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Coexpression cluster:C2581: Difference between revisions

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|full_id=C2581_Renal_Endothelial_extraskeletal_Hepatic_Lymphatic_Mesenchymal_Smooth
|full_id=C2581_Renal_Endothelial_extraskeletal_Hepatic_Lymphatic_Mesenchymal_Smooth
|id=C2581
|id=C2581
|ontology_enrichment_celltype=CL:0000222!4.64e-28!119;CL:0000055!2.33e-21!180;CL:0000183!1.42e-18!59;CL:0000680!6.41e-17!57;CL:0000056!6.41e-17!57;CL:0000355!6.41e-17!57;CL:0002139!1.29e-16!24;CL:0000187!2.89e-16!54;CL:0000115!4.30e-16!35;CL:0000359!1.90e-15!32;CL:0000393!3.20e-15!60;CL:0000211!3.20e-15!60;CL:0000192!3.72e-15!42;CL:0000514!3.72e-15!42;CL:0002078!2.62e-14!44;CL:0000071!3.57e-13!18;CL:0002546!3.57e-13!18;CL:0000213!1.59e-11!57;CL:0000215!1.59e-11!57;CL:0000220!2.17e-10!246;CL:0002321!2.97e-10!248;CL:1000413!2.09e-07!9;CL:0002494!8.40e-07!16
|ontology_enrichment_celltype=CL:0000222!9.78e-29!121;CL:0000183!3.69e-18!59;CL:0000680!4.21e-17!58;CL:0000056!4.21e-17!58;CL:0000355!4.21e-17!58;CL:0000115!8.77e-17!36;CL:0002139!1.03e-16!24;CL:0000187!2.13e-16!55;CL:0000055!1.23e-15!106;CL:0000359!1.46e-15!32;CL:0000192!2.31e-15!43;CL:0000514!2.31e-15!43;CL:0002078!3.59e-15!45;CL:0000393!5.20e-15!61;CL:0000211!5.20e-15!61;CL:0000071!2.88e-13!18;CL:0002546!2.88e-13!18;CL:0000213!1.01e-11!58;CL:0000215!1.01e-11!58;CL:0002321!4.86e-11!250;CL:1000413!2.18e-07!9;CL:0002494!4.08e-07!16
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002049!3.58e-35!79;UBERON:0007798!3.58e-35!79;UBERON:0000055!1.64e-30!69;UBERON:0000477!1.21e-29!286;UBERON:0000119!6.95e-29!312;UBERON:0000025!3.60e-28!194;UBERON:0001981!1.23e-27!60;UBERON:0007500!1.23e-27!60;UBERON:0004537!1.23e-27!60;UBERON:0006965!1.23e-27!60;UBERON:0000483!1.42e-27!309;UBERON:0004872!2.98e-27!84;UBERON:0004111!9.07e-27!241;UBERON:0004535!3.22e-26!110;UBERON:0003914!5.16e-26!118;UBERON:0001009!2.02e-24!113;UBERON:0001637!9.17e-22!42;UBERON:0003509!9.17e-22!42;UBERON:0004572!9.17e-22!42;UBERON:0000490!2.60e-20!138;UBERON:0000481!1.56e-17!347;UBERON:0004573!9.89e-17!33;UBERON:0004571!9.89e-17!33;UBERON:0002385!3.95e-16!63;UBERON:0001015!3.95e-16!63;UBERON:0000383!3.95e-16!63;UBERON:0001134!4.17e-16!61;UBERON:0002036!4.17e-16!61;UBERON:0003082!4.17e-16!61;UBERON:0004290!1.29e-15!70;UBERON:0000914!1.80e-14!83;UBERON:0002329!1.80e-14!83;UBERON:0003077!1.80e-14!83;UBERON:0003059!1.80e-14!83;UBERON:0007282!1.80e-14!83;UBERON:0009618!1.80e-14!83;UBERON:0007285!1.80e-14!83;UBERON:0005256!4.33e-14!143;UBERON:0000475!2.69e-13!365;UBERON:0001986!3.57e-13!18;UBERON:0004638!3.57e-13!18;UBERON:0004852!3.57e-13!18;UBERON:0000486!2.54e-12!82;UBERON:0006914!9.37e-12!25;UBERON:0000487!2.22e-11!22;UBERON:0000947!1.21e-10!21;UBERON:0010191!1.21e-10!21;UBERON:0002100!3.66e-09!216;UBERON:0003104!4.38e-09!238;UBERON:0009142!4.38e-09!238;UBERON:0000468!4.02e-08!659;UBERON:0003915!2.09e-07!9;UBERON:0004700!2.09e-07!9;UBERON:0001917!2.09e-07!9;UBERON:0000922!2.58e-07!612;UBERON:0003103!4.66e-07!69;UBERON:0002050!5.76e-07!605;UBERON:0005423!5.76e-07!605;UBERON:0000467!6.06e-07!625;UBERON:0000923!8.20e-07!604;UBERON:0005291!8.20e-07!604;UBERON:0006598!8.20e-07!604;UBERON:0002532!8.20e-07!604;UBERON:0000480!8.28e-07!626
|ontology_enrichment_uberon=UBERON:0002049!2.29e-35!78;UBERON:0007798!2.29e-35!78;UBERON:0000477!1.12e-31!373;UBERON:0000055!8.48e-31!68;UBERON:0000119!1.50e-30!309;UBERON:0000483!2.75e-29!306;UBERON:0000025!7.59e-29!192;UBERON:0007500!5.10e-28!59;UBERON:0001981!5.10e-28!59;UBERON:0004537!5.10e-28!59;UBERON:0006965!5.10e-28!59;UBERON:0004872!5.65e-28!83;UBERON:0004111!5.47e-27!240;UBERON:0004535!2.46e-26!109;UBERON:0003914!4.07e-26!117;UBERON:0001009!2.45e-24!112;UBERON:0001637!5.87e-22!42;UBERON:0003509!5.87e-22!42;UBERON:0004572!5.87e-22!42;UBERON:0000490!5.34e-20!148;UBERON:0000481!1.66e-19!342;UBERON:0007503!4.90e-19!78;UBERON:0004573!6.52e-17!33;UBERON:0004571!6.52e-17!33;UBERON:0002385!1.32e-16!64;UBERON:0001015!1.32e-16!64;UBERON:0000383!1.32e-16!64;UBERON:0001134!2.20e-16!62;UBERON:0002036!2.20e-16!62;UBERON:0003082!2.20e-16!62;UBERON:0007524!8.23e-16!73;UBERON:0003104!1.16e-15!160;UBERON:0009142!1.16e-15!160;UBERON:0003077!1.20e-15!72;UBERON:0007285!1.20e-15!72;UBERON:0002329!1.32e-15!71;UBERON:0003059!1.32e-15!71;UBERON:0007282!1.32e-15!71;UBERON:0004290!1.32e-15!71;UBERON:0009618!1.32e-15!71;UBERON:0004638!2.88e-13!18;UBERON:0001986!2.88e-13!18;UBERON:0004852!2.88e-13!18;UBERON:0005256!1.13e-12!122;UBERON:0000486!2.77e-12!83;UBERON:0006914!1.63e-11!25;UBERON:0000487!3.81e-11!22;UBERON:0000947!8.13e-11!21;UBERON:0010191!8.13e-11!21;UBERON:0010314!3.27e-10!132;UBERON:0000475!1.74e-08!264;UBERON:0000468!3.14e-08!656;UBERON:0000467!6.01e-08!624;UBERON:0002100!6.30e-08!199;UBERON:0000480!8.18e-08!625;UBERON:0003075!1.67e-07!82;UBERON:0007284!1.67e-07!82;UBERON:0003103!1.80e-07!68;UBERON:0003915!2.18e-07!9;UBERON:0004700!2.18e-07!9;UBERON:0001917!2.18e-07!9;UBERON:0002346!4.06e-07!86
|tf_chipseq_enrich=EBF1#1879;3:6.67985013492675:0.00518429411827891:0.0240502151387612!FOS#2353;4:8.9979553088944:0.000152514771116863:0.00195034776303099
|tf_chipseq_enrich=EBF1#1879;3:6.67985013492675:0.00518429411827891:0.0240502151387612!FOS#2353;4:8.9979553088944:0.000152514771116863:0.00195034776303099
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}}
}}

