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Coexpression cluster:C4510

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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
artery4.13e-1642
arterial blood vessel4.13e-1642
arterial system4.13e-1642
endoderm-derived structure3.92e-15160
endoderm3.92e-15160
presumptive endoderm3.92e-15160
unilaminar epithelium8.62e-15148
systemic artery1.36e-1433
systemic arterial system1.36e-1433
organism subdivision1.51e-13264
multilaminar epithelium1.16e-1283
skeletal muscle tissue1.57e-1262
striated muscle tissue1.57e-1262
myotome1.57e-1262
multi-tissue structure1.99e-12342
trunk mesenchyme2.22e-12122
digestive system6.64e-12145
digestive tract6.64e-12145
primitive gut6.64e-12145
somite1.00e-1171
presomitic mesoderm1.00e-1171
presumptive segmental plate1.00e-1171
dermomyotome1.00e-1171
trunk paraxial mesoderm1.00e-1171
dense mesenchyme tissue1.01e-1173
muscle tissue1.13e-1164
musculature1.13e-1164
musculature of body1.13e-1164
paraxial mesoderm2.40e-1172
presumptive paraxial mesoderm2.40e-1172
aorta1.90e-1021
aortic system1.90e-1021
trunk1.99e-10199
epithelial tube open at both ends4.18e-1059
blood vessel4.18e-1059
blood vasculature4.18e-1059
vascular cord4.18e-1059
endo-epithelium9.44e-1082
respiratory system1.66e-0974
splanchnic layer of lateral plate mesoderm1.99e-0983
anatomical conduit2.43e-09240
epithelial vesicle2.54e-0978
epithelium1.43e-08306
cell layer1.93e-08309
blood vessel smooth muscle2.41e-0810
arterial system smooth muscle2.41e-0810
artery smooth muscle tissue2.41e-0810
aorta smooth muscle tissue2.41e-0810
thoracic cavity element3.43e-0834
thoracic cavity3.43e-0834
mucosa5.95e-0820
surface structure6.05e-0899
anatomical cluster6.56e-08373
orifice6.84e-0836
thoracic segment organ9.98e-0835
mouth1.05e-0729
stomodeum1.05e-0729
mesenchyme1.22e-07160
entire embryonic mesenchyme1.22e-07160
mouth mucosa3.46e-0713
vessel3.64e-0768
epithelial tube3.74e-07117
reproductive structure5.49e-0759
reproductive system5.49e-0759
tracheobronchial tree7.60e-0715
lower respiratory tract7.60e-0715
Disease
Ontology termp-valuen
squamous cell carcinoma8.78e-0914


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.