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(Created page with "{{Coexpression_clusters |full_id=C4506_mesothelioma_schwannoma_Smooth_thyroid_leiomyoma_osteosarcoma_fibrous |id=C4506 }}")
 
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|full_id=C4506_mesothelioma_schwannoma_Smooth_thyroid_leiomyoma_osteosarcoma_fibrous
 
|full_id=C4506_mesothelioma_schwannoma_Smooth_thyroid_leiomyoma_osteosarcoma_fibrous
 
|id=C4506
 
|id=C4506
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|ontology_enrichment_celltype=CL:0000222!1.74e-33!119;CL:0002139!1.20e-21!24;CL:0000359!1.56e-19!32;CL:0000680!2.44e-18!57;CL:0000056!2.44e-18!57;CL:0000355!2.44e-18!57;CL:0000115!1.41e-17!35;CL:0000055!2.85e-17!180;CL:0000071!6.89e-17!18;CL:0002546!6.89e-17!18;CL:0000187!9.78e-17!54;CL:0000213!2.18e-16!57;CL:0000215!2.18e-16!57;CL:0000183!2.63e-16!59;CL:0000192!7.31e-15!42;CL:0000514!7.31e-15!42;CL:0000393!9.17e-14!60;CL:0000211!9.17e-14!60;CL:0002078!9.08e-13!44;CL:0000220!1.41e-12!246;CL:0002321!2.95e-12!248;CL:0002539!2.51e-10!10;CL:1000413!2.25e-09!9;CL:0000076!6.09e-07!62;CL:0002595!6.19e-07!5;CL:0000057!6.43e-07!75;CL:0002494!8.82e-07!16
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|ontology_enrichment_disease=DOID:2394!8.64e-08!14
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|ontology_enrichment_uberon=UBERON:0000055!2.84e-37!69;UBERON:0001637!1.89e-35!42;UBERON:0003509!1.89e-35!42;UBERON:0004572!1.89e-35!42;UBERON:0001981!8.95e-34!60;UBERON:0007500!8.95e-34!60;UBERON:0004537!8.95e-34!60;UBERON:0006965!8.95e-34!60;UBERON:0004872!6.71e-30!84;UBERON:0004573!1.15e-28!33;UBERON:0004571!1.15e-28!33;UBERON:0002049!1.20e-28!79;UBERON:0007798!1.20e-28!79;UBERON:0003914!6.75e-25!118;UBERON:0004535!1.44e-24!110;UBERON:0001009!2.80e-23!113;UBERON:0000490!7.78e-19!138;UBERON:0000947!5.61e-17!21;UBERON:0010191!5.61e-17!21;UBERON:0001986!6.89e-17!18;UBERON:0004638!6.89e-17!18;UBERON:0004852!6.89e-17!18;UBERON:0001134!3.34e-16!61;UBERON:0002036!3.34e-16!61;UBERON:0003082!3.34e-16!61;UBERON:0002385!3.01e-15!63;UBERON:0001015!3.01e-15!63;UBERON:0000383!3.01e-15!63;UBERON:0004290!4.95e-15!70;UBERON:0000487!1.79e-14!22;UBERON:0000486!2.58e-14!82;UBERON:0006914!4.83e-13!25;UBERON:0004111!1.10e-12!241;UBERON:0000914!1.38e-12!83;UBERON:0002329!1.38e-12!83;UBERON:0003077!1.38e-12!83;UBERON:0003059!1.38e-12!83;UBERON:0007282!1.38e-12!83;UBERON:0009618!1.38e-12!83;UBERON:0007285!1.38e-12!83;UBERON:0000119!1.63e-12!312;UBERON:0000025!1.63e-12!194;UBERON:0000483!1.67e-11!309;UBERON:0004237!2.51e-10!10;UBERON:0004695!2.51e-10!10;UBERON:0002111!2.51e-10!10;UBERON:0004178!2.51e-10!10;UBERON:0000477!6.51e-10!286;UBERON:0003915!2.25e-09!9;UBERON:0004700!2.25e-09!9;UBERON:0001917!2.25e-09!9;UBERON:0005256!8.22e-09!143;UBERON:0002100!6.74e-08!216;UBERON:0003834!6.19e-07!5;UBERON:0001533!6.19e-07!5
 
}}
 
}}

Revision as of 05:49, 21 May 2012


Full id: C4506_mesothelioma_schwannoma_Smooth_thyroid_leiomyoma_osteosarcoma_fibrous



