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Coexpression cluster:C3898: Difference between revisions

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|ontology_enrichment_disease=DOID:305!2.06e-13!106;DOID:0050687!2.11e-10!143
|ontology_enrichment_disease=DOID:305!2.06e-13!106;DOID:0050687!2.11e-10!143
|ontology_enrichment_uberon=UBERON:0000468!7.90e-19!659;UBERON:0000467!3.57e-18!625;UBERON:0000481!5.73e-18!347;UBERON:0003104!6.61e-18!238;UBERON:0009142!6.61e-18!238;UBERON:0000480!8.15e-18!626;UBERON:0003914!6.95e-17!118;UBERON:0000119!1.02e-16!312;UBERON:0000483!3.62e-16!309;UBERON:0004119!3.63e-16!169;UBERON:0000925!3.63e-16!169;UBERON:0006595!3.63e-16!169;UBERON:0001048!2.73e-15!168;UBERON:0005177!2.19e-14!107;UBERON:0000466!3.63e-14!126;UBERON:0000922!4.69e-14!612;UBERON:0002049!5.76e-14!79;UBERON:0007798!5.76e-14!79;UBERON:0002100!1.14e-13!216;UBERON:0000477!1.35e-13!286;UBERON:0002050!2.20e-13!605;UBERON:0005423!2.20e-13!605;UBERON:0000475!2.37e-13!365;UBERON:0000923!2.84e-13!604;UBERON:0005291!2.84e-13!604;UBERON:0006598!2.84e-13!604;UBERON:0002532!2.84e-13!604;UBERON:0004111!2.43e-12!241;UBERON:0000464!2.83e-12!104;UBERON:0001007!3.48e-12!155;UBERON:0001555!3.48e-12!155;UBERON:0007026!3.48e-12!155;UBERON:0000077!2.13e-11!130;UBERON:0000490!3.39e-11!138;UBERON:0000055!4.44e-11!69;UBERON:0009569!1.46e-10!113;UBERON:0004921!1.60e-10!129;UBERON:0004185!1.60e-10!129;UBERON:0001041!2.48e-10!98;UBERON:0006554!5.07e-10!44;UBERON:0001008!6.47e-10!45;UBERON:0005085!1.41e-09!29;UBERON:0000064!1.64e-09!219;UBERON:0000062!1.82e-09!511;UBERON:0000487!1.88e-09!22;UBERON:0001981!4.22e-09!60;UBERON:0007500!4.22e-09!60;UBERON:0004537!4.22e-09!60;UBERON:0006965!4.22e-09!60;UBERON:0005256!6.03e-09!143;UBERON:0001986!8.36e-09!18;UBERON:0004638!8.36e-09!18;UBERON:0004852!8.36e-09!18;UBERON:0004211!1.51e-08!16;UBERON:0001285!1.51e-08!16;UBERON:0007684!1.51e-08!16;UBERON:0003220!1.51e-08!16;UBERON:0004208!1.51e-08!16;UBERON:0001444!2.97e-08!48;UBERON:0003103!2.98e-08!69;UBERON:0000058!3.50e-08!26;UBERON:0004872!3.82e-08!84;UBERON:0005911!4.56e-08!82;UBERON:0006914!5.34e-08!25;UBERON:0003064!5.41e-08!37;UBERON:0006555!5.55e-08!17;UBERON:0005103!5.55e-08!17;UBERON:0000083!5.55e-08!17;UBERON:0009201!5.55e-08!17;UBERON:0004819!5.55e-08!17;UBERON:0006553!5.55e-08!17;UBERON:0003074!5.55e-08!17;UBERON:0003060!5.55e-08!17;UBERON:0001851!5.59e-08!16;UBERON:0001004!7.54e-08!72;UBERON:0000020!8.90e-08!23;UBERON:0005172!9.57e-08!55;UBERON:0005173!9.57e-08!55;UBERON:0000926!1.00e-07!448;UBERON:0004120!1.00e-07!448;UBERON:0006603!1.00e-07!448;UBERON:0000025!1.03e-07!194;UBERON:0001009!1.30e-07!113;UBERON:0004535!1.53e-07!110;UBERON:0000063!1.61e-07!97;UBERON:0000353!1.62e-07!17;UBERON:0000019!1.63e-07!19;UBERON:0000047!1.63e-07!19;UBERON:0004088!1.63e-07!19;UBERON:0003072!1.63e-07!19;UBERON:0003071!1.63e-07!19;UBERON:0004128!1.63e-07!19;UBERON:0002553!1.71e-07!70;UBERON:0002113!1.91e-07!27;UBERON:0003918!1.91e-07!27;UBERON:0005095!1.91e-07!27;UBERON:0007687!1.91e-07!27;UBERON:0000970!1.94e-07!20;UBERON:0000080!2.12e-07!18;UBERON:0002120!2.12e-07!18;UBERON:0004875!2.12e-07!18;UBERON:0005721!2.12e-07!18;UBERON:0005754!2.12e-07!18;UBERON:0007297!2.12e-07!18;UBERON:0001032!3.05e-07!24;UBERON:0004456!3.05e-07!24;UBERON:0001225!3.99e-07!13;UBERON:0008987!3.99e-07!13;UBERON:0000489!5.03e-07!32;UBERON:0001456!5.06e-07!21;UBERON:0001801!5.87e-07!14;UBERON:0002104!7.14e-07!21;UBERON:0004876!9.74e-07!20
