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Coexpression cluster:C142: Difference between revisions

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|tf_chipseq_enrich=ESR1#2099;15:3.75226869465299:1.20118707854347e-05:0.000300841192556358!GATA3#2625;11:2.43578601568509:0.00578043597670573:0.0259936685886402!POLR2A#5430;122:2.12999420764296:2.02515758995374e-39:1.14948605183249e-36
|tf_chipseq_enrich=ESR1#2099;15:3.75226869465299:1.20118707854347e-05:0.000300841192556358!GATA3#2625;11:2.43578601568509:0.00578043597670573:0.0259936685886402!POLR2A#5430;122:2.12999420764296:2.02515758995374e-39:1.14948605183249e-36
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|tfbs_overrepresentation_for_novel_motifs=0.0494758,5.37935e-06,0.0440386,3.63189,1.36297,3.15795,0.616918,0.288916,0.0949513,0.00537324,0.627363,3.11282,0.0511997,0.0153294,0.205619,1.33605,0.0264237,4.61582,4.32768,0.0698014,0.635955,0.000134916,0.0580559,0.195753,0.909201,0.10113,2.49122,1.53282,0.00911236,0.00822373,0.241871,0.585225,0.00566996,0.0192661,0.38901,0.00747332,3.51496e-05,0.133083,0.0248538,7.96562e-05,8.84418,0.120314,2.31072,0.129322,5.80715e-05,0.0695649,0.413427,1.59683,3.65856,0.141125,0.647502,0.14622,1.40172,0.4441,0.113183,0.388217,1.70261,0.0907296,0.00818421,0.683069,0.68379,0.0586848,0.279359,0.23328,0.289046,1.28662,0.476027,0.405303,2.7736,0.285172,0.0218004,0.0728283,8.88856e-11,0.730544,3.26143e-06,1.4501e-06,0.65933,0.0186993,4.62334,0.0784077,0.172018,0.231929,0.288355,0.0116938,0.0900678,1.19094e-11,8.92678e-05,0.354098,0.00982828,0.485231,0.2113,0.0794624,0.0381646,0.642891,1.08041e-05,2.04323,0.00704118,0.185629,0.0102859,2.74409e-11,0.0121839,0.611445,0.0479241,0.11375,2.55872,0.0150874,0.0241383,0.371977,0.00114009,0.168692,5.19321e-05,0.401077,1.47526,0.0498599,0.182646,0.0397463,7.8994e-05,0.368705,2.1358,0.403447,0.108521,2.69414,1.27712,0.310828,0.251317,0.0188162,0.83762,0.0394013,0.128502,0.0732711,0.0797246,4.27318,0.135627,0.0240794,1.83151,1.63895e-05,0.511915,2.62589,0.193442,0.889919,0.528969,1.56688,1.81331,0.40898,1.64064,0.0334181,0.06123,0.742828,4.35875,0.00637152,0.0129395,3.10996e-14,1.45282,0.0288917,0.254122,0.306705,3.07295,0.257713,0.909576,0.0265388,0.171209,2.50487,0.552016,0.0032092,0.386836,0.286812,0.226766,3.60607,1.6478e-09
}}
}}