Phase1 CAGE Peaks

  Short description
Hg19::chr5:54281586..54281597,- p5@ESM1
Hg19::chr5:54281688..54281697,- p6@ESM1
Hg19::chr5:54281739..54281753,- p3@ESM1


Enriched pathways on this co-expression clusterSummary:
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.
Analyst: Emmanuel Dimont

link to source dataset
data


No results for this coexpression

Enriched Gene Ontology terms on this co-expression clusterSummary: 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.
Analyst: Erik Arner

link to source dataset
data


No GOStat results

Enriched sample ontology terms on this co-expression clusterSummary: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. Analyst: Hideya Kawaji

links to source dataset

cell_data
uberon_data
disease_data


Cell Type
Ontology termp-valuen
mesodermal cell1.74e-33119
endothelial cell of vascular tree1.20e-2124
vascular associated smooth muscle cell1.56e-1932
muscle precursor cell2.44e-1857
myoblast2.44e-1857
multi-potent skeletal muscle stem cell2.44e-1857
endothelial cell1.41e-1735
non-terminally differentiated cell2.85e-17180
blood vessel endothelial cell6.89e-1718
embryonic blood vessel endothelial progenitor cell6.89e-1718
muscle cell9.78e-1754
lining cell2.18e-1657
barrier cell2.18e-1657
contractile cell2.63e-1659
smooth muscle cell7.31e-1542
smooth muscle myoblast7.31e-1542
electrically responsive cell9.17e-1460
electrically active cell9.17e-1460
meso-epithelial cell9.08e-1344
embryonic cell2.95e-12248
aortic smooth muscle cell2.51e-1010
endothelial cell of artery2.25e-099
squamous epithelial cell6.09e-0762
smooth muscle cell of the subclavian artery6.19e-075
fibroblast6.43e-0775
cardiocyte8.82e-0716
Uber Anatomy
Ontology termp-valuen
vessel2.84e-3769
artery1.89e-3542
arterial blood vessel1.89e-3542
arterial system1.89e-3542
blood vessel8.95e-3460
epithelial tube open at both ends8.95e-3460
blood vasculature8.95e-3460
vascular cord8.95e-3460
splanchnic layer of lateral plate mesoderm6.71e-3084
systemic artery1.15e-2833
systemic arterial system1.15e-2833
vasculature1.20e-2879
vascular system1.20e-2879
epithelial tube6.75e-25118
cardiovascular system1.44e-24110
circulatory system2.80e-23113
unilaminar epithelium7.78e-19138
aorta5.61e-1721
aortic system5.61e-1721
endothelium6.89e-1718
blood vessel endothelium6.89e-1718
cardiovascular system endothelium6.89e-1718
skeletal muscle tissue3.34e-1661
striated muscle tissue3.34e-1661
myotome3.34e-1661
muscle tissue3.01e-1563
musculature3.01e-1563
musculature of body3.01e-1563
dermomyotome4.95e-1570
simple squamous epithelium1.79e-1422
multilaminar epithelium2.58e-1482
squamous epithelium4.83e-1325
anatomical conduit1.10e-12241
somite1.38e-1283
paraxial mesoderm1.38e-1283
presomitic mesoderm1.38e-1283
presumptive segmental plate1.38e-1283
trunk paraxial mesoderm1.38e-1283
presumptive paraxial mesoderm1.38e-1283
cell layer1.63e-12312
tube1.63e-12194
epithelium1.67e-11309
blood vessel smooth muscle2.51e-1010
arterial system smooth muscle2.51e-1010
artery smooth muscle tissue2.51e-1010
aorta smooth muscle tissue2.51e-1010
anatomical cluster6.51e-10286
endothelial tube2.25e-099
arterial system endothelium2.25e-099
endothelium of artery2.25e-099
trunk mesenchyme8.22e-09143
trunk6.74e-08216
thoracic segment blood vessel6.19e-075
subclavian artery6.19e-075
Disease
Ontology termp-valuen
ovarian cancer8.64e-0814


Overrepresented TFBS (DNA) motifs on this co-expression clusterSummary: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. Analyst: Michiel de Hoon

link to source data
Novel motifs
data

Jaspar motifs
data


Novel motifs



JASPAR motifs

Motifs-log10(p-value)

{{{tfbs_overrepresentation_jaspar}}}



ENCODE TF ChIP-seq peak enrichment analysisSummary: 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.
Analyst: Erik Arner

link to source dataset

data


No analysis results for this cluster

Relative expression of the co-expression clusterSummary:Co-expression clusters are compared against FANTOM5 samples to obtain relative expression.
Analyst:NA

link to data source
data


This analysis result is provided for C0 - C305 clusters.