|ontology_enrichment_uberon=UBERON:0000468!7.90e-19!659;UBERON:0000467!3.57e-18!625;UBERON:0000481!5.73e-18!347;UBERON:0003104!6.61e-18!238;UBERON:0009142!6.61e-18!238;UBERON:0000480!8.15e-18!626;UBERON:0003914!6.95e-17!118;UBERON:0000119!1.02e-16!312;UBERON:0000483!3.62e-16!309;UBERON:0004119!3.63e-16!169;UBERON:0000925!3.63e-16!169;UBERON:0006595!3.63e-16!169;UBERON:0001048!2.73e-15!168;UBERON:0005177!2.19e-14!107;UBERON:0000466!3.63e-14!126;UBERON:0000922!4.69e-14!612;UBERON:0002049!5.76e-14!79;UBERON:0007798!5.76e-14!79;UBERON:0002100!1.14e-13!216;UBERON:0000477!1.35e-13!286;UBERON:0002050!2.20e-13!605;UBERON:0005423!2.20e-13!605;UBERON:0000475!2.37e-13!365;UBERON:0000923!2.84e-13!604;UBERON:0005291!2.84e-13!604;UBERON:0006598!2.84e-13!604;UBERON:0002532!2.84e-13!604;UBERON:0004111!2.43e-12!241;UBERON:0000464!2.83e-12!104;UBERON:0001007!3.48e-12!155;UBERON:0001555!3.48e-12!155;UBERON:0007026!3.48e-12!155;UBERON:0000077!2.13e-11!130;UBERON:0000490!3.39e-11!138;UBERON:0000055!4.44e-11!69;UBERON:0009569!1.46e-10!113;UBERON:0004921!1.60e-10!129;UBERON:0004185!1.60e-10!129;UBERON:0001041!2.48e-10!98;UBERON:0006554!5.07e-10!44;UBERON:0001008!6.47e-10!45;UBERON:0005085!1.41e-09!29;UBERON:0000064!1.64e-09!219;UBERON:0000062!1.82e-09!511;UBERON:0000487!1.88e-09!22;UBERON:0001981!4.22e-09!60;UBERON:0007500!4.22e-09!60;UBERON:0004537!4.22e-09!60;UBERON:0006965!4.22e-09!60;UBERON:0005256!6.03e-09!143;UBERON:0001986!8.36e-09!18;UBERON:0004638!8.36e-09!18;UBERON:0004852!8.36e-09!18;UBERON:0004211!1.51e-08!16;UBERON:0001285!1.51e-08!16;UBERON:0007684!1.51e-08!16;UBERON:0003220!1.51e-08!16;UBERON:0004208!1.51e-08!16;UBERON:0001444!2.97e-08!48;UBERON:0003103!2.98e-08!69;UBERON:0000058!3.50e-08!26;UBERON:0004872!3.82e-08!84;UBERON:0005911!4.56e-08!82;UBERON:0006914!5.34e-08!25;UBERON:0003064!5.41e-08!37;UBERON:0006555!5.55e-08!17;UBERON:0005103!5.55e-08!17;UBERON:0000083!5.55e-08!17;UBERON:0009201!5.55e-08!17;UBERON:0004819!5.55e-08!17;UBERON:0006553!5.55e-08!17;UBERON:0003074!5.55e-08!17;UBERON:0003060!5.55e-08!17;UBERON:0001851!5.59e-08!16;UBERON:0001004!7.54e-08!72;UBERON:0000020!8.90e-08!23;UBERON:0005172!9.57e-08!55;UBERON:0005173!9.57e-08!55;UBERON:0000926!1.00e-07!448;UBERON:0004120!1.00e-07!448;UBERON:0006603!1.00e-07!448;UBERON:0000025!1.03e-07!194;UBERON:0001009!1.30e-07!113;UBERON:0004535!1.53e-07!110;UBERON:0000063!1.61e-07!97;UBERON:0000353!1.62e-07!17;UBERON:0000019!1.63e-07!19;UBERON:0000047!1.63e-07!19;UBERON:0004088!1.63e-07!19;UBERON:0003072!1.63e-07!19;UBERON:0003071!1.63e-07!19;UBERON:0004128!1.63e-07!19;UBERON:0002553!1.71e-07!70;UBERON:0002113!1.91e-07!27;UBERON:0003918!1.91e-07!27;UBERON:0005095!1.91e-07!27;UBERON:0007687!1.91e-07!27;UBERON:0000970!1.94e-07!20;UBERON:0000080!2.12e-07!18;UBERON:0002120!2.12e-07!18;UBERON:0004875!2.12e-07!18;UBERON:0005721!2.12e-07!18;UBERON:0005754!2.12e-07!18;UBERON:0007297!2.12e-07!18;UBERON:0001032!3.05e-07!24;UBERON:0004456!3.05e-07!24;UBERON:0001225!3.99e-07!13;UBERON:0008987!3.99e-07!13;UBERON:0000489!5.03e-07!32;UBERON:0001456!5.06e-07!21;UBERON:0001801!5.87e-07!14;UBERON:0002104!7.14e-07!21;UBERON:0004876!9.74e-07!20
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}}
}}