Revision as of 13:34, 26 November 2012


Full id: C142_Preadipocyte_Fibroblast_hepatic_Ewing_Adipocyte_Olfactory_Hair



Phase1 CAGE Peaks

Hg19::chr15:39873268..39873287,+p1@THBS1
Hg19::chr15:39873352..39873390,-p@chr15:39873352..39873390
-
Hg19::chr15:39874384..39874412,+p@chr15:39874384..39874412
+
Hg19::chr15:39874415..39874435,+p@chr15:39874415..39874435
+
Hg19::chr15:39874416..39874433,-p@chr15:39874416..39874433
-
Hg19::chr15:39874450..39874555,+p@chr15:39874450..39874555
+
Hg19::chr15:39874545..39874592,-p@chr15:39874545..39874592
-
Hg19::chr15:39874573..39874603,+p@chr15:39874573..39874603
+
Hg19::chr15:39874611..39874645,-p@chr15:39874611..39874645
-
Hg19::chr15:39874624..39874636,+p@chr15:39874624..39874636
+
Hg19::chr15:39874646..39874658,+p@chr15:39874646..39874658
+
Hg19::chr15:39874647..39874660,-p@chr15:39874647..39874660
-
Hg19::chr15:39874673..39874718,+p@chr15:39874673..39874718
+
Hg19::chr15:39874750..39874781,-p@chr15:39874750..39874781
-
Hg19::chr15:39874775..39874799,+p@chr15:39874775..39874799
+
Hg19::chr15:39874801..39874813,+p@chr15:39874801..39874813
+
Hg19::chr15:39874814..39874827,+p@chr15:39874814..39874827
+
Hg19::chr15:39874833..39874882,-p@chr15:39874833..39874882
-
Hg19::chr15:39874839..39874842,+p@chr15:39874839..39874842
+
Hg19::chr15:39874845..39874911,+p@chr15:39874845..39874911
+
Hg19::chr15:39874927..39874939,+p@chr15:39874927..39874939
+
Hg19::chr15:39875809..39875867,+p@chr15:39875809..39875867
+
Hg19::chr15:39876176..39876314,+p@chr15:39876176..39876314
+
Hg19::chr15:39876228..39876300,-p@chr15:39876228..39876300
-
Hg19::chr15:39876325..39876356,+p@chr15:39876325..39876356
+
Hg19::chr15:39876334..39876355,-p@chr15:39876334..39876355
-
Hg19::chr15:39876490..39876590,+p@chr15:39876490..39876590
+
Hg19::chr15:39876528..39876544,-p@chr15:39876528..39876544
-
Hg19::chr15:39876566..39876609,-p@chr15:39876566..39876609
-
Hg19::chr15:39876615..39876625,-p@chr15:39876615..39876625
-
Hg19::chr15:39877655..39877744,+p15@THBS1
Hg19::chr15:39877742..39877767,-p@chr15:39877742..39877767
-
Hg19::chr15:39879545..39879692,+p7@THBS1
Hg19::chr15:39879648..39879683,-p@chr15:39879648..39879683
-
Hg19::chr15:39880241..39880341,+p8@THBS1
Hg19::chr15:39880315..39880385,-p@chr15:39880315..39880385
-
Hg19::chr15:39880345..39880367,+p19@THBS1
Hg19::chr15:39880370..39880395,+p25@THBS1
Hg19::chr15:39880723..39880752,+p2@THBS1
Hg19::chr15:39880753..39880767,+p9@THBS1
Hg19::chr15:39880777..39880827,+p3@THBS1
Hg19::chr15:39880843..39880887,-p@chr15:39880843..39880887
-
Hg19::chr15:39880854..39880863,+p35@THBS1
Hg19::chr15:39881152..39881262,+p4@THBS1
Hg19::chr15:39881200..39881244,-p@chr15:39881200..39881244
-
Hg19::chr15:39881392..39881514,+p@chr15:39881392..39881514
+
Hg19::chr15:39881480..39881526,-p@chr15:39881480..39881526
-
Hg19::chr15:39881517..39881536,+p@chr15:39881517..39881536
+
Hg19::chr15:39881528..39881548,-p@chr15:39881528..39881548
-
Hg19::chr15:39881997..39882024,+p@chr15:39881997..39882024
+
Hg19::chr15:39882038..39882076,+p@chr15:39882038..39882076
+
Hg19::chr15:39882038..39882106,-p@chr15:39882038..39882106
-
Hg19::chr15:39882120..39882131,-p@chr15:39882120..39882131
-
Hg19::chr15:39882147..39882159,+p@chr15:39882147..39882159
+
Hg19::chr15:39882160..39882178,+p@chr15:39882160..39882178
+
Hg19::chr15:39882174..39882185,-p@chr15:39882174..39882185
-
Hg19::chr15:39882188..39882206,+p@chr15:39882188..39882206
+
Hg19::chr15:39882711..39882733,+p14@THBS1
Hg19::chr15:39882740..39882785,+p6@THBS1
