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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C4510_bone_mesenchymal_Small_squamous_Fibroblast_thyroid_glioblastoma
|full_id=C4510_bone_mesenchymal_Small_squamous_Fibroblast_thyroid_glioblastoma
|id=C4510
|id=C4510

Revision as of 17:36, 12 September 2012


Full id: C4510_bone_mesenchymal_Small_squamous_Fibroblast_thyroid_glioblastoma



Phase1 CAGE Peaks

Hg19::chr5:60600415..60600431,-p@chr5:60600415..60600431
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Hg19::chr5:60600469..60600488,-p@chr5:60600469..60600488
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Hg19::chr5:60600512..60600563,-p@chr5:60600512..60600563
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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>disease_data<br>

Uber Anatomy
Ontology termp-valuen
artery5.29e-1642
arterial blood vessel5.29e-1642
arterial system5.29e-1642
systemic artery2.49e-1533
systemic arterial system2.49e-1533
somite3.25e-1583
paraxial mesoderm3.25e-1583
presomitic mesoderm3.25e-1583
presumptive segmental plate3.25e-1583
trunk paraxial mesoderm3.25e-1583
presumptive paraxial mesoderm3.25e-1583
organism subdivision5.20e-15365
unilaminar epithelium7.38e-15138
trunk mesenchyme1.54e-13143
trunk3.40e-13216
multi-tissue structure6.09e-13347
multilaminar epithelium9.30e-1382
skeletal muscle tissue1.08e-1161
striated muscle tissue1.08e-1161
myotome1.08e-1161
blood vessel1.16e-1160
epithelial tube open at both ends1.16e-1160
blood vasculature1.16e-1160
vascular cord1.16e-1160
epithelium1.67e-11309
cell layer3.03e-11312
dermomyotome3.22e-1170
muscle tissue3.88e-1163
musculature3.88e-1163
musculature of body3.88e-1163
mesenchyme4.68e-11238
entire embryonic mesenchyme4.68e-11238
splanchnic layer of lateral plate mesoderm8.07e-1184
endoderm-derived structure9.21e-11169
endoderm9.21e-11169
presumptive endoderm9.21e-11169
aorta1.57e-1021
aortic system1.57e-1021
anatomical system1.85e-10625
anatomical group2.71e-10626
surface structure1.08e-0995
multi-cellular organism1.75e-09659
anatomical conduit2.08e-09241
vessel5.12e-0969
reproductive structure7.62e-0959
reproductive system7.62e-0959
anatomical cluster1.32e-08286
vasculature1.54e-0879
vascular system1.54e-0879
epithelial tube2.03e-08118
digestive system3.72e-08155
digestive tract3.72e-08155
primitive gut3.72e-08155
female reproductive organ4.03e-0837
female reproductive system4.03e-0837
blood vessel smooth muscle1.75e-0710
arterial system smooth muscle1.75e-0710
artery smooth muscle tissue1.75e-0710
aorta smooth muscle tissue1.75e-0710
germ layer2.44e-07604
embryonic tissue2.44e-07604
presumptive structure2.44e-07604
epiblast (generic)2.44e-07604
embryonic structure3.35e-07605
developing anatomical structure3.35e-07605
endo-epithelium4.01e-0782
female organism4.11e-0741
mouth7.07e-0728
stomodeum7.07e-0728
embryo7.25e-07612
orifice8.24e-0735
respiratory system9.77e-0772
Disease
Ontology termp-valuen
reproductive organ cancer1.00e-0729
female reproductive organ cancer2.55e-0727
squamous cell carcinoma3.83e-0714
ovarian cancer5.22e-0714


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#672320.18423064322380.0001215704860271640.00164465025779676
CEBPB#105137.971147625824820.001974187055288560.0115644243573549
CTCF#1066435.360256373075030.0064925092527670.0280949315868959
EP300#203336.77394172622320.003216880500103790.0168168877039914
ESR1#2099330.76860329615453.43136389821584e-050.00067872767834425
GTF2F1#2962312.73966087675770.0004835525047438590.00435585130610177
JUN#3725312.51282919233630.0005103313992726250.00445975240637885
JUND#372736.994663941871030.002921845042734990.0157466625944682
MAX#414936.452555509007120.003721913834265510.0187259350099651
MXI1#460139.96157162875930.001011470541259020.00722600532584657
MYC#460935.22228187160940.007020843755740150.0295724904620184
NR3C1#2908314.9730233311730.0002978331194675480.00309876401315713
RFX5#5993312.04791082719510.0005717246050312580.004862802021733
SMARCB1#6598318.25271578115740.000164397760679890.00203816924592201
SMC3#9126315.04493284493280.0002935825420371870.00310464430010346
STAT3#6774310.51946499715420.0008589184530415310.00644939135216079
TFAP2A#7020316.5186343730450.0002218033880766340.00249246008686632
TFAP2C#7022310.80922860986020.0007916746575753130.00618273458180723



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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