Revision as of 11:48, 5 September 2012


Full id: C3898_Alveolar_immature_serous_Bronchial_Tracheal_Keratinocyte_embryonic



Phase1 CAGE Peaks

Hg19::chr1:16482507..16482514,-p3@EPHA2
Hg19::chr1:16482527..16482546,-p2@EPHA2
Hg19::chr1:16482554..16482576,-p1@EPHA2


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>disease_data<br>

Uber Anatomy
Ontology termp-valuen
multi-cellular organism7.90e-19659
anatomical system3.57e-18625
multi-tissue structure5.73e-18347
mesenchyme6.61e-18238
entire embryonic mesenchyme6.61e-18238
anatomical group8.15e-18626
epithelial tube6.95e-17118
cell layer1.02e-16312
epithelium3.62e-16309
endoderm-derived structure3.63e-16169
endoderm3.63e-16169
presumptive endoderm3.63e-16169
primordium2.73e-15168
trunk region element2.19e-14107
immaterial anatomical entity3.63e-14126
embryo4.69e-14612
vasculature5.76e-1479
vascular system5.76e-1479
trunk1.14e-13216
anatomical cluster1.35e-13286
embryonic structure2.20e-13605
developing anatomical structure2.20e-13605
organism subdivision2.37e-13365
germ layer2.84e-13604
embryonic tissue2.84e-13604
presumptive structure2.84e-13604
epiblast (generic)2.84e-13604
anatomical conduit2.43e-12241
anatomical space2.83e-12104
digestive system3.48e-12155
digestive tract3.48e-12155
primitive gut3.48e-12155
mixed endoderm/mesoderm-derived structure2.13e-11130
unilaminar epithelium3.39e-11138
vessel4.44e-1169
subdivision of trunk1.46e-10113
subdivision of digestive tract1.60e-10129
endodermal part of digestive tract1.60e-10129
foregut2.48e-1098
urinary system structure5.07e-1044
renal system6.47e-1045
ectodermal placode1.41e-0929
organ part1.64e-09219
organ1.82e-09511
simple squamous epithelium1.88e-0922
blood vessel4.22e-0960
epithelial tube open at both ends4.22e-0960
blood vasculature4.22e-0960
vascular cord4.22e-0960
trunk mesenchyme6.03e-09143
endothelium8.36e-0918
blood vessel endothelium8.36e-0918
cardiovascular system endothelium8.36e-0918
nephron epithelium1.51e-0816
nephron1.51e-0816
uriniferous tubule1.51e-0816
metanephric mesenchyme1.51e-0816
nephrogenic mesenchyme1.51e-0816
subdivision of head2.97e-0848
compound organ2.98e-0869
duct3.50e-0826
splanchnic layer of lateral plate mesoderm3.82e-0884
endo-epithelium4.56e-0882
squamous epithelium5.34e-0825
intermediate mesoderm5.41e-0837
excretory tube5.55e-0817
mesonephric epithelium5.55e-0817
mesonephric tubule5.55e-0817
nephric duct5.55e-0817
kidney epithelium5.55e-0817
renal duct5.55e-0817
mesonephric duct5.55e-0817
pronephric duct5.55e-0817
cortex5.59e-0816

Disease
Ontology termp-valuen


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
BRCA1#672320.18423064322380.0001215704860271640.00164231017852683
CEBPB#105137.971147625824820.001974187055288560.0115249928377463
CTBP2#1488362.71700033932814.049570681927e-060.000129853580733735
EP300#203336.77394172622320.003216880500103790.0167523202468382
FOS#235338.99795530889440.001372499272417130.0089802312687616
FOSL2#2355316.93020060456170.0002060162053171620.0024314754737393
JUN#3725312.51282919233630.0005103313992726250.00444376363253574
JUND#372736.994663941871030.002921845042734990.0156851490320329
MXI1#460139.96157162875930.001011470541259020.0072053046762534
REST#597839.650028716128020.001112636247114590.00767926361435373
RFX5#5993312.04791082719510.0005717246050312580.00484779946617354
SIN3A#2594235.408884726815140.006318961977991520.0276950803650785
SP1#666735.69838137814090.005403962701712170.024666074935716
TAF7#6879311.43306940492390.0006690181981945830.0054328272763583
TCF7L2#6934310.77017656313730.0008003181298398380.0061409466727164
TFAP2A#7020316.5186343730450.0002218033880766340.0024831090199738
TFAP2C#7022310.80922860986020.0007916746575753130.00616108118945664
YY1#752834.911170749853860.008441455341808260.0329588827411534



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.

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