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Coexpression cluster:C4265: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C4265_heart_Fibroblast_Endothelial_smooth_mesodermal_Ciliary_mature
|full_id=C4265_heart_Fibroblast_Endothelial_smooth_mesodermal_Ciliary_mature
|id=C4265
|id=C4265

Revision as of 17:19, 12 September 2012


Full id: C4265_heart_Fibroblast_Endothelial_smooth_mesodermal_Ciliary_mature



Phase1 CAGE Peaks

Hg19::chr3:111578558..111578576,+p6@PHLDB2
Hg19::chr3:111578583..111578620,+p4@PHLDB2
Hg19::chr3:111578650..111578707,+p2@PHLDB2


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>


Uber Anatomy
Ontology termp-valuen
splanchnic layer of lateral plate mesoderm3.37e-2184
circulatory system1.04e-19113
vasculature3.57e-1979
vascular system3.57e-1979
cardiovascular system1.89e-18110
epithelial tube7.19e-17118
unilaminar epithelium1.03e-16138
blood vessel2.29e-1560
epithelial tube open at both ends2.29e-1560
blood vasculature2.29e-1560
vascular cord2.29e-1560
vessel3.81e-1569
muscle tissue2.43e-1463
musculature2.43e-1463
musculature of body2.43e-1463
skeletal muscle tissue7.27e-1461
striated muscle tissue7.27e-1461
myotome7.27e-1461
dermomyotome4.05e-1370
somite4.15e-1383
paraxial mesoderm4.15e-1383
presomitic mesoderm4.15e-1383
presumptive segmental plate4.15e-1383
trunk paraxial mesoderm4.15e-1383
presumptive paraxial mesoderm4.15e-1383
trunk mesenchyme2.75e-12143
cell layer5.02e-12312
epithelium1.03e-11309
multi-tissue structure6.96e-11347
artery1.34e-1042
arterial blood vessel1.34e-1042
arterial system1.34e-1042
trunk1.66e-10216
multilaminar epithelium2.19e-1082
primary circulatory organ3.36e-1027
mesenchyme4.09e-10238
entire embryonic mesenchyme4.09e-10238
anatomical cluster4.79e-10286
organism subdivision5.86e-10365
multi-cellular organism1.40e-09659
heart7.26e-0924
primitive heart tube7.26e-0924
primary heart field7.26e-0924
anterior lateral plate mesoderm7.26e-0924
heart tube7.26e-0924
heart primordium7.26e-0924
cardiac mesoderm7.26e-0924
cardiogenic plate7.26e-0924
heart rudiment7.26e-0924
systemic artery9.92e-0933
systemic arterial system9.92e-0933
anatomical conduit1.09e-07241
anatomical system3.07e-07625
aorta3.50e-0721
aortic system3.50e-0721
anatomical group4.81e-07626


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
CTCF#1066435.360256373075030.0064925092527670.0280345298652058
E2F1#186934.907389214879320.008460985347239390.0326482246612109
EP300#203336.77394172622320.003216880500103790.0167883161378343
JUND#372736.994663941871030.002921845042734990.015715845620755
SMARCC2#6601394.15537442689761.19621075407887e-064.86113054261646e-05
TCF7L2#6934310.77017656313730.0008003181298398380.00615723205615785



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.