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Coexpression cluster:C3898: Difference between revisions

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|full_id=C3898_Alveolar_immature_serous_Bronchial_Tracheal_Keratinocyte_embryonic
|full_id=C3898_Alveolar_immature_serous_Bronchial_Tracheal_Keratinocyte_embryonic
|id=C3898
|id=C3898
|ontology_enrichment_celltype=CL:0000066!3.02e-57!254;CL:0000220!6.95e-34!246;CL:0002321!1.11e-33!248;CL:0000076!1.92e-18!62;CL:0000223!5.40e-14!59;CL:0000222!7.14e-14!119;CL:0000213!1.42e-13!57;CL:0000215!1.42e-13!57;CL:0002076!1.98e-13!43;CL:0002078!2.48e-12!44;CL:0002139!3.03e-11!24;CL:0000115!3.80e-11!35;CL:1000497!4.96e-09!18;CL:0002518!4.96e-09!18;CL:0000071!8.36e-09!18;CL:0002546!8.36e-09!18;CL:0002368!1.11e-08!13;CL:1000449!1.51e-08!16;CL:0000548!5.61e-08!679;CL:0000004!5.61e-08!679;CL:0000255!5.61e-08!679;CL:0000012!2.56e-07!682;CL:0002681!3.99e-07!13;CL:0002584!3.99e-07!13;CL:0002202!6.74e-07!9;CL:0002632!6.74e-07!9
|ontology_enrichment_celltype=CL:0000066!7.29e-57!253;CL:0002321!5.18e-33!250;CL:0000076!3.22e-17!63;CL:0000223!1.98e-14!58;CL:0000213!2.78e-14!58;CL:0000215!2.78e-14!58;CL:0000222!3.50e-14!121;CL:0002076!8.52e-14!42;CL:0002078!3.27e-13!45;CL:0000115!2.73e-12!36;CL:0002139!8.59e-12!24;CL:1000497!2.17e-09!17;CL:0002518!2.17e-09!17;CL:0000071!4.20e-09!18;CL:0002546!4.20e-09!18;CL:1000449!5.62e-09!15;CL:0002368!1.90e-08!13;CL:0000548!3.82e-08!679;CL:0000255!3.82e-08!679;CL:0002681!1.39e-07!12;CL:0002584!1.39e-07!12;CL:0002202!6.64e-07!9;CL:0002632!6.64e-07!9
|ontology_enrichment_disease=DOID:305!2.06e-13!106;DOID:0050687!2.11e-10!143
|ontology_enrichment_disease=DOID:305!1.95e-13!106;DOID:0050687!7.27e-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:0000477!1.17e-20!373;UBERON:0000475!1.25e-20!264;UBERON:0003914!6.84e-17!117;UBERON:0000468!1.06e-16!656;UBERON:0000467!2.69e-16!624;UBERON:0005177!5.05e-16!101;UBERON:0000480!5.47e-16!625;UBERON:0000119!1.61e-14!309;UBERON:0004119!3.80e-14!160;UBERON:0000925!3.80e-14!160;UBERON:0006595!3.80e-14!160;UBERON:0002049!3.95e-14!78;UBERON:0007798!3.95e-14!78;UBERON:0000483!4.86e-14!306;UBERON:0000481!6.94e-14!342;UBERON:0002100!2.26e-13!199;UBERON:0004111!2.19e-12!240;UBERON:0001048!2.82e-12!160;UBERON:0000466!1.21e-11!117;UBERON:0000055!1.84e-11!68;UBERON:0009569!3.55e-11!112;UBERON:0006554!1.26e-10!47;UBERON:0000922!1.43e-10!592;UBERON:0001008!1.79e-10!48;UBERON:0001007!1.90e-10!145;UBERON:0001555!1.90e-10!145;UBERON:0007026!1.90e-10!145;UBERON:0000490!3.73e-10!148;UBERON:0000464!1.00e-09!95;UBERON:0000487!1.10e-09!22;UBERON:0007500!3.62e-09!59;UBERON:0001981!3.62e-09!59;UBERON:0004537!3.62e-09!59;UBERON:0006965!3.62e-09!59;UBERON:0004638!4.20e-09!18;UBERON:0001986!4.20e-09!18;UBERON:0004852!4.20e-09!18;UBERON:0001041!4.74e-09!87;UBERON:0000064!4.77e-09!218;UBERON:0004211!5.62e-09!15;UBERON:0009773!5.62e-09!15;UBERON:0001231!5.62e-09!15;UBERON:0001285!5.62e-09!15;UBERON:0007684!5.62e-09!15;UBERON:0004208!5.62e-09!