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Coexpression cluster:C2766: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C2766_Smooth_Hair_spindle_leiomyoma_Endothelial_bone_Multipotent
|full_id=C2766_Smooth_Hair_spindle_leiomyoma_Endothelial_bone_Multipotent
|id=C2766
|id=C2766

Revision as of 15:32, 12 September 2012


Full id: C2766_Smooth_Hair_spindle_leiomyoma_Endothelial_bone_Multipotent



Phase1 CAGE Peaks

Hg19::chr4:10117949..10117979,-p8@WDR1
Hg19::chr4:10118001..10118022,-p7@WDR1
Hg19::chr4:10118034..10118074,-p6@WDR1
Hg19::chr4:10118075..10118107,-p5@WDR1


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
non-terminally differentiated cell2.57e-38180
mesodermal cell7.25e-37119
somatic cell1.12e-21591
muscle precursor cell1.68e-2057
myoblast1.68e-2057
multi-potent skeletal muscle stem cell1.68e-2057
contractile cell1.82e-2059
fibroblast4.79e-2075
smooth muscle cell1.01e-1942
smooth muscle myoblast1.01e-1942
muscle cell1.09e-1954
vascular associated smooth muscle cell3.30e-1832
electrically responsive cell3.14e-1760
electrically active cell3.14e-1760
embryonic cell3.80e-17248
lining cell2.85e-1557
barrier cell2.85e-1557
animal cell1.02e-13679
eukaryotic cell1.02e-13679
multi fate stem cell1.25e-13430
somatic stem cell1.79e-12436
meso-epithelial cell6.82e-1244
endothelial cell1.19e-1135
endothelial cell of vascular tree1.38e-1124
stem cell3.89e-11444
blood vessel endothelial cell7.16e-1018
embryonic blood vessel endothelial progenitor cell7.16e-1018
cardiocyte8.52e-0716
Uber Anatomy
Ontology termp-valuen
vasculature3.48e-3279
vascular system3.48e-3279
vessel3.27e-2869
splanchnic layer of lateral plate mesoderm8.75e-2784
cardiovascular system1.02e-26110
blood vessel3.32e-2660
epithelial tube open at both ends3.32e-2660
blood vasculature3.32e-2660
vascular cord3.32e-2660
circulatory system8.12e-26113
artery1.05e-2242
arterial blood vessel1.05e-2242
arterial system1.05e-2242
somite1.88e-2183
paraxial mesoderm1.88e-2183
presomitic mesoderm1.88e-2183
presumptive segmental plate1.88e-2183
trunk paraxial mesoderm1.88e-2183
presumptive paraxial mesoderm1.88e-2183
epithelial tube1.03e-20118
dermomyotome1.97e-1970
trunk mesenchyme6.65e-18143
lateral plate mesoderm1.28e-17216
systemic artery1.43e-1733
systemic arterial system1.43e-1733
skeletal muscle tissue2.19e-1761
striated muscle tissue2.19e-1761
myotome2.19e-1761
multilaminar epithelium2.46e-1782
muscle tissue5.92e-1763
musculature5.92e-1763
musculature of body5.92e-1763
unilaminar epithelium9.93e-16138
mesoderm1.78e-15448
mesoderm-derived structure1.78e-15448
presumptive mesoderm1.78e-15448
musculoskeletal system9.16e-14167
multi-cellular organism4.12e-12659
anatomical system6.62e-12625
anatomical group1.03e-11626
trunk2.49e-11216
aorta5.47e-1121
aortic system5.47e-1121
endothelium7.16e-1018
blood vessel endothelium7.16e-1018
cardiovascular system endothelium7.16e-1018
simple squamous epithelium1.79e-0822
anatomical cluster2.71e-08286
squamous epithelium2.83e-0825
cell layer3.46e-08312
epithelium1.06e-07309
embryonic structure4.51e-07605
developing anatomical structure4.51e-07605
germ layer5.78e-07604
embryonic tissue5.78e-07604
presumptive structure5.78e-07604
epiblast (generic)5.78e-07604


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
E2F1#186944.907389214879320.001724022357361790.010669303803064
ELF1#199744.258097958807540.003041525565781240.0161180174834903
ETS1#211337.296570691651750.00400857377511390.0192103627999413
GABPB1#255335.300762877136630.01012678824234270.0378780759702755
HEY1#2346244.040111043105710.00375304636917980.0186454385762901
HMGN3#932436.133910792512940.006640696683324720.0283092257198151
POU2F2#545249.106124057742520.000145395665174930.00188609835737231
SIN3A#2594245.408884726815140.001168172384885160.00797612158113368
TAF1#687243.343046285745290.008005664898701650.032296957523003
TBP#690843.706770687096390.005296377814784350.0244799257655453
ZBTB7A#5134147.35190930787590.000342223540015990.00347139513361791
ZEB1#6935312.66632401315790.000793336075912850.00613378934203895



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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