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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 ==
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$(document).ready(function() {
var motifs = 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u_f1','CNhs11786_bl_f2','CNhs11786_bu_f1','CNhs11789_bl_f2','CNhs11793_bu_f1','CNhs11811_bl_f2','CNhs11822_bl_f1','CNhs11822_bl_f2','CNhs11828_bl_f2','CNhs11828_bu_f0','CNhs11828_bu_f1','CNhs11828_bu_f2','CNhs11833_bl_f2','CNhs11840_bl_f0','CNhs11840_bl_f2','CNhs11842_bl_f0','CNhs11848_bu_f2','CNhs11853_bu_f1','CNhs11862_bl_f2','CNhs11882_bl_f2','CNhs11882_bu_f2','CNhs11892_bl_f2','CNhs11893_bl_f1','CNhs11893_bu_f2','CNhs11931_bu_f2','CNhs11986_bl_f2','CNhs11986_bu_f1','CNhs11990_bl_f1','CNhs11990_bl_f2','CNhs12001_bu_f0','CNhs12008_bl_f1','CNhs12008_bu_f2','CNhs12013_bu_f2','CNhs12028_bl_f2','CNhs12030_bl_f0','CNhs12035_bu_f0','CNhs12036_bu_f2','CNhs12040_bu_f2','CNhs12043_bu_f1','CNhs12065_bl_f2','CNhs12087_bl_f0','CNhs12087_bu_f1','CNhs12092_bu_f2','CNhs12093_bu_f2','CNhs12096_bl_f2','CNhs12098_bu_f2','CNhs12102_bl_f1','CNhs12103_bl_f1','CNhs12105_bl_f2','CNhs12128_bu_f2','CNhs12192_bu_f0','CNhs12316_bu_f2','CNhs12323_bu_f0','CNhs12341_bl_f2','CNhs12345_bu_f2','CNhs12348_bl_f1','CNhs12494_bl_f0','CNhs12494_bu_f1','CNhs12497_bu_f2','CNhs12498_bl_f2','CNhs12500_bl_f2','CNhs12500_bu_f2','CNhs12502_bl_f1','CNhs12518_bu_f0','CNhs12522_bl_f0','CNhs12523_bl_f1','CNhs12524_bu_f2','CNhs12525_bl_f0','CNhs12530_bu_f2','CNhs12545_bl_f2','CNhs12546_bu_f2','CNhs12566_bl_f1','CNhs12574_bl_f1','CNhs12622_bl_f1','CNhs12623_bl_f2','CNhs12623_bu_f2','CNhs12625_bl_f1','CNhs12625_bu_f2','CNhs12626_bu_f0','CNhs12626_bu_f2','CNhs12627_bu_f2','CNhs12703_bl_f2','CNhs12727_bl_f1','CNhs12733_bl_f2','CNhs12825_bl_f2','CNhs12838_bl_f1','CNhs12839_bu_f2','CNhs12846_bl_f1','CNhs12846_bl_f2','CNhs12849_bu_f0','CNhs12849_bu_f1','CNhs12851_bu_f0','CNhs12856_bu_f2','CNhs12857_bu_f2','CNhs12859_bu_f2','CNhs12920_bl_f2','CNhs12922_bu_f1','CNhs12952_bu_f0','CNhs13059_bl_f0','CNhs13060_bl_f1','CNhs13063_bl_f2','CNhs13063_bu_f1','CNhs13068_bl_f2','CNhs13099_bl_f0','CNhs13099_bu_f2','CNhs13156_bu_f0','CNhs13435_bu_f1','CNhs13439_bl_f1','CNhs13449_bl_f1','CNhs13458_bl_f1','CNhs13458_bl_f2','CNhs13458_bu_f2','CNhs13460_bu_f2','CNhs13464_bu_f2','CNhs13480_bl_f0','CNhs13498_bu_f1','CNhs13505_bu_f1','CNhs13549_bu_f2','CNhs13550_bl_f1','CNhs13793_bl_f2','CNhs13800_bu_f2','CNhs13801_bl_f2','CNhs13847_bu_f0','COE1_f2','CRACCWA','CRATCGC','CREB1_f1','CRX_Retina-Crx-ChIP-Seq/Homer','CSAAYWAG','CTACCAGTAC','CTACTTC','CTBGTCBTC','CTCCTGTTCC','CTCF_f2','CTCTCGATC','CTCTTAGTCATG','CTCTTCCAGTTC','CTSTTTCTTTAAG','CTTCTTTCC','DBP','DDIT3_f1','DMC1_Testis-DMC1-ChIP-Seq/Homer','E2F4_do','EBNA1_Raji-EBNA1-ChIP-Seq(GSE30709)/Homer','EGR1_K562-EGR1-ChIP-Seq/Homer','EOMES_f1','EPAS1_si','ESR1_do','ETV1_GIST48-ETV1-ChIP-Seq/Homer','EVI1_f1','FOSL2_f1','FOXA1_LNCAP-FOXA1-ChIP-Seq/Homer','FOXC2_f1','FOXD1_si','FOXM1','FOXO1_si','FOXP3','FOXP3_f1','FOX{C1','FUBP1_f1','GAAAAGC','GAAGSCG','GAATTSGA','GAGAGACAAAGG','GATA1..3','GATA1_si','GATCGCT','GATTGGTGCAG','GATTTTTWT','GAYCAGG','GCAGGAAACCACAG','GCCGCAAAC','GCCGCTTTAA','GCGCGCG','GCGGACTGAA','GCM1_f1','GCTCCGCTC','GFI1_f1','GGAAGAACTAG','GGACAAG','GGACCCCCTA','GGACCGCCG','GGAGKYTTAA','GGATGACGAA','GGCAACTTCT','GGGAATTTTTG','GGGGGAAAGAAA','GGGTGACTCGTA','GGGTTGCGTCA','GGTGACACAKC','GLI3_si','GTACGRC','GTAGATGTTGA','GTAGTCGA','GTATTAGG','GTCACCCTCA','GTGAATG','GTGACTSGG','GTTCCTATT','GTTGCTCAACAG','GTTGTAGCCC','GTWCAACA','GZF1','HES1_f1','HEY2_f1','HLTF_f1','HMGA2_f1','HNF1A','HNF4A_f1','HNF4G_f1','HNF6_f1','HOXC9_Ainv15-Hoxc9-ChIP-Seq/Homer','HOX{A5','HSF1_f2','HXA13_f1','HXB7_si','HXC8_f1','HXD13_f1','HXD4_f1','HXD9_f1','INSM1_f1','IRF2_f1','IRF5_f1','ISL1_f1','KAISO_f1','KCCGCCDY','KLF12','KLF4_mES-Klf4-ChIP-Seq/Homer','KLF8_f1','LHX2_f1','LHX3','MAFA_f1','MCR_f1','MEF2{A','MEIS1_f2','MLXPL_f1','MSX2_f1','MTE{core}','MTF1_f1','MYBB_f1','MYB_ERMYB-Myb-ChIPSeq(GSE22095)/Homer','NAAAGTT','NANOG_mES-Nanog-ChIP-Seq/Homer','NEUROD1_Islet-NeuroD1-ChIP-Seq(GSE30298)/Homer','NFAC2_f1','NFAT5_f1','NFATC1_motifA:Jurkat-NFATC1-ChIP-Seq/Homer','NFIX','NFKB1_REL_RELA','NFYB_f1','NKX2-1','NKX21_f1','NKX22_si','NKX3-2','NR0B1_si','NR1H4_f1','NR1I3_f2','NR1I3_si','NR2C2_Hela-TR4-ChIP-Seq/Homer','NR6A1_do','NRF1_MCF7-NRF1-ChIP-Seq/Homer','P73_si','PAX3_Rh4-PAX3:FKHR-ChIP-Seq/Homer','PAX4','PAX5_f1','PAX5_motifB:GM12878-PAX5-ChIP-Seq/Homer','PAX6_f1','PAX8_f1','PBX3_GM12878-PBX3-ChIP-Seq/Homer','PKNX1_si','PLAG1_f1','PLAG1_si','PO3F2_si','PO5F1_do','PO6F1_f1','POU1F1','POU3F1..4','POU5F1_mES-Oct4-ChIP-Seq/Homer','PRGR_f1','PROP1_f1','PRRX2_f1','PTF1A_f1','PURA_f1','RAGAGAGAGAGAG','RARA_f1','RARG_do','REST_f1','RFX1_NPC-Rfx1-ChIP-Seq/Homer','RGAAAGSAGAAG','RGCGGCSGC','RORA_f1','RRCGAACC','RREB1_si','RTATACTKT','RUNX1..3','RXR{A','SGAGMKTAK','SMAD3_f1','SNAI2_f1','SOX17_f2','SOX18_f1','SOX2','SP1_f1','SP4_f1','SPDEF_VCaP-SPDEF-ChIP-Seq/Homer','SPZ1','SREBP1A_HepG2-Srebp1a-ChIP-Seq/Homer','SRF_do','STAT4_CD4-Stat4-ChIP-Seq/Homer','STCGWAG','STTCGVC','SUH_f1','TAACTGTACA','TACAGTATTC','TACCGGATC','TACCGGT','TACCTCCGC','TACTGYAG','TAGAMCCTAT','TAGGAAAC','TAGGCGA','TAGTCTGACG','TATCCCATT','TBP','TBX20_Heart-Tbx20-ChIP-Seq(GSE29636)/Homer','TBX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    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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