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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
== enrichment analysis ==
<html>
<html>
<script type="text/javascript" language="javascript" src="/resource_browser/rb_js/datatables/media/js/jquery.dataTables.js"></script>
<script type="text/javascript" language="javascript" src="/resource_browser/rb_js/datatables/media/js/jquery.dataTables.min.js"></script>
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<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";
.table_title{
text-align:left;
font-size:small;
text-decoration:underline;
color:darkgoldenrod;
}
</style>
</style>
<script type="text/javascript">
                      <script>


$(document).ready(function() {
$(document).ready(function() {
var motifs = ['9-AATRCATCGC,CNhs12311,BestGuessHOXA2(Homeobox)mES-Hoxa2-ChIP-SeqHomer(0.61615700032211),T1085.0(24.58),B7771.7(17.68),P1e-30','9-ACTTMCTHC,CNhs13493,BestGuessEP300.p2.SwissRegulon.nucfreq(0.665506750413533),T2818.0(39.99),B12528.2(29.94),P1e-71','9-CGGAAACAA,CNhs11957,BestGuessFOXO1,3,4.p2.SwissRegulon.nucfreq(0.721285301542419),T1250.0(25.22),B6798.2(16.04),P1e-60','9-CTGTTGCGT,CNhs13539,BestGuessMYB.p2.SwissRegulon.nucfreq(0.68195734924287),T452.0(17.24),B4321.7(9.78),P1e-31','9-CTSASTCACTG,CNhs13543,BestGuessNFE2.p2.SwissRegulon.nucfreq(0.727267229928719),T717.0(9.78),B1675.4(4.03),P1e-100','9-GATCCGCTA,CNhs13799,BestGuessSPIB.p2.SwissRegulon.nucfreq(0.570792469807206),T1309.0(27.04),B8805.0(20.32),P1e-28','9-GCTAGCAAAA,CNhs13793,BestGuessDBP.p2.SwissRegulon.nucfreq(0.728928404467759),T2240.0(45.56),B16055.4(37.11),P1e-33','9-GGGGTTT,CNhs11958,BestGuessREL_do_HM09(0.715499181166044),T3541.0(67.28),B24463.4(56.33),P1e-58','9-GTAGGAT,CNhs13793,BestGuessDBP.p2.SwissRegulon.nucfreq(0.647270678335512),T1365.0(27.76),B9057.4(20.93),P1e-29','9-HGASWSVGYG,CNhs11049,BestGuessEGR3_f1_HM09(0.70241249964471),T910.0(37.05),B11649.9(25.90),P1e-33','9-RTKACAA,CNhs13472,BestGuessNF2L1_f1_HM09(0.747270056750428),T2114.0(48.54),B17431.8(38.80),P1e-38','9-TAGTTACCG,CNhs12354,BestGuessTLX2.p2.SwissRegulon.nucfreq(0.695631589497027),T1640.0(53.47),B18986.6(42.47),P1e-33','9-TATAWACGC,CNhs13227,BestGuessGZF1.p2.SwissRegulon.nucfreq(0.693521774730849),T1373.0(43.67),B14343.1(32.03),P1e-41','9-TATCCGMH,CNhs12592,BestGuessGATA4_f1_HM09(0.743624209455324),T711.0(21.51),B5961.7(13.21),P1e-38','9-TDDCRNMASM,CNhs10860,BestGuessCEBPB_f1_HM09(0.709901533954884),T948.0(36.59),B11030.9(23.95),P1e-46','9-TTTCSCT,CNhs13465,BestGuessPRDM1_f1_HM09(0.744373968197745),T2971.0(42.71),B14173.2(33.73),P1e-54','9-VCTTKCTKC,CNhs13512,BestGuessETS1,2.p2.SwissRegulon.nucfreq(0.628080460919971),T529.0(20.76),B5677.6(12.79),P1e-28','AAAAGCACTGC,motif961,CNhs10641,T748.0(21.57),B9310.8(14.67),P1e-27','AAAARAAG,motif736,CNhs12620,T1550.0(44.93),B26897.8(35.63),P1e-28','AAACCCCCCC,motif448,CNhs10859,T1212.0(25.67),B14114.0(18.58),P1e-32','AAACTATA,motif684,CNhs11065,T1202.0(43.35),B23571.4(33.01),P1e-29','AAATAGGGAAGT,motif184,CNhs13543,T336.0(5.80),B2009.5(2.52),P1e-41','AAGACTACCA,motif544,CNhs12641,T803.0(24.83),B12552.7(16.71),P1e-31','AAGATCGAS,motif641,CNhs13817,T2008.0(51.63),B32508.3(42.50),P1e-29','