15;UBERON:0004921!7.47e-09!118;UBERON:0000062!9.37e-09!503;UBERON:0005423!1.07e-08!581;UBERON:0006555!1.55e-08!16;UBERON:0004819!1.55e-08!16;UBERON:0001851!1.97e-08!15;UBERON:0003104!2.02e-08!160;UBERON:0009142!2.02e-08!160;UBERON:0000353!2.94e-08!15;UBERON:0003103!2.99e-08!68;UBERON:0005911!3.12e-08!82;UBERON:0005172!4.08e-08!54;UBERON:0005173!4.08e-08!54;UBERON:0000033!5.42e-08!56;UBERON:0001004!6.47e-08!74;UBERON:0005085!6.71e-08!31;UBERON:0006914!6.72e-08!25;UBERON:0004872!6.76e-08!83;UBERON:0002113!8.12e-08!26;UBERON:0003918!8.12e-08!26;UBERON:0011143!8.12e-08!26;UBERON:0005095!8.12e-08!26;UBERON:0007687!8.12e-08!26;UBERON:0000025!1.02e-07!192;UBERON:0001444!1.06e-07!49;UBERON:0001009!1.10e-07!112;UBERON:0004535!1.27e-07!109;UBERON:0001225!1.39e-07!12;UBERON:0008987!1.39e-07!12;UBERON:0000063!2.17e-07!98;UBERON:0000020!3.25e-07!24;UBERON:0001032!3.25e-07!24;UBERON:0004456!3.25e-07!24;UBERON:0000489!4.22e-07!31;UBERON:0000153!7.16e-07!62;UBERON:0007811!7.16e-07!62;UBERON:0002417!9.76e-07!60;UBERON:0000916!9.76e-07!60
|tf_chipseq_enrich=BRCA1#672;3:20.1842306432238:0.000121570486027164:0.00164231017852683!CEBPB#1051;3:7.97114762582482:0.00197418705528856:0.0115249928377463!CTBP2#1488;3:62.7170003393281:4.049570681927e-06:0.000129853580733735!EP300#2033;3:6.7739417262232:0.00321688050010379:0.0167523202468382!FOS#2353;3:8.9979553088944:0.00137249927241713:0.0089802312687616!FOSL2#2355;3:16.9302006045617:0.000206016205317162:0.0024314754737393!JUN#3725;3:12.5128291923363:0.000510331399272625:0.00444376363253574!JUND#3727;3:6.99466394187103:0.00292184504273499:0.0156851490320329!MXI1#4601;3:9.9615716287593:0.00101147054125902:0.0072053046762534!REST#5978;3:9.65002871612802:0.00111263624711459:0.00767926361435373!RFX5#5993;3:12.0479108271951:0.000571724605031258:0.00484779946617354!SIN3A#25942;3:5.40888472681514:0.00631896197799152:0.0276950803650785!SP1#6667;3:5.6983813781409:0.00540396270171217:0.024666074935716!TAF7#6879;3:11.4330694049239:0.000669018198194583:0.0054328272763583!TCF7L2#6934;3:10.7701765631373:0.000800318129839838:0.0061409466727164!TFAP2A#7020;3:16.518634373045:0.000221803388076634:0.0024831090199738!TFAP2C#7022;3:10.8092286098602:0.000791674657575313:0.00616108118945664!YY1#7528;3:4.91117074985386:0.00844145534180826:0.0329588827411534
|tf_chipseq_enrich=BRCA1#672;3:20.1842306432238:0.000121570486027164:0.00164231017852683!CEBPB#1051;3:7.97114762582482:0.00197418705528856:0.0115249928377463!CTBP2#1488;3:62.7170003393281:4.049570681927e-06:0.000129853580733735!EP300#2033;3:6.7739417262232:0.00321688050010379:0.0167523202468382!FOS#2353;3:8.9979553088944:0.00137249927241713:0.0089802312687616!FOSL2#2355;3:16.9302006045617:0.000206016205317162:0.0024314754737393!JUN#3725;3:12.5128291923363:0.000510331399272625:0.00444376363253574!JUND#3727;3:6.99466394187103:0.00292184504273499:0.0156851490320329!MXI1#4601;3:9.9615716287593:0.00101147054125902:0.0072053046762534!REST#5978;3:9.65002871612802:0.00111263624