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motif without matrices
[[Swissregulon:SRY.p1]]
[[Swissregulon:HOX(A,B,D)3.p1]]
doubled top motif tables
CNhs10855 & CNhs11062
CNhs11245 & CNhs11183
CNhs11248 & CNhs11185
CNhs11772 & CNhs12996
CNhs11781 & CNhs12997
{{REVISIONTIMESTAMP}}
{{#ifexpr: {{#expr: {{REVISIONTIMESTAMP}}-20120731160000 }} > 0 | yes }}
{{CURRENTTIMESTAMP}}
<html>
<style type="text/css"> 
.rotate90 {
  -webkit-transform: rotate(-90deg);
  -moz-transform: rotate(-90deg);
-webkit-transform-origin: 6px 18px;
-moz-transform-origin: 6px 18px;
width:1px;
}
</style>
<script type="text/javascript">
$(document).ready(function() {
    var oTable =  $('#gene_exptable').dataTable({
"sScrollY": "300px",
"bPaginate": false,
"bScrollCollapse": true,
"iDisplayLength": -1,
"aaSorting": [[1,'desc']],
"aoColumnDefs": [ { "asSorting": [ "desc", "asc" ], "aTargets": [ "_all" ] }  , { "bSortable": false, "aTargets": [ 0 ] }]
});
$('#gene_exptable_wrapper .dataTables_scrollHead th').css("height", "100px").css("vertical-align", "bottom");
var data = [];
var plotdata = [];
// chart checkbox
for (var i2=1; i2<oTable.fnSettings().aoColumns.length; i2++){
key2 = i2-1;
        $("#gene_exptable_chart_chkbox").append('<input type="checkbox" name="' + key2 +
                              '" checked="checked" id="id' + key2 + '"><label for="id' + key2 + '">'
                                + $(oTable.fnSettings().aoColumns[i2].sTitle).text() + '</label><br/>');
}
function collectdata(){
data = [];
for (var i2=1; i2<oTable.fnSettings().aoColumns.length; i2++){
var plots = [];
for (var i1=1; i1<$('#gene_exptable tr').length; i1++) {
    plots.push([i1,$("#gene_exptable tr")[i1].cells[i2].innerHTML]);
}
data.push({"label": oTable.fnSettings().aoColumns[i2].sTitle.replace(/<(?:.|\n)*?>/gm, '').replace(/(^\s+)|(\s+$)/g, ""), "data": plots});
}
}
function drawchart(){
plotdata = [];
$("#gene_exptable_chart_chkbox").find("input:checked").each(function () {
var key = $(this).attr("name");
plotdata.push(data[$(this).attr("name")]);
});
var plot1 = $.plot($("#gene_exptable_chart"), plotdata, {
                yaxis : { axisLabel : 'TPM' },
lines : { show : false },
points : { show : true },
                grid: { hoverable: true, clickable: true },
xaxis : { tickDecimals : 0, show: false },
                legend: { show: false }
});
//test
var data_series = plot1.getData();
$("#gene_exptable_chart_chkbox label").css("background-color", "white");
$.each(data_series , function(){
$("#gene_exptable_chart_chkbox label:contains(" + this.label + ")").css("background-color", this.color);
});
//test
//$('#test').text(oTable.fnSettings().aoData[1]._aData[0]);
$('#test').text(oTable.fnGetData(2, 2));
//test1 = oTable.fnSettings().oRow;
}
collectdata();
drawchart();
// re-draw chart event
$(window).resize(function() { drawchart(); });
$("th").click(function() {collectdata(); drawchart(); } );
$("#gene_exptable_paginate").click(function() {collectdata(); drawchart(); } );
$('#gene_exptable').bind('filter', function() {
setTimeout(function(){
collectdata(); drawchart();}, 1000);
} );
$('#gene_exptable_length').change(function() {collectdata(); drawchart(); } );
$("#gene_exptable_chart_chkbox").find("input").click(function() { drawchart(); });
// tooltip function start
    function showTooltip(x, y, contents) {
        $('<div id="tooltip">' + contents + '</div>').css( {
            position: 'absolute',
            display: 'none',
            top: y + 5,
            left: x + 5,
            border: '1px solid #aaa',
            padding: '2px',
            'background-color': '#fff',
            opacity: 0.80
        }).appendTo("body").fadeIn(200);
    }
    var previousPoint = null;
    $("#gene_exptable_chart").bind("plothover", function (event, pos, item) {
        $("#x").text(pos.x.toFixed(2));
        $("#y").text(pos.y.toFixed(2));
            if (item) {
                if (previousPoint != item.dataIndex) {
                    previousPoint = item.dataIndex;
                   