AAGCAGGAA,motif523,CNhs12858,T1008.0(23.49),B12051.4(16.48),P1e-31','AATGGGG,motif928,CNhs11973,T1645.0(49.52),B29608.4(40.14),P1e-27','AATTCCCGG,motif577,CNhs12560,T1350.0(48.95),B26720.6(38.03),P1e-30','AAYAATC,motif540,CNhs10645,T2136.0(58.04),B31315.1(48.39),P1e-31','ACGAGACGGATGA,motif936,CNhs13469,T2517.0(39.98),B26480.2(33.41),P1e-27','ACGTCACAA,motif25,CNhs10632,T722.0(14.44),B3997.1(5.56),P1e-117','AGACTCAGA,motif213,CNhs11954,T2894.0(47.76),B30571.8(39.29),P1e-40','AGAGAAAGAG,motif627,CNhs13800,T1307.0(31.40),B16632.6(23.59),P1e-30','AGCASAGGA,motif488,CNhs10633,T759.0(25.44),B12115.7(16.81),P1e-32','AGKAGGACCA,motif546,CNhs12639,T328.0(9.62),B3566.5(4.78),P1e-31','AGTCTCAAGTT,motif953,CNhs10616,T349.0(10.26),B3876.2(5.52),P1e-27','AGTTTCCGC,motif855,CNhs11086,T446.0(21.91),B8660.3(13.01),P1e-27','AHR_si','AIRE','AIRE_f2','ALX1','AP2A_f2','ARAGGGGK,motif561,CNhs13793,T2326.0(51.61),B30125.2(42.94),P1e-31','ARI3A_do','ARI5B_f1','AR_LNCAP-AR-ChIP-SeqHomer','ATAGCGAC,motif639,CNhs13802,T2743.0(58.30),B34247.7(49.97),P1e-29','ATCATTTCC,motif740,CNhs13494,T486.0(8.40),B3892.4(4.91),P1e-28','ATF5_si','ATF6','ATGATGGTGGC,motif457,CNhs12843,T50.0(1.78),B127.6(0.17),P1e-32','ATGGAGGTCGTC,motif943,CNhs12639,T1721.0(50.48),B30752.6(41.23),P1e-27','ATTGGCGGCG,motif630,CNhs12908,T541.0(17.89),B7449.1(10.87),P1e-29','ATYACCC,motif728,CNhs12546,T3248.0(60.25),B39802.9(52.64),P1e-28','BPTF_si','CAAACTTAGCC,motif480,CNhs11765,T810.0(22.10),B10902.5(14.70),P1e-32','CAATGATGG,motif925,CNhs11923,T611.0(22.85),B10770.1(14.86),P1e-27','CACACTTTTTA,motif844,CNhs13817,T598.0(15.38),B7445.3(9.73),P1e-27','CACGAAG,motif790,CNhs12639,T1550.0(45.47),B26976.9(36.16),P1e-28','CACTTCCTTCCT,motif281,CNhs13543,T307.0(5.30),B1859.8(2.33),P1e-37','CAGAGTTCTAG,motif792,CNhs10632,T515.0(10.30),B4438.2(6.17),P1e-28','CARGWTGY,motif333,CNhs13223,T664.0(25.10),B11666.0(15.61),P1e-35','CATCCATGTC,motif545,CNhs11972,T1380.0(42.86),B24137.1(32.95),P1e-31','CATTAGGACCAG,motif719,CNhs12639,T215.0(6.31),B1988.9(2.67),P1e-28','CATTRTGACG,motif6,CNhs12998,T457.0(10.92),B1694.9(2.30),P1e-161','CAYAAST,motif606,CNhs13474,T1925.0(38.98),B24678.6(31.21),P1e-30','CCAATCCGGT,motif823,CNhs11913,T370.0(14.93),B5558.6(8.19),P1e-28','CCAGTACA,motif794,CNhs11974,T2601.0(47.87),B30203.6(40.41),P1e-28','CCCACAGACTCAG,motif858,CNhs11672,T90.0(2.92),B567.3(0.70),P1e-27','CCCCCTATTA,motif248,CNhs11772,T1384.0(40.03),B20640.3(29.61),P1e-38','CCCCCTCTCTCC,motif580,CNhs11772,T482.0(13.94),B5609.6(8.05),P1e-30','CCCGAAC,motif795,CNhs13421,T857.0(30.27),B14974.5(21.33),P1e-28','CCCGATCC,motif958,CNhs12065,T1270.0(44.20),B24777.2(34.39),P1e-27','CCGCCAATYC,motif849,CNhs12065,T944.0(32.86),B17115.1(23.75),P1e-27'];
    var oTable = $('.ff_sample_list').dataTable({
