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Coexpression cluster:C4265: Difference between revisions

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|full_id=C4265_heart_Fibroblast_Endothelial_smooth_mesodermal_Ciliary_mature
|full_id=C4265_heart_Fibroblast_Endothelial_smooth_mesodermal_Ciliary_mature
|id=C4265
|id=C4265
|ontology_enrichment_celltype=CL:0000055!3.97e-18!180;CL:0000222!2.48e-17!119;CL:0000680!1.26e-13!57;CL:0000056!1.26e-13!57;CL:0000355!1.26e-13!57;CL:0000187!2.69e-13!54;CL:0000183!3.66e-12!59;CL:0000393!1.74e-11!60;CL:0000211!1.74e-11!60;CL:0000220!4.10e-10!246;CL:0002321!4.88e-10!248;CL:0000192!2.90e-09!42;CL:0000514!2.90e-09!42;CL:0000359!9.48e-09!32;CL:0000057!2.50e-08!75;CL:0002139!9.43e-07!24
|ontology_enrichment_celltype=CL:0000222!7.36e-20!121;CL:0000680!1.17e-15!58;CL:0000056!1.17e-15!58;CL:0000355!1.17e-15!58;CL:0000187!1.85e-15!55;CL:0000183!2.02e-14!59;CL:0000393!6.13e-13!61;CL:0000211!6.13e-13!61;CL:0000192!9.05e-11!43;CL:0000514!9.05e-11!43;CL:0002321!1.36e-10!250;CL:0000359!3.70e-10!32;CL:0000055!4.24e-10!106;CL:0000057!7.69e-08!76;CL:0002139!1.98e-07!24
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0004872!3.37e-21!84;UBERON:0001009!1.04e-19!113;UBERON:0002049!3.57e-19!79;UBERON:0007798!3.57e-19!79;UBERON:0004535!1.89e-18!110;UBERON:0003914!7.19e-17!118;UBERON:0000490!1.03e-16!138;UBERON:0001981!2.29e-15!60;UBERON:0007500!2.29e-15!60;UBERON:0004537!2.29e-15!60;UBERON:0006965!2.29e-15!60;UBERON:0000055!3.81e-15!69;UBERON:0002385!2.43e-14!63;UBERON:0001015!2.43e-14!63;UBERON:0000383!2.43e-14!63;UBERON:0001134!7.27e-14!61;UBERON:0002036!7.27e-14!61;UBERON:0003082!7.27e-14!61;UBERON:0004290!4.05e-13!70;UBERON:0000914!4.15e-13!83;UBERON:0002329!4.15e-13!83;UBERON:0003077!4.15e-13!83;UBERON:0003059!4.15e-13!83;UBERON:0007282!4.15e-13!83;UBERON:0009618!4.15e-13!83;UBERON:0007285!4.15e-13!83;UBERON:0005256!2.75e-12!143;UBERON:0000119!5.02e-12!312;UBERON:0000483!1.03e-11!309;UBERON:0000481!6.96e-11!347;UBERON:0001637!1.34e-10!42;UBERON:0003509!1.34e-10!42;UBERON:0004572!1.34e-10!42;UBERON:0002100!1.66e-10!216;UBERON:0000486!2.19e-10!82;UBERON:0007100!3.36e-10!27;UBERON:0003104!4.09e-10!238;UBERON:0009142!4.09e-10!238;UBERON:0000477!4.79e-10!286;UBERON:0000475!5.86e-10!365;UBERON:0000468!1.40e-09!659;UBERON:0000948!7.26e-09!24;UBERON:0005498!7.26e-09!24;UBERON:0004140!7.26e-09!24;UBERON:0009881!7.26e-09!24;UBERON:0004141!7.26e-09!24;UBERON:0003084!7.26e-09!24;UBERON:0007005!7.26e-09!24;UBERON:0004139!7.26e-09!24;UBERON:0004291!7.26e-09!24;UBERON:0004573!9.92e-09!33;UBERON:0004571!9.92e-09!33;UBERON:0004111!1.09e-07!241;UBERON:0000467!3.07e-07!625;UBERON:0000947!3.50e-07!21;UBERON:0010191!3.50e-07!21;UBERON:0000480!4.81e-07!626
|ontology_enrichment_uberon=UBERON:0004872!6.54e-22!83;UBERON:0001009!4.79e-21!112;UBERON:0002049!1.75e-20!78;UBERON:0007798!1.75e-20!78;UBERON:0004535!1.02e-19!109;UBERON:0003914!3.85e-17!117;UBERON:0000490!7.43e-17!148;UBERON:0007500!2.50e-16!59;UBERON:0001981!2.50e-16!59;UBERON:0004537!2.50e-16!59;UBERON:0006965!2.50e-16!59;UBERON:0000055!3.24e-16!68;UBERON:0002385!4.85e-16!64;UBERON:0001015!4.85e-16!64;UBERON:0000383!4.85e-16!64;UBERON:0001134!1.51e-15!62;UBERON:0002036!1.51e-15!62;UBERON:0003082!1.51e-15!62;UBERON:0002329!2.57e-14!71;UBERON:0003059!2.57e-14!71;UBERON:0007282!2.57e-14!71;UBERON:0004290!2.57e-14!71;UBERON:0009618!2.57e-14!71;UBERON:0003077!4.47e-14!72;UBERON:0007285!4.47e-14!72;UBERON:0007524!5.55e-14!73;UBERON:0007503!1.40e-13!78;UBERON:0005256!1.68e-13!122;UBERON:0003104!4.70e-13!160;UBERON:0009142!4.70e-13!160;UBERON:0000475!1.51e-12!264;UBERON:0001637!4.06e-12!42;UBERON:0003509!4.06e-12!42;UBERON:0004572!4.06e-12!42;UBERON:0000486!1.35e-11!83;UBERON:0000119!2.02e-11!309;UBERON:0000483!3.79e-11!306;UBERON:0000477!8.52e-11!373;UBERON:0007100!2.79e-10!27;UBERON:0002100!3.63e-10!199;UBERON:0004573!6.04e-10!33;UBERON:0004571!6.04e-10!33;UBERON:0000481!9.57e-10!342;UBERON:0000468!2.70e-09!656;UBERON:0000948!6.79e-09!24;UBERON:0005498!6.79e-09!24;UBERON:0004140!6.79e-09!24;UBERON:0009881!6.79e-09!24;UBERON:0004141!6.79e-09!24;UBERON:0003084!6.79e-09!24;UBERON:0007005!6.79e-09!24;UBERON:0004139!6.79e-09!24;UBERON:0004291!6.79e-09!24;UBERON:0004111!8.40e-08!240;UBERON:0000947!1.17e-07!21;UBERON:0010191!1.17e-07!21;UBERON:0000467!2.72e-07!624;UBERON:0000480!4.52e-07!625
|tf_chipseq_enrich=CTCF#10664;3:5.36025637307503:0.006492509252767:0.0280345298652058!E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0326482246612109!EP300#2033;3:6.7739417262232:0.00321688050010379:0.0167883161378343!JUND#3727;3:6.99466394187103:0.00292184504273499:0.015715845620755!SMARCC2#6601;3:94.1553744268976:1.19621075407887e-06:4.86113054261646e-05!TCF7L2#6934;3:10.7701765631373:0.000800318129839838:0.00615723205615785
|tf_chipseq_enrich=CTCF#10664;3:5.36025637307503:0.006492509252767:0.0280345298652058!E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0326482246612109!EP300#2033;3:6.7739417262232:0.00321688050010379:0.0167883161378343!JUND#3727;3:6.99466394187103:0.00292184504273499:0.015715845620755!SMARCC2#6601;3:94.1553744268976:1.19621075407887e-06:4.86113054261646e-05!TCF7L2#6934;3:10.7701765631373:0.000800318129839838:0.00615723205615785
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}}
}}