                    $("#tooltip").remove();
                    var x = item.datapoint[0].toFixed(0),
                        y = item.datapoint[1].toFixed(2);
                 
                    showTooltip(item.pageX, item.pageY,
                              "Gene: "+ item.series.label +"<br>TPM: "+y);
                }
            }
            else {
                $("#tooltip").remove();
                previousPoint = null;           
            }
    });
// tooltip function end
// clicking point function
    $("#gene_exptable_chart").bind("plotclick", function (event, pos, item) {
if (item){
var vdata = Math.round($('#gene_exptable').height())/item.series.data.length*item.dataIndex;
$('#gene_exptable_wrapper .dataTables_scrollBody').animate({ scrollTop: vdata-150 }, 'slow');
$("#gene_exptable_wrapper .dataTables_scrollBody tbody td").removeClass('highlight');
$('#gene_exptable_wrapper .dataTables_scrollBody tbody tr:eq(' + item.dataIndex+ ') td').addClass('highlight');
}
    });
// clicking point function end
} );
</script>
</html>
{{#gene_exptable_hg19:ACTB|{{#ask:[[Category:FFCP]][[Short description::p1@ACTB]]|mainlabel=-|?phase1_expression|link=none|format=list|headers=hide|limit=1|intro=p1@ACTB,|searchlabel=}}|{{#ask:[[Category:FFCP]][[Short description::p2@ACTB]]|mainlabel=-|?phase1_expression|link=none|format=list|headers=hide|limit=1|intro=p2@ACTB,|searchlabel=}}|{{#ask:[[Category:FFCP]][[Short description::p3@ACTB]]|mainlabel=-|?phase1_expression|link=none|format=list|headers=hide|limit=1|intro=p3@ACTB,|searchlabel=}}|{{#ask:[[Category:FFCP]][[Short description::p4@ACTB]]|mainlabel=-|?phase1_expression|link=none|format=list|headers=hide|limit=1|intro=p4@ACTB,|searchlabel=}}|{{#ask:[[Category:FFCP]][[Short description::p5@ACTB]]|mainlabel=-|?phase1_expression|link=none|format=list|headers=hide|limit=1|intro=p5@ACTB,|searchlabel=}}
}}
<div id="gene_exptable_chart" style="float:left;width:600px;height:300px;"></div>
<div id="gene_exptable_chart_chkbox" style="float:left;"></div>
<div style="clear:both;"></div>
<div id="test"></div>
== gene mouse ==
<html>
<html>
<script type="text/javascript" language="javascript" src="/resource_browser/rb_js/datatables/media/js/jquery.dataTables.min.js"></script>
<script type="text/javascript" language="javascript" src="/resource_browser/rb_js/datatables/media/js/jquery.dataTables.min.js"></script>
<script type="text/javascript" language="javascript" src="/resource_browser/rb_js/datatables/extras/TableTools/media/js/TableTools.min.js"></script>
<script type="text/javascript" language="javascript" src="/resource_browser/rb_js/datatables/extras/TableTools/media/js/TableTools.min.js"></script>
<script type="text/javascript" language="javascript" src="/resource_browser/rb_js/flot/jquery.flot.min.js"></script>
<style type="text/css" title="currentStyle">
<style type="text/css" title="currentStyle">
@import "/resource_browser/rb_js/datatables/media/css/jquery.dataTables.css";
@import "/resource_browser/rb_js/datatables/media/css/jquery.dataTables.css";
@import "/resource_browser/rb_js/datatables/extras/TableTools/media/css/TableTools.css";
@import "/resource_browser/rb_js/datatables/extras/TableTools/media/css/TableTools.css";
</style>
</style>
                      <script>


