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Coexpression cluster:C3021: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000055!6.26e-50!69;UBERON:0001981!1.92e-44!60;UBERON:0007500!1.92e-44!60;UBERON:0004537!1.92e-44!60;UBERON:0006965!1.92e-44!60;UBERON:0001637!3.11e-43!42;UBERON:0003509!3.11e-43!42;UBERON:0004572!3.11e-43!42;UBERON:0002049!9.19e-43!79;UBERON:0007798!9.19e-43!79;UBERON:0004872!1.70e-41!84;UBERON:0004535!2.53e-36!110;UBERON:0001009!8.25e-35!113;UBERON:0004573!3.99e-33!33;UBERON:0004571!3.99e-33!33;UBERON:0003914!3.09e-26!118;UBERON:0001986!3.15e-22!18;UBERON:0004638!3.15e-22!18;UBERON:0004852!3.15e-22!18;UBERON:0000947!1.06e-20!21;UBERON:0010191!1.06e-20!21;UBERON:0000487!2.35e-19!22;UBERON:0006914!4.76e-18!25;UBERON:0000490!2.37e-14!138;UBERON:0000914!1.55e-13!83;UBERON:0002329!1.55e-13!83;UBERON:0003077!1.55e-13!83;UBERON:0003059!1.55e-13!83;UBERON:0007282!1.55e-13!83;UBERON:0009618!1.55e-13!83;UBERON:0007285!1.55e-13!83;UBERON:0004111!1.88e-13!241;UBERON:0003915!4.04e-13!9;UBERON:0004700!4.04e-13!9;UBERON:0001917!4.04e-13!9;UBERON:0000486!1.33e-12!82;UBERON:0004290!1.50e-12!70;UBERON:0000477!3.07e-12!286;UBERON:0000025!5.78e-11!194;UBERON:0001134!3.19e-10!61;UBERON:0002036!3.19e-10!61;UBERON:0003082!3.19e-10!61;UBERON:0002385!1.17e-09!63;UBERON:0001015!1.17e-09!63;UBERON:0000383!1.17e-09!63;UBERON:0002199!4.13e-09!45;UBERON:0002416!4.13e-09!45;UBERON:0004237!4.69e-09!10;UBERON:0004695!4.69e-09!10;UBERON:0002111!4.69e-09!10;UBERON:0004178!4.69e-09!10;UBERON:0000483!5.09e-09!309;UBERON:0002097!6.45e-09!40;UBERON:0000119!9.53e-09!312;UBERON:0000948!2.92e-08!24;UBERON:0005498!2.92e-08!24;UBERON:0004140!2.92e-08!24;UBERON:0009881!2.92e-08!24;UBERON:0004141!2.92e-08!24;UBERON:0003084!2.92e-08!24;UBERON:0007005!2.92e-08!24;UBERON:0004139!2.92e-08!24;UBERON:0004291!2.92e-08!24;UBERON:0003081!6.81e-08!216;UBERON:0003102!1.41e-07!95;UBERON:0001473!1.69e-07!8;UBERON:0004536!1.69e-07!8;UBERON:0006558!1.69e-07!8;UBERON:0003498!1.97e-07!5;UBERON:0005985!1.97e-07!5;UBERON:0000415!4.11e-07!4;UBERON:0007240!4.11e-07!4;UBERON:0005742!4.11e-07!4;UBERON:0005734!4.11e-07!4;UBERON:0004664!4.11e-07!4;UBERON:0004663!4.11e-07!4;UBERON:0005256!4.71e-07!143;UBERON:0000467!4.85e-07!625;UBERON:0000480!5.58e-07!626;UBERON:0007100!5.90e-07!27
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}}
}}

Revision as of 18:50, 8 August 2012


Full id: C3021_large_Fibroblast_giant_Lymphatic_medulloblastoma_Endothelial_squamous



