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Coexpression cluster:C4642

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Full id: C4642_liposarcoma_extraskeletal_Endothelial_Lymphatic_Mesenchymal_large_glioblastoma



Phase1 CAGE Peaks

Hg19::chr7:107643362..107643373,-p7@LAMB1
Hg19::chr7:107643412..107643428,-p2@LAMB1
Hg19::chr7:107643432..107643443,-p4@LAMB1


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
mesodermal cell1.47e-27119
non-terminally differentiated cell4.42e-22180
embryonic cell8.34e-20248
endothelial cell of vascular tree3.91e-1724
muscle precursor cell4.52e-1557
myoblast4.52e-1557
multi-potent skeletal muscle stem cell4.52e-1557
contractile cell2.11e-1459
muscle cell3.43e-1454
lining cell5.52e-1457
barrier cell5.52e-1457
blood vessel endothelial cell4.15e-1318
embryonic blood vessel endothelial progenitor cell4.15e-1318
electrically responsive cell9.59e-1260
electrically active cell9.59e-1260
endothelial cell2.36e-1135
smooth muscle cell5.10e-1142
smooth muscle myoblast5.10e-1142
meso-epithelial cell7.00e-1044
vascular associated smooth muscle cell1.19e-0932
fibroblast1.30e-0975
cardiocyte2.86e-0816
endothelial cell of artery2.07e-079
squamous epithelial cell2.14e-0762
Uber Anatomy
Ontology termp-valuen
splanchnic layer of lateral plate mesoderm5.81e-2784
vasculature3.44e-2679
vascular system3.44e-2679
epithelial tube6.36e-24118
unilaminar epithelium1.46e-22138
vessel2.87e-2269
circulatory system1.50e-20113
cardiovascular system1.96e-20110
blood vessel2.20e-2060
epithelial tube open at both ends2.20e-2060
blood vasculature2.20e-2060
vascular cord2.20e-2060
cell layer4.12e-20312
multi-cellular organism8.69e-20659
epithelium2.00e-19309
anatomical cluster1.11e-16286
skeletal muscle tissue1.29e-1561
striated muscle tissue1.29e-1561
myotome1.29e-1561
trunk mesenchyme1.31e-15143
artery2.23e-1542
arterial blood vessel2.23e-1542
arterial system2.23e-1542
muscle tissue2.30e-1563
musculature2.30e-1563
musculature of body2.30e-1563
organism subdivision2.61e-15365
dermomyotome3.99e-1570
trunk4.77e-15216
anatomical system1.07e-14625
multi-tissue structure1.10e-14347
anatomical conduit1.83e-14241
anatomical group2.07e-14626
multilaminar epithelium2.64e-1482
somite2.91e-1483
paraxial mesoderm2.91e-1483
presomitic mesoderm2.91e-1483
presumptive segmental plate2.91e-1483
trunk paraxial mesoderm2.91e-1483
presumptive paraxial mesoderm2.91e-1483
endothelium4.15e-1318
blood vessel endothelium4.15e-1318
cardiovascular system endothelium4.15e-1318
mesenchyme1.09e-12238
entire embryonic mesenchyme1.09e-12238
embryo1.53e-11612
embryonic structure3.29e-11605
developing anatomical structure3.29e-11605
tube3.90e-11194
simple squamous epithelium4.66e-1122
systemic artery5.23e-1133
systemic arterial system5.23e-1133
germ layer7.53e-11604
embryonic tissue7.53e-11604
presumptive structure7.53e-11604
epiblast (generic)7.53e-11604
squamous epithelium3.13e-1025
heart3.15e-0924
primitive heart tube3.15e-0924
primary heart field3.15e-0924
anterior lateral plate mesoderm3.15e-0924
heart tube3.15e-0924
heart primordium3.15e-0924
cardiac mesoderm3.15e-0924
cardiogenic plate3.15e-0924
heart rudiment3.15e-0924
primary circulatory organ4.58e-0927
compound organ3.38e-0869
mesoderm5.67e-08448
mesoderm-derived structure5.67e-08448
presumptive mesoderm5.67e-08448
aorta5.86e-0821
aortic system5.86e-0821
endothelial tube2.07e-079


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
CCNT2#90536.336201576962630.003930750035764890.0191083412299967
E2F1#186934.907389214879320.008460985347239390.0327571488982924
E2F6#187635.017155731697390.00791769806886330.0324191974208654
NRF1#4899312.21027944771090.0005492172401020010.00473342955430045
RAD21#5885310.35503389545630.0009004912073565420.00668275429582249
TFAP2C#7022310.80922860986020.0007916746575753130.00618782439473942
USF1#739136.361499277207960.00388404057290560.0191116755426944
YY1#752834.911170749853860.008441455341808260.0331123813875348



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.