</html>
$(document).ready(function() {
    var oTable =  $('.ff_sample_list').dataTable({


});


<!--
});
 
</script>
== Enrichment analysis: top 100 MCL coexpression mm9 enriched with this ontology term v019 var. ==
</html>
{{#info:TOP 100 FANTOM5 Cage Peaks enriched with {{{id}}} ({{{name}}}), sorted by p-values <br>Analyst: Hideya Kawaji}}
{{#ask:[[MCL_coexpression_mm9_ontology_enrichment_uberon_id::UBERON:0002048]]
|?MCL_coexpression_mm9_ontology_enrichment_uberon_p-value|format=ttable|sort=MCL_coexpression_mm9_ontology_enrichment_uberon_p-value|order=asc|limit=100|searchlabel=}}
 
 
 
{{#sparql:select * where { ?x ?y ?z . } LIMIT 100  |endpoint=http://localhost:8080/sparql/}}
 
{{#ask:[[Category:FFCP]][[Coexpression_cluster_id::C297]]|?id|?Short_description|?Phase1_expression|format=template|template=Datatable_sampledata|sep=,|limit=20000}}
 
{{#jstest:
{{#ask:[[Category:FF Ontology]][[Sample_species::Mouse (Mus musculus)]]|?id|?Name|?sample_tissue|?sample_cell_line=|?sample_cell_type|?rna_sample_type|format=template|template=Datatable_sampledata|sep=,|limit=2000}}
}}
 
{{#sparql:
SELECT * WHERE { ?x ?y ?z FILTER regex(?z, "GO")
} LIMIT 10
|endpoint=http://go.bio2rdf.org/sparql/
|footer=NO
}}
 
 
{{#sparql:select * where { ?x ?y ?z . } LIMIT 10  |endpoint=http://localhost:8080/sparql/}}
 
{{#sparql:
PREFIX prop:<http://f5-webapp2/resource_browser/index.php/Special:URIResolver/Property-3A>
PREFIX page:<http://f5-webapp2/resource_browser/index.php/Special:URIResolver/>
SELECT ?x,?y WHERE {
?x
prop:Sample_species
?y FILTER regex(?y, "OMO", "i" )
} LIMIT 100
|endpoint=http://localhost:8080/sparql/
|headers=Page,Id
|footer=NO
}}
 


-->
{{#ask:[[Concept:FF_samples_withname]]|[[Sample_species::Human (Homo sapiens)]]|mainlabel=FF ontology id|?Name|?Sample_category|?datafreeze_phase
|format=ttable|class=ff_sample_list|limit=20|searchlabel=}}

Latest revision as of 18:50, 20 February 2014

FF ontology idNameSample categoryDatafreeze phase
10000-101A1Clontech Human Universal Reference Total RNA, pool1tissues2
10001-101A3Clontech Mouse Universal Reference Total RNA, pool1tissues2
10002-101A5SABiosciences XpressRef Human Universal Total RNA, pool1tissues2
10003-101A7SABiosciences XpressRef Mouse Universal Total RNA, pool1tissues2
10004-101A9chicken embryo whole body, day10 (HH37)tissues-1
10005-101B1{{{name}}}{{{sample_category}}}-1
10006-101B2Universal RNA - Dog Normal Tissues Biochain, pool1tissues-1
10007-101B4Universal RNA - Human Normal Tissues Biochain, pool1tissues2
10008-101B6Universal RNA - Mouse Normal Tissues Biochain, pool1tissues2
10009-101B8Universal RNA - Rat Normal Tissues Biochain, pool1tissues-1
10010-101C1adipose tissue, adult, pool1tissues2
10011-101C2bladder, adult, pool1tissues2
10012-101C3brain, adult, pool1tissues2
10013-101C4cervix, adult, pool1tissues2
10014-101C5colon, adult, pool1tissues2
10015-101C6esophagus, adult, pool1tissues2
10016-101C7heart, adult, pool1tissues2
10017-101C8kidney, adult, pool1tissues2
10018-101C9liver, adult, pool1tissues2
10019-101D1lung, adult, pool1tissues2