Hg19::chr15:39882788..39882816,-p@chr15:39882788..39882816
-
Hg19::chr15:39883385..39883407,+p5@THBS1
Hg19::chr15:39883443..39883468,+p10@THBS1
Hg19::chr15:39883501..39883528,-p@chr15:39883501..39883528
-
Hg19::chr15:39883509..39883520,+p23@THBS1
Hg19::chr15:39883697..39883741,+p@chr15:39883697..39883741
+
Hg19::chr15:39883769..39883790,+p@chr15:39883769..39883790
+
Hg19::chr15:39884760..39884827,+p17@THBS1
Hg19::chr15:39884839..39884858,+p29@THBS1
Hg19::chr15:39884859..39884872,+p36@THBS1
Hg19::chr15:39884872..39884923,-p@chr15:39884872..39884923
-
Hg19::chr15:39884878..39884898,+p30@THBS1
Hg19::chr15:39884901..39884916,+p22@THBS1
Hg19::chr15:39884917..39884949,+p24@THBS1
Hg19::chr15:39884924..39884945,-p@chr15:39884924..39884945
-
Hg19::chr15:39884950..39884967,+p28@THBS1
Hg19::chr15:39885197..39885322,+p13@THBS1
Hg19::chr15:39885323..39885396,+p16@THBS1
Hg19::chr15:39885590..39885644,+p20@THBS1
Hg19::chr15:39885653..39885673,+p32@THBS1
Hg19::chr15:39885701..39885737,+p27@THBS1
Hg19::chr15:39885742..39885808,+p18@THBS1
Hg19::chr15:39885810..39885845,+p21@THBS1
Hg19::chr15:39886290..39886353,+p11@THBS1
Hg19::chr15:39886357..39886368,+p31@THBS1
Hg19::chr15:39886495..39886505,+p39@THBS1
Hg19::chr15:39886511..39886611,+p12@THBS1
Hg19::chr15:39887636..39887649,+p@chr15:39887636..39887649
+
Hg19::chr15:39887636..39887649,-p@chr15:39887636..39887649
-
Hg19::chr15:39887667..39887675,+p@chr15:39887667..39887675
+
Hg19::chr15:39887702..39887713,+p@chr15:39887702..39887713
+
Hg19::chr15:39887744..39887747,+p@chr15:39887744..39887747
+
Hg19::chr15:39887886..39887897,+p@chr15:39887886..39887897
+
Hg19::chr15:39887918..39887929,+p@chr15:39887918..39887929
+
Hg19::chr15:39887951..39887958,+p@chr15:39887951..39887958
+
Hg19::chr15:39887969..39887972,+p@chr15:39887969..39887972
+
Hg19::chr15:39888008..39888026,+p@chr15:39888008..39888026
+
Hg19::chr15:39888011..39888097,-p@chr15:39888011..39888097
-
Hg19::chr15:39888029..39888054,+p@chr15:39888029..39888054
+
Hg19::chr15:39888070..39888084,+p@chr15:39888070..39888084
+
Hg19::chr15:39888092..39888103,+p@chr15:39888092..39888103
+
Hg19::chr15:39888108..39888125,+p@chr15:39888108..39888125
+
Hg19::chr15:39888129..39888145,+p@chr15:39888129..39888145
+
Hg19::chr15:39888147..39888161,+p@chr15:39888147..39888161
+
Hg19::chr15:39888222..39888232,+p@chr15:39888222..39888232
+
Hg19::chr15:39888305..39888312,+p@chr15:39888305..39888312
+
Hg19::chr15:39888341..39888350,+p@chr15:39888341..39888350
+
Hg19::chr15:39888375..39888402,-p@chr15:39888375..39888402
-
Hg19::chr15:39888386..39888393,+p@chr15:39888386..39888393
+
Hg19::chr15:39888428..39888447,+p@chr15:39888428..39888447
+
Hg19::chr15:39888451..39888489,+p@chr15:39888451..39888489
+
Hg19::chr15:39888509..39888542,+p@chr15:39888509..39888542
+
Hg19::chr15:39888616..39888632,+p@chr15:39888616..39888632
+
Hg19::chr15:39888645..39888657,+p@chr15:39888645..39888657
+
Hg19::chr15:39888667..39888675,+p@chr15:39888667..39888675
+
Hg19::chr15:39888763..39888780,+p@chr15:39888763..39888780
+
Hg19::chr15:39888814..39888825,+p@chr15:39888814..39888825
+
Hg19::chr15:39888860..39888866,+p@chr15:39888860..39888866
+
Hg19::chr15:39888868..39888879,+p@chr15:39888868..39888879
+
Hg19::chr15:39888881..39888913,+p@chr15:39888881..39888913
+
Hg19::chr15:39888950..39888983,+p@chr15:39888950..39888983
+
Hg19::chr15:39888995..39889015,+p@chr15:39888995..39889015
+
Hg19::chr15:39889494..39889515,+p1@BC015134
Hg19::chr1:231005310..231005347,-p2@C1orf198


