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Coexpression cluster:C506: Difference between revisions

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|tf_chipseq_enrich=CTCF#10664;12:3.3854250777316:2.39602138640007e-05:0.000522308657011557!GATA3#2625;6:8.60100516543348:4.38557728836884e-05:0.000777764147427328!HEY1#23462;19:4.04011104310571:3.00127317794054e-12:3.98791309708564e-10!JUN#3725;7:4.6099897024397:0.000441885070713004:0.00411612869248978!JUND#3727;16:5.89024331947034:1.90674971775736e-11:2.29422849968734e-09!NR3C1#2908;7:5.51637701674796:0.00014542250124313:0.00187967581773901!POLR2A#5430;19:2.14745317655807:4.9316078952508e-07:2.31380142395372e-05!POU5F1#5460;3:52.9640844397746:2.46415883246597e-05:0.00053404084727934!RAD21#5885;10:5.45001783971386:2.85321341547804e-06:9.81511053686135e-05!STAT3#6774;6:3.32193631489081:0.00671975157504051:0.0285622943610621!TAF7#6879;18:10.8313289099279:1.55076047024434e-18:3.52853753272002e-16!USF2#7392;7:4.78659903660459:0.000350930992195822:0.00353261512230742
|tf_chipseq_enrich=CTCF#10664;12:3.3854250777316:2.39602138640007e-05:0.000522308657011557!GATA3#2625;6:8.60100516543348:4.38557728836884e-05:0.000777764147427328!HEY1#23462;19:4.04011104310571:3.00127317794054e-12:3.98791309708564e-10!JUN#3725;7:4.6099897024397:0.000441885070713004:0.00411612869248978!JUND#3727;16:5.89024331947034:1.90674971775736e-11:2.29422849968734e-09!NR3C1#2908;7:5.51637701674796:0.00014542250124313:0.00187967581773901!POLR2A#5430;19:2.14745317655807:4.9316078952508e-07:2.31380142395372e-05!POU5F1#5460;3:52.9640844397746:2.46415883246597e-05:0.00053404084727934!RAD21#5885;10:5.45001783971386:2.85321341547804e-06:9.81511053686135e-05!STAT3#6774;6:3.32193631489081:0.00671975157504051:0.0285622943610621!TAF7#6879;18:10.8313289099279:1.55076047024434e-18:3.52853753272002e-16!USF2#7392;7:4.78659903660459:0.000350930992195822:0.00353261512230742
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|tfbs_overrepresentation_for_novel_motifs=0.38505,0.387747,0.751989,0.212191,0.311264,1.14145,0.267678,0.638099,0.349778,0.162676,1.05757,0.301621,1.55205,0.258863,0.309279,0.343795,0.450873,0.234631,0.284708,2.29871,1.23153,0.106218,0.205464,0.30387,0.14499,0.3198,1.39439,2.4704,0.0951691,0.0158228,0.997362,1.21322,0.0517705,0.492735,0.943201,0.0158821,0.257826,0.6081,0.0631864,0.0325761,0.0750527,0.492059,0.605973,0.0919607,0.184169,0.135566,0.268517,0.53703,0.78545,0.0952386,0.331306,0.760991,0.00874967,0.551494,0.691633,0.723091,0.662384,0.236404,0.0157984,0.235655,0.519357,0.270343,0.152232,0.426924,0.284296,0.397545,0.774525,1.12911,0.473932,0.971498,0.470686,0.36817,0.0433928,0.689771,0.0237,0.701812,0.38945,1.0608,0.471083,0.435465,0.542387,1.9132,0.284019,0.157796,0.642096,1.22187,0.199201,0.889441,0.352635,1.2264,0.863265,0.617268,0.497892,0.201541,0.0939013,0.0604965,0.281646,0.535841,0.937936,0.153578,0.0637978,0.492893,0.530844,0.45406,0.387815,0.186536,1.12127,0.256236,0.873416,0.602594,0.123668,0.528368,1.21021,0.570939,0.817503,0.544005,1.74804,0.173882,0.395564,0.786082,0.682065,0.350633,0.209033,0.292875,0.923346,0.413094,1.33772,0.502315,0.721838,0.0609207,0.617901,0.176632,0.73532,0.290252,0.875585,0.335759,0.980958,0.204325,0.83506,1.67608,1.2779,0.799588,0.730043,0.532681,1.01026,0.651215,0.375295,1.51807,0.486639,0.763964,1.99015,0.223402,0.618251,0.142739,0.269969,1.0011,0.339339,0.0861459,0.874255,0.399932,0.798435,0.601304,2.06255,0.129103,0.402913,0.283401,0.182347,0.266654,0.0266587
}}
}}

