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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C4552_Lymphatic_Endothelial_Renal_pharyngeal_papillary_amniotic_Fibroblast
|full_id=C4552_Lymphatic_Endothelial_Renal_pharyngeal_papillary_amniotic_Fibroblast
|id=C4552
|id=C4552

Revision as of 17:39, 12 September 2012


Full id: C4552_Lymphatic_Endothelial_Renal_pharyngeal_papillary_amniotic_Fibroblast



Phase1 CAGE Peaks

Hg19::chr6:12296648..12296663,+p@chr6:12296648..12296663
+
Hg19::chr6:12296671..12296685,+p@chr6:12296671..12296685
+
Hg19::chr6:12296687..12296706,+p@chr6:12296687..12296706
+


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
vessel5.08e-1569
vasculature8.21e-1579
vascular system8.21e-1579
splanchnic layer of lateral plate mesoderm2.17e-1484
blood vessel8.42e-1360
epithelial tube open at both ends8.42e-1360
blood vasculature8.42e-1360
vascular cord8.42e-1360
cardiovascular system4.15e-12110
epithelial tube9.84e-12118
circulatory system1.28e-11113
tube1.79e-11194
anatomical cluster2.44e-11286
anatomical conduit6.74e-11241
artery7.60e-1142
arterial blood vessel7.60e-1142
arterial system7.60e-1142
endothelium1.28e-0918
blood vessel endothelium1.28e-0918
cardiovascular system endothelium1.28e-0918
cell layer3.52e-09312
epithelium3.59e-09309
multi-cellular organism5.72e-09659
anatomical system1.02e-08625
simple squamous epithelium1.35e-0822
anatomical group1.38e-08626
aorta5.24e-0821
aortic system5.24e-0821
systemic artery5.38e-0833
systemic arterial system5.38e-0833
squamous epithelium2.27e-0725


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#1066435.360256373075030.0064925092527670.0281019177690635
JUND#372736.994663941871030.002921845042734990.0157547924218184
NR3C1#2908314.9730233311730.0002978331194675480.0030996904000071
RAD21#5885310.35503389545630.0009004912073565420.00667895754599175



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.