Revision as of 15:48, 19 October 2012


Full id: C4265_heart_Fibroblast_Endothelial_smooth_mesodermal_Ciliary_mature



Phase1 CAGE Peaks

Hg19::chr3:111578558..111578576,+p6@PHLDB2
Hg19::chr3:111578583..111578620,+p4@PHLDB2
Hg19::chr3:111578650..111578707,+p2@PHLDB2


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
splanchnic layer of lateral plate mesoderm6.54e-2283
circulatory system4.79e-21112
vasculature1.75e-2078
vascular system1.75e-2078
cardiovascular system1.02e-19109
epithelial tube3.85e-17117
unilaminar epithelium7.43e-17148
epithelial tube open at both ends2.50e-1659
blood vessel2.50e-1659
blood vasculature2.50e-1659
vascular cord2.50e-1659
vessel3.24e-1668
muscle tissue4.85e-1664
musculature4.85e-1664
musculature of body4.85e-1664
skeletal muscle tissue1.51e-1562
striated muscle tissue1.51e-1562
myotome1.51e-1562
somite2.57e-1471
presomitic mesoderm2.57e-1471
presumptive segmental plate2.57e-1471
dermomyotome2.57e-1471
trunk paraxial mesoderm2.57e-1471
paraxial mesoderm4.47e-1472
presumptive paraxial mesoderm4.47e-1472
dense mesenchyme tissue5.55e-1473
epithelial vesicle1.40e-1378
trunk mesenchyme1.68e-13122
mesenchyme4.70e-13160
entire embryonic mesenchyme4.70e-13160
organism subdivision1.51e-12264
artery4.06e-1242
arterial blood vessel4.06e-1242
arterial system4.06e-1242
multilaminar epithelium1.35e-1183
cell layer2.02e-11309
epithelium3.79e-11306
anatomical cluster8.52e-11373
primary circulatory organ2.79e-1027
trunk3.63e-10199
systemic artery6.04e-1033
systemic arterial system6.04e-1033
multi-tissue structure9.57e-10342
multi-cellular organism2.70e-09656
heart6.79e-0924
primitive heart tube6.79e-0924
primary heart field6.79e-0924
anterior lateral plate mesoderm6.79e-0924
heart tube6.79e-0924
heart primordium6.79e-0924
cardiac mesoderm6.79e-0924
cardiogenic plate6.79e-0924
heart rudiment6.79e-0924
anatomical conduit8.40e-08240
aorta1.17e-0721
aortic system1.17e-0721
anatomical system2.72e-07624
anatomical group4.52e-07625


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#1066435.360256373075030.0064925092527670.0280345298652058
E2F1#186934.907389214879320.008460985347239390.0326482246612109
EP300#203336.77394172622320.003216880500103790.0167883161378343
JUND#372736.994663941871030.002921845042734990.015715845620755
SMARCC2#6601394.15537442689761.19621075407887e-064.86113054261646e-05
TCF7L2#6934310.77017656313730.0008003181298398380.00615723205615785



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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