Revision as of 14:16, 26 November 2012


Full id: C506_Smooth_Renal_Endothelial_hepatic_Adipocyte_Fibroblast_Preadipocyte



Phase1 CAGE Peaks

Hg19::chr6:132269835..132269894,-p7@CTGF
Hg19::chr6:132269939..132269966,-p12@CTGF
Hg19::chr6:132270118..132270130,-p13@CTGF
Hg19::chr6:132270276..132270290,-p10@CTGF
Hg19::chr6:132270471..132270530,-p5@CTGF
Hg19::chr6:132270532..132270550,-p9@CTGF
Hg19::chr6:132270563..132270604,-p3@CTGF
Hg19::chr6:132270672..132270706,-p8@CTGF
Hg19::chr6:132271115..132271160,-p@chr6:132271115..132271160
-
Hg19::chr6:132271128..132271174,+p@chr6:132271128..132271174
+
Hg19::chr6:132271161..132271207,-p@chr6:132271161..132271207
-
Hg19::chr6:132271279..132271304,-p@chr6:132271279..132271304
-
Hg19::chr6:132271546..132271561,-p@chr6:132271546..132271561
-
Hg19::chr6:132271569..132271590,-p@chr6:132271569..132271590
-
Hg19::chr6:132271627..132271658,-p@chr6:132271627..132271658
-
Hg19::chr6:132271932..132271967,-p6@CTGF
Hg19::chr6:132271980..132271991,-p16@CTGF
Hg19::chr6:132271998..132272086,-p2@CTGF
Hg19::chr6:132272504..132272519,-p1@CTGF


Enriched pathways on this co-expression cluster<b>Summary:</b><br>Canonical pathway gene sets were compiled from Reactome, Wikipathways and KEGG. For the major signaling pathways, the transcriptionally-regulated genes (downstream targets) were obtained from Netpath. Combined, the canonical pathways and downstream targets totaled 489 human gene sets. The corresponding M. musculus gene sets were inferred by homology using the HomoloGene database. Enrichment for each of the canonical 489 pathways and gene sets included in the co-expression cluster was assessed by the hypergeometric probability. The resulting P values were also then adjusted by the Benjamini-Hochberg method for multiple comparisons.<br><b>Analyst: </b>Emmanuel Dimont<br><br>link to source dataset<br>data


No results for this coexpression

Enriched Gene Ontology terms on this co-expression cluster<b>Summary:</b> Results for GOStat analysis on co-expressed clusters. Each cluster with promoters mapping to at least two different genes was analysed with GOStat (PMID: 14962934) with default parameter. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br>data


No GOStat results

Enriched sample ontology terms on this co-expression cluster<b>Summary:</b>To summarize promoter activities (expression profile of a TSS region) across ~1000 samples, we performed enrichment analysis based on FANTOM5 Sample Ontology (FF ontology). The question here is “in which type of samples the promoter is more active”. To answer this question, we compared expressions (TPMs) in the samples associated with a sample ontology term and the rest of the samples by using the Mann-Whitney rank sum test. To summarize ontologies enriched in this co-expression cluster, we ran the same analysis on an averaged expression profile of all promoters that make up. <b>Analyst:</b> Hideya Kawaji <br><br>links to source dataset<br><br>cell_data<br>uberon_data<br><br>