var pval = [1,1,1,1,6.13482e-09,1,1,1,1,1,0.999604,1,1,1,1,1,1,1,1,1,1,0.00708028,1,1,1,1,0.999946,1,1,1,1,1,0.997015,1,1,1,1,1,1,1,1,0.999984,1,1,1,0.00816367,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,0.0100364,1,1,0.96714,1,1,1,1,1,1,1,1,1,1,1,1,1,0.999993,1,1,1,1,1,1,1,1,1,1,5.89797e-08,0.999999,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,0.993238,1,1,1,1,1,1,1,1,0.0390238,1,1,0.343053,1,1,0.980803,1,1,1,0.999689,1,1,1,1,1,1,1,1,1,1,1,1,0.825871,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,0.997359,1,1,1,1,1,1,1,1,1,1,1,1,0.999947,1,1,0.998966,1,1,1,1,1,1,1,1,1,1,1,1,1,0.911901,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,0.999755,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,0.000493084,8.77295e-51,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,0.998598,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,0.999987,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,0.999974,1,1,1,1,1,1,1,1,1,1,1,1,0,1,1,1,1,1,1,1,0.991086,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,0.906871,1,0.994737,1,0.834479,1,0.997178,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,0.993321,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1.05417e-08,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,0.835013,1,9.23934e-10,1,1,1,1,1,1,1,1,1,1,1,1,1,0.997324,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,0.999999,0.938664,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,0.337207,1,1,1,1,1,1,0.999988,1,1,1,0.645058,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,0.999992,1.51362e-09,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,0.988897,1,0.99984,1,1,1,0.999998,1,1,0.989695,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,9.93892e-06,1,1,1,1,1,1,1,1,1,1,1,1,1,0.702219,1,1,1,1,1,1,1,1,1,1,1,1,6.60378e-15,1.49915e-09,1,1,1,7.26153e-12,1.56756e-07,1,1,0.560302,1,1,0.199247,1.76124e-05,0.99994,1,1,1,2.55112e-06,0.323866,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1.42689e-05,1,1,1,0.561362,1,1,1,0.0545097,1,5.60293e-08,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,0.003232,1,0.999999,1,1,1,1,1.86691e-11,1,1,1,1,0.879851,0.953685,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,0.606544,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,0.999975,1,1,1,0.999998,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,0.00434176,1,1,1,0.999999,1,1,1,1,1,1,1,0.999999,1,1,1,1,1,1,1,0.99999,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,0.999976,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,0.998762,1,0.303727,1,1,2.07678e-05,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,0.999991,1,2.07441e-34,1,0.957223,1,1,1,1,1,1,1,1,1,0.999946,1,1,1,0.999943,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1];
var data = [];
for(i1=0;i1<motifs.length;i1++){
data.push([motifs[i1],pval[i1]]);
}


    $('#tfbs_overexpression_table').dataTable({
//"aaData": [["one", 1],["two", 3],["three", 0]],
"aaData": data,
"aoColumns": [{ "sTitle": "Motifs", "sWidth": "200pt", "fnRender": function(obj) {
return sReturn = obj.aData[ obj.iDataColumn ].replace("BestGuess","<br>BestGuess");
} },{ "sTitle": "p-value" }]
});
});
});
});
</script>
</script>
<table id="tfbs_overexpression_table"></table>
</html>
</html>


 
{{#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=}}
{{REVISIONTIMESTAMP}}
{{#ifexpr: {{#expr: {{REVISIONTIMESTAMP}}-20120731160000 }} > 0 | yes }}
 
{{CURRENTTIMESTAMP}}
 
<!--
{{#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
}}
 
 
-->

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
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