711459:0.00767926361435373!RFX5#5993;3:12.0479108271951:0.000571724605031258:0.00484779946617354!SIN3A#25942;3:5.40888472681514:0.00631896197799152:0.0276950803650785!SP1#6667;3:5.6983813781409:0.00540396270171217:0.024666074935716!TAF7#6879;3:11.4330694049239:0.000669018198194583:0.0054328272763583!TCF7L2#6934;3:10.7701765631373:0.000800318129839838:0.0061409466727164!TFAP2A#7020;3:16.518634373045:0.000221803388076634:0.0024831090199738!TFAP2C#7022;3:10.8092286098602:0.000791674657575313:0.00616108118945664!YY1#7528;3:4.91117074985386:0.00844145534180826:0.0329588827411534
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}}
}}

Revision as of 15:29, 19 October 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
anatomical cluster1.17e-20373
organism subdivision1.25e-20264
epithelial tube6.84e-17117
multi-cellular organism1.06e-16656
anatomical system2.69e-16624
trunk region element5.05e-16101
anatomical group5.47e-16625
cell layer1.61e-14309
endoderm-derived structure3.80e-14160
endoderm3.80e-14160
presumptive endoderm3.80e-14160
vasculature3.95e-1478
vascular system3.95e-1478
epithelium4.86e-14306
multi-tissue structure6.94e-14342
trunk2.26e-13199
anatomical conduit2.19e-12240
primordium2.82e-12160
immaterial anatomical entity1.21e-11117
vessel1.84e-1168
subdivision of trunk3.55e-11112
urinary system structure1.26e-1047
embryo1.43e-10592
renal system1.79e-1048
digestive system1.90e-10145
digestive tract1.90e-10145
primitive gut1.90e-10145
unilaminar epithelium3.73e-10148
anatomical space1.00e-0995
simple squamous epithelium1.10e-0922
epithelial tube open at both ends3.62e-0959
blood vessel3.62e-0959
blood vasculature3.62e-0959
vascular cord3.62e-0959
blood vessel endothelium4.20e-0918
endothelium4.20e-0918
cardiovascular system endothelium4.20e-0918
foregut4.74e-0987
organ part4.77e-09218
nephron epithelium5.62e-0915
renal tubule5.62e-0915
nephron tubule5.62e-0915
nephron5.62e-0915
uriniferous tubule5.62e-0915
nephrogenic mesenchyme5.62e-0915
subdivision of digestive tract7.47e-09118
organ9.37e-09503
developing anatomical structure1.07e-08581
excretory tube1.55e-0816
kidney epithelium1.55e-0816
cortex1.97e-0815
mesenchyme2.02e-08160
entire embryonic mesenchyme2.02e-08160
parenchyma2.94e-0815
compound organ2.99e-0868
endo-epithelium3.12e-0882
abdomen element4.08e-0854
abdominal segment element4.08e-0854
head5.42e-0856
respiratory system6.47e-0874
ectodermal placode6.71e-0831
squamous epithelium6.72e-0825
splanchnic layer of lateral plate mesoderm6.76e-0883
kidney8.12e-0826
kidney mesenchyme8.12e-0826
upper urinary tract8.12e-0826
kidney rudiment8.12e-0826
kidney field8.12e-0826
tube1.02e-07192
subdivision of head1.06e-0749
circulatory system1.10e-07112
cardiovascular system1.27e-07109
cortex of kidney1.39e-0712
renal parenchyma1.39e-0712
organ segment2.17e-0798
sense organ3.25e-0724
sensory system3.25e-0724

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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