Uber Anatomy
Ontology termp-valuen
vasculature1.21e-3278
vascular system1.21e-3278
vessel5.01e-2868
splanchnic layer of lateral plate mesoderm1.99e-2783
epithelial tube1.48e-26117
cardiovascular system3.07e-26109
circulatory system7.70e-26112
epithelial tube open at both ends5.57e-2559
blood vessel5.57e-2559
blood vasculature5.57e-2559
vascular cord5.57e-2559
artery3.52e-2242
arterial blood vessel3.52e-2242
arterial system3.52e-2242
unilaminar epithelium6.40e-20148
systemic artery4.66e-1733
systemic arterial system4.66e-1733
trunk mesenchyme1.01e-16122
epithelial vesicle8.39e-1678
muscle tissue1.04e-1564
musculature1.04e-1564
musculature of body1.04e-1564
skeletal muscle tissue1.70e-1562
striated muscle tissue1.70e-1562
myotome1.70e-1562
mesenchyme3.13e-14160
entire embryonic mesenchyme3.13e-14160
dense mesenchyme tissue1.07e-1373
somite1.26e-1371
presomitic mesoderm1.26e-1371
presumptive segmental plate1.26e-1371
dermomyotome1.26e-1371
trunk paraxial mesoderm1.26e-1371
paraxial mesoderm3.77e-1372
presumptive paraxial mesoderm3.77e-1372
trunk6.37e-13199
aorta5.44e-1221
aortic system5.44e-1221
organism subdivision1.32e-11264
squamous epithelium9.88e-1125
multilaminar epithelium1.01e-1083
simple squamous epithelium1.69e-1022
mesoderm3.27e-10315
mesoderm-derived structure3.27e-10315
presumptive mesoderm3.27e-10315
anatomical cluster3.50e-10373
cell layer6.17e-10309
anatomical conduit7.30e-10240
epithelium1.51e-09306
blood vessel endothelium3.01e-0918
endothelium3.01e-0918
cardiovascular system endothelium3.01e-0918
tube1.74e-08192
multi-cellular organism1.77e-07656
heart3.17e-0724
primitive heart tube3.17e-0724
primary heart field3.17e-0724
anterior lateral plate mesoderm3.17e-0724
heart tube3.17e-0724
heart primordium3.17e-0724
cardiac mesoderm3.17e-0724
cardiogenic plate3.17e-0724
heart rudiment3.17e-0724
smooth muscle tissue6.23e-0715
primary circulatory organ9.14e-0727


Overrepresented TFBS (DNA) motifs on this co-expression cluster<b>Summary:</b>The values shown are the p-values for overrepresentation of the motif in this coexpression cluster. So a small p-value means a strong overrepresentation. <b>Analyst:</b> Michiel de Hoon <br><br>link to source data <br> Novel motifs <br>data <br><br> Jaspar motifs <br>data


Novel motifs



JASPAR motifs

Motifs-log10(p-value)

{{{tfbs_overrepresentation_jaspar}}}



ENCODE TF ChIP-seq peak enrichment analysis<b>Summary:</b> For each TF and each co-expression cluster, the number of promoters with ENCODE TF ChIP signal was compared with the rest of promoters from the robust set using Fisher's exact test. Clusters with significant ChIP enrichment (q <= 0.05) after Benjamini-Hochberg correction were retained. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br><br>data


(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
CTCF#10664123.38542507773162.39602138640007e-050.000522308657011557
GATA3#262568.601005165433484.38557728836884e-050.000777764147427328
HEY1#23462194.040111043105713.00127317794054e-123.98791309708564e-10
JUN#372574.60998970243970.0004418850707130040.00411612869248978
JUND#3727165.890243319470341.90674971775736e-112.29422849968734e-09
NR3C1#290875.516377016747960.000145422501243130.00187967581773901
POLR2A#5430192.147453176558074.9316078952508e-072.31380142395372e-05
POU5F1#5460352.96408443977462.46415883246597e-050.00053404084727934
RAD21#5885105.450017839713862.85321341547804e-069.81511053686135e-05
STAT3#677463.321936314890810.006719751575040510.0285622943610621
TAF7#68791810.83132890992791.55076047024434e-183.52853753272002e-16
USF2#739274.786599036604590.0003509309921958220.00353261512230742



Relative expression of the co-expression cluster<b>Summary:</b>Co-expression clusters are compared against FANTOM5 samples to obtain relative expression. <br><b>Analyst:</b>NA<br><br>link to data source<br> data


This analysis result is provided for C0 - C305 clusters.