Phase1 CAGE Peaks

Hg19::chr10:4823011..4823022,-p@chr10:4823011..4823022
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Hg19::chr10:4823096..4823144,-p@chr10:4823096..4823144
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Hg19::chr10:4823152..4823165,-p@chr10:4823152..4823165
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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>

Cell Type
Ontology termp-valuen
endothelial cell of vascular tree5.07e-3124
mesodermal cell5.27e-25119
blood vessel endothelial cell3.15e-2218
embryonic blood vessel endothelial progenitor cell3.15e-2218
vascular associated smooth muscle cell3.97e-2132
endothelial cell2.79e-2035
non-terminally differentiated cell1.22e-19180
fibroblast1.28e-1675
lining cell9.65e-1657
barrier cell9.65e-1657
meso-epithelial cell1.01e-1544
skin fibroblast1.04e-1523
smooth muscle cell1.75e-1542
smooth muscle myoblast1.75e-1542
embryonic cell3.32e-13248
endothelial cell of artery4.04e-139
muscle precursor cell1.74e-1157
myoblast1.74e-1157
multi-potent skeletal muscle stem cell1.74e-1157
lymphangioblast2.03e-106
endothelial cell of lymphatic vessel2.03e-106
vascular lymphangioblast2.03e-106
muscle cell2.27e-1054
contractile cell9.29e-1059
aortic endothelial cell1.56e-096
aortic smooth muscle cell4.69e-0910
cardiocyte7.02e-0916
squamous epithelial cell7.22e-0962
electrically responsive cell1.23e-0860
electrically active cell1.23e-0860
animal cell1.97e-08679
eukaryotic cell1.97e-08679
somatic cell3.76e-07591
fibroblast of tunica adventitia of artery4.11e-074
fibroblast of the aortic adventitia4.11e-074
Uber Anatomy
Ontology termp-valuen
vessel6.26e-5069
blood vessel1.92e-4460
epithelial tube open at both ends1.92e-4460
blood vasculature1.92e-4460
vascular cord1.92e-4460
artery3.11e-4342
arterial blood vessel3.11e-4342
arterial system3.11e-4342
vasculature9.19e-4379
vascular system9.19e-4379
splanchnic layer of lateral plate mesoderm1.70e-4184
cardiovascular system2.53e-36110
circulatory system8.25e-35113
systemic artery3.99e-3333
systemic arterial system3.99e-3333
epithelial tube3.09e-26118
endothelium3.15e-2218
blood vessel endothelium3.15e-2218
cardiovascular system endothelium3.15e-2218
aorta1.06e-2021
aortic system1.06e-2021
simple squamous epithelium2.35e-1922
squamous epithelium4.76e-1825
unilaminar epithelium2.37e-14138
somite1.55e-1383
paraxial mesoderm1.55e-1383
presomitic mesoderm1.55e-1383
presumptive segmental plate1.55e-1383
trunk paraxial mesoderm1.55e-1383
presumptive paraxial mesoderm1.55e-1383
anatomical conduit1.88e-13241
endothelial tube4.04e-139
arterial system endothelium4.04e-139
endothelium of artery4.04e-139
multilaminar epithelium1.33e-1282
dermomyotome1.50e-1270
anatomical cluster3.07e-12286
tube5.78e-11194
skeletal muscle tissue3.19e-1061
striated muscle tissue3.19e-1061
myotome3.19e-1061
muscle tissue1.17e-0963
musculature1.17e-0963
musculature of body1.17e-0963
integument4.13e-0945
integumental system4.13e-0945
blood vessel smooth muscle4.69e-0910
arterial system smooth muscle4.69e-0910
artery smooth muscle tissue4.69e-0910
aorta smooth muscle tissue4.69e-0910
epithelium5.09e-09309
skin of body6.45e-0940
cell layer9.53e-09312
heart2.92e-0824
primitive heart tube2.92e-0824
primary heart field2.92e-0824
anterior lateral plate mesoderm2.92e-0824
heart tube2.92e-0824
heart primordium2.92e-0824
cardiac mesoderm2.92e-0824


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

No analysis results for this cluster

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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