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Coexpression cluster:C1687: Difference between revisions

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|tf_chipseq_enrich=EP300#2033;5:6.7739417262232:7.00901578206049e-05:0.00110726758321376!FOS#2353;5:8.9979553088944:1.69470025615156e-05:0.000388824253190274!GATA2#2624;5:12.744931733554:2.9719152914525e-06:0.00010113517794852!JUN#3725;5:12.5128291923363:3.25800591331781e-06:0.00010905861525032!JUND#3727;5:6.99466394187103:5.97069468343598e-05:0.000983399120081012!STAT3#6774;5:10.5194649971542:7.759040745861e-06:0.000220262695421847!TCF7L2#6934;5:10.7701765631373:6.89693748574565e-06:0.000199586936567966
|tf_chipseq_enrich=EP300#2033;5:6.7739417262232:7.00901578206049e-05:0.00110726758321376!FOS#2353;5:8.9979553088944:1.69470025615156e-05:0.000388824253190274!GATA2#2624;5:12.744931733554:2.9719152914525e-06:0.00010113517794852!JUN#3725;5:12.5128291923363:3.25800591331781e-06:0.00010905861525032!JUND#3727;5:6.99466394187103:5.97069468343598e-05:0.000983399120081012!STAT3#6774;5:10.5194649971542:7.759040745861e-06:0.000220262695421847!TCF7L2#6934;5:10.7701765631373:6.89693748574565e-06:0.000199586936567966
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}}
}}

Revision as of 15:02, 26 November 2012


Full id: C1687_liposarcoma_basal_Preadipocyte_Fibroblast_mesenchymal_Smooth_leiomyoma



Phase1 CAGE Peaks

Hg19::chr12:78333942..78333956,+p4@NAV3
Hg19::chr12:78334017..78334054,+p2@NAV3
Hg19::chr12:78334061..78334110,+p1@NAV3
Hg19::chr12:78334115..78334165,+p3@NAV3
Hg19::chr12:78334166..78334180,+p6@NAV3


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>


Cell Type
Ontology termp-valuen
mesodermal cell1.09e-30121
fibroblast3.58e-2376
animal cell1.42e-20679
eukaryotic cell1.42e-20679
embryonic cell7.68e-20250
muscle precursor cell2.14e-1958
myoblast2.14e-1958
multi-potent skeletal muscle stem cell2.14e-1958
muscle cell7.12e-1855
contractile cell9.35e-1759
smooth muscle cell7.09e-1643
smooth muscle myoblast7.09e-1643
electrically responsive cell8.01e-1561
electrically active cell8.01e-1561
non-terminally differentiated cell1.66e-14106
vascular associated smooth muscle cell3.01e-1432
skin fibroblast1.15e-1223
somatic cell1.26e-12588
native cell1.40e-12722
squamous epithelial cell5.56e-1163
lining cell5.71e-1158
barrier cell5.71e-1158
mesothelial cell9.40e-1019
preadipocyte2.98e-0712
endothelial cell of vascular tree6.42e-0724
somatic stem cell6.52e-07433
multi fate stem cell7.36e-07427
aortic smooth muscle cell9.30e-0710
Uber Anatomy
Ontology termp-valuen
somite4.36e-2071
presomitic mesoderm4.36e-2071
presumptive segmental plate4.36e-2071
dermomyotome4.36e-2071
trunk paraxial mesoderm4.36e-2071
unilaminar epithelium8.76e-20148
dense mesenchyme tissue1.67e-1973
paraxial mesoderm1.86e-1972
presumptive paraxial mesoderm1.86e-1972
epithelial vesicle6.45e-1978
vasculature2.04e-1878
vascular system2.04e-1878
multilaminar epithelium4.13e-1883
skeletal muscle tissue1.52e-1762
striated muscle tissue1.52e-1762
myotome1.52e-1762
muscle tissue6.31e-1764
musculature6.31e-1764
musculature of body6.31e-1764
vessel7.07e-1768
trunk mesenchyme1.48e-16122
epithelial tube open at both ends7.52e-1659
blood vessel7.52e-1659
blood vasculature7.52e-1659
vascular cord7.52e-1659
artery2.25e-1542
arterial blood vessel2.25e-1542
arterial system2.25e-1542
trunk2.43e-14199
splanchnic layer of lateral plate mesoderm5.05e-1483
organism subdivision1.87e-13264
epithelial tube3.57e-13117
cardiovascular system4.72e-13109
systemic artery2.20e-1233
systemic arterial system2.20e-1233
circulatory system5.03e-12112
mesenchyme2.29e-11160
entire embryonic mesenchyme2.29e-11160
surface structure3.37e-1199
skin of body1.25e-1041
integument1.42e-1046
integumental system1.42e-1046
aorta1.89e-0821
aortic system1.89e-0821
smooth muscle tissue1.45e-0715
cell layer9.15e-07309
blood vessel smooth muscle9.30e-0710
arterial system smooth muscle9.30e-0710
artery smooth muscle tissue9.30e-0710
aorta smooth muscle tissue9.30e-0710
Disease
Ontology termp-valuen
ovarian cancer1.09e-0814


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
EP300#203356.77394172622327.00901578206049e-050.00110726758321376
FOS#235358.99795530889441.69470025615156e-050.000388824253190274
GATA2#2624512.7449317335542.9719152914525e-060.00010113517794852
JUN#3725512.51282919233633.25800591331781e-060.00010905861525032
JUND#372756.994663941871035.97069468343598e-050.000983399120081012
STAT3#6774510.51946499715427.759040745861e-060.000220262695421847
TCF7L2#6934510.77017656313736.89693748574565e-060.000199586936567966



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.