation\" type=\"number\" value=\"1000\" class=\"{validate:{required:true, messages:{required:'Please enter numbers only'}}} location\" />\r\n </div>\r\n <div class=\"snper-input-wrapper\">\r\n <span class=\"snper-label\">Region Length</span>\r\n <input id=\"sregion\" name=\"sregion\" type=\"number\" value=\"1\" />\r\n </div>\r\n </div>\r\n \r\n <div id=\"snper-filters-wrapper\" class=\"ui-widget ui-widget-content ui-corner-all\">\r\n <h4 class=\"ui-widget-header small-label\">Filters:</h4>\r\n <div id=\"snper-filters\">\r\n <div class=\"inner-filter\">\r\n <label class=\"label\">Conservation Scores</label>\r\n <div style=\"float:left;\">\r\n <span style=\"display:block;\">BBLS</span>\r\n <span style=\"display:block;\">BLS</span>\r\n </div>\r\n <div style=\"float:left; text-align: right;\">\r\n <input style=\"display:block;\" id=\"sbbls\" name=\"sbbls\" type=\"number\" value=\"0.00\" />\r\n <input style=\"display:block;\" id=\"sbls\" name=\"sbls\" type=\"number\" value=\"0.00\" />\r\n </div>\r\n </div> \r\n <div class=\"inner-filter\">\r\n <label class=\"label\">False Discovery Rate</label> \r\n <div style=\"float:left;\">\r\n <span style=\"display:block;\" class=\"spinner-label\">FDR </span>\r\n </div>\r\n <div style=\"float:left; text-align: right;\">\r\n <input style=\"display:block;\" id=\"sfdr\" name=\"sfdr\" type=\"number\" value=\"0.50\" />\r\n </div>\r\n </div> \r\n <div class=\"inner-filter\">\r\n <label class=\"label\">Motif Scores</label>\r\n <div style=\"float:left;\">\r\n <span style=\"display:block;\" class=\"spinner-label\">NLOD </span>\r\n <span style=\"display:block;\" class=\"spinner-label\">Z-Score </span>\r\n </div>\r\n <div style=\"float:left; text-align: right;\">\r\n <input style=\"display:block;\" id=\"snlod\" name=\"snlod\" type=\"number\" value=\"0.65\" /> \r\n <input style=\"display:block;\" id=\"szscore\" name=\"szscore\" type=\"number\" value=\"1\" />\r\n </div> \r\n </div> \r\n </div>\r\n \n <button id=\"snperSearch\">Search</button> \r\n </div> \r\n \r\n <div id=\"snperExport\">\r\n <button class=\"export\">Other</button>\r\n <ul id=\"snper-export-menu\">\r\n <li><a href=\"#\">BED</a></li>\r\n <li><a href=\"#\">CSV</a></li>\r\n <li><a href=\"#\">GFF3</a></li>\r\n <li><a href=\"#\">TXT</a></li>\r\n <li><a href=\"#\">UCSC Browser</a></li>\r\n </ul>\r\n </div>\r\n <div id=\"snperMotifsTableTools\"></div>\r\n <label class=\"export-label\">Export:</label> \r\n <table id=\"snperSearchMotifs\" class=\"display\">\r\n <thead>\r\n <th></th> <th>cid</th> <th>Location</th> <th>Strand</th> <th>BBLS</th> <th>BLS</th> <th>NLOD</th> <th>Z-Score</th> <th>FDR</th> <th>Motif ID</th> <th>TF Name</th>\r\n </thead>\r\n <tbody></tbody>\r\n </table>\r\n </div>\r\n \r\n <div class=\"button-wrapper\"><button id=\"snperBack\">Back</button> <button id=\"snperNext\">Next</button></div>\r\n </div> \r\n </div>\r\n \r\n <div id=\"footer\">M o t i f M a p :: Copyright © <a target=\"_blank\" href=\"http://uci.edu\">University of California, Irvine</a> :: <a target=\"_blank\" href=\"http://ics.uci.edu\">ICS</a> :: <a target=\"_blank\" href=\"http://www.igb.uci.edu\">IGB</a></div>\r\n </body>\r\n</html>\r\n\r\n\r\n", "encoding": "ascii"} |