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

GO IDGO nameFDR corrected p-value
GO:0008201heparin binding0.0154244672082892
GO:0007596blood coagulation0.0154244672082892
GO:0050817coagulation0.0154244672082892
GO:0007599hemostasis0.0154244672082892
GO:0005539glycosaminoglycan binding0.0154244672082892
GO:0030247polysaccharide binding0.0154244672082892
GO:0050878regulation of body fluid levels0.0154244672082892
GO:0001871pattern binding0.0154244672082892
GO:0042060wound healing0.0154244672082892
GO:0004866endopeptidase inhibitor activity0.0256253813300793
GO:0030414protease inhibitor activity0.0256253813300793
GO:0051674localization of cell0.0298834334157541
GO:0006928cell motility0.0298834334157541
GO:0004857enzyme inhibitor activity0.0298834334157541
GO:0009611response to wounding0.0298834334157541
GO:0030246carbohydrate binding0.0316584245849523
GO:0009605response to external stimulus0.039458100442579
GO:0007399nervous system development0.042152360767691
GO:0065008regulation of biological quality0.0484432557904829
GO:0022610biological adhesion0.0484432557904829
GO:0007155cell adhesion0.0484432557904829



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
splanchnic layer of lateral plate mesoderm8.18e-2183
vasculature1.06e-2078
vascular system1.06e-2078
vessel2.99e-2068
epithelial tube open at both ends7.61e-1959
blood vessel7.61e-1959
blood vasculature7.61e-1959
vascular cord7.61e-1959
cardiovascular system2.65e-15109
circulatory system1.10e-14112
artery2.76e-1442
arterial blood vessel2.76e-1442
arterial system2.76e-1442
epithelial tube6.39e-14117
multi-cellular organism5.72e-11656
blood vessel endothelium8.53e-1118
endothelium8.53e-1118
cardiovascular system endothelium8.53e-1118
mesoderm8.57e-11315
mesoderm-derived structure8.57e-11315
presumptive mesoderm8.57e-11315
anatomical system1.20e-10624
anatomical group1.65e-10625
unilaminar epithelium4.19e-10148
systemic artery4.63e-1033
systemic arterial system4.63e-1033
simple squamous epithelium8.49e-1022
organ component layer9.79e-1066
surface structure1.47e-0999
squamous epithelium1.92e-0925
multilaminar epithelium2.08e-0883
lateral plate mesoderm3.37e-08203
integument5.75e-0846
integumental system5.75e-0846
extraembryonic membrane7.50e-0814
membranous layer7.50e-0814
aorta9.80e-0821
aortic system9.80e-0821
skin of body1.49e-0741
epithelial vesicle4.21e-0778


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
ESR1#2099153.752268694652991.20118707854347e-050.000300841192556358
GATA3#2625112.435786015685090.005780435976705730.0259936685886402
POLR2A#54301222.129994207642962.02515758995374e-391.14948605183249e-36



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

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