Revision as of 14:11, 19 October 2012


Full id: C2581_Renal_Endothelial_extraskeletal_Hepatic_Lymphatic_Mesenchymal_Smooth



Phase1 CAGE Peaks

Hg19::chr1:32538492..32538508,+p2@TMEM39B
Hg19::chr4:145567043..145567058,-p3@ENST00000503066
Hg19::chr4:145567059..145567099,-p1@ENST00000503066
Hg19::chr4:145567114..145567191,-p1@LOC646576


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
vasculature2.29e-3578
vascular system2.29e-3578
anatomical cluster1.12e-31373
vessel8.48e-3168
cell layer1.50e-30309
epithelium2.75e-29306
tube7.59e-29192
epithelial tube open at both ends5.10e-2859
blood vessel5.10e-2859
blood vasculature5.10e-2859
vascular cord5.10e-2859
splanchnic layer of lateral plate mesoderm5.65e-2883
anatomical conduit5.47e-27240
cardiovascular system2.46e-26109
epithelial tube4.07e-26117
circulatory system2.45e-24112
artery5.87e-2242
arterial blood vessel5.87e-2242
arterial system5.87e-2242
unilaminar epithelium5.34e-20148
multi-tissue structure1.66e-19342
epithelial vesicle4.90e-1978
systemic artery6.52e-1733
systemic arterial system6.52e-1733
muscle tissue1.32e-1664
musculature1.32e-1664
musculature of body1.32e-1664
skeletal muscle tissue2.20e-1662
striated muscle tissue2.20e-1662
myotome2.20e-1662
dense mesenchyme tissue8.23e-1673
mesenchyme1.16e-15160
entire embryonic mesenchyme1.16e-15160
paraxial mesoderm1.20e-1572
presumptive paraxial mesoderm1.20e-1572
somite1.32e-1571
presomitic mesoderm1.32e-1571
presumptive segmental plate1.32e-1571
dermomyotome1.32e-1571
trunk paraxial mesoderm1.32e-1571
blood vessel endothelium2.88e-1318
endothelium2.88e-1318
cardiovascular system endothelium2.88e-1318
trunk mesenchyme1.13e-12122
multilaminar epithelium2.77e-1283
squamous epithelium1.63e-1125
simple squamous epithelium3.81e-1122
aorta8.13e-1121
aortic system8.13e-1121
structure with developmental contribution from neural crest3.27e-10132
organism subdivision1.74e-08264
multi-cellular organism3.14e-08656
anatomical system6.01e-08624
trunk6.30e-08199
anatomical group8.18e-08625
neural plate1.67e-0782
presumptive neural plate1.67e-0782
compound organ1.80e-0768
endothelial tube2.18e-079
arterial system endothelium2.18e-079
endothelium of artery2.18e-079
neurectoderm4.06e-0786


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)

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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
EBF1#187936.679850134926750.005184294118278910.0240502151387612
FOS#235348.99795530889440.0001525147711168630.00195034776303099



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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