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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C823_Fibroblast_Endothelial_hepatic_Pericytes_umbilical_Adipocyte_Lymphatic
|full_id=C823_Fibroblast_Endothelial_hepatic_Pericytes_umbilical_Adipocyte_Lymphatic
|id=C823
|id=C823

Revision as of 18:34, 12 September 2012


Full id: C823_Fibroblast_Endothelial_hepatic_Pericytes_umbilical_Adipocyte_Lymphatic



Phase1 CAGE Peaks

Hg19::chr13:110827583..110827627,+p@chr13:110827583..110827627
+
Hg19::chr13:110829031..110829044,+p@chr13:110829031..110829044
+
Hg19::chr13:110830539..110830556,-p@chr13:110830539..110830556
-
Hg19::chr13:110845203..110845217,+p@chr13:110845203..110845217
+
Hg19::chr13:110847360..110847381,+p@chr13:110847360..110847381
+
Hg19::chr13:111077159..111077201,-p@chr13:111077159..111077201
-
Hg19::chr13:111086779..111086789,-p@chr13:111086779..111086789
-
Hg19::chr13:111118370..111118403,-p@chr13:111118370..111118403
-
Hg19::chr13:111137319..111137361,-p@chr13:111137319..111137361
-
Hg19::chr13:111164338..111164351,+p@chr13:111164338..111164351
+


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
vasculature5.74e-1779
vascular system5.74e-1779
epithelial tube1.86e-16118
trunk mesenchyme1.15e-14143
circulatory system1.44e-13113
splanchnic layer of lateral plate mesoderm1.67e-1384
cardiovascular system3.62e-13110
vessel3.91e-1369
cell layer1.05e-11312
muscle tissue2.66e-1163
musculature2.66e-1163
musculature of body2.66e-1163
epithelium3.91e-11309
skeletal muscle tissue4.73e-1161
striated muscle tissue4.73e-1161
myotome4.73e-1161
blood vessel4.85e-1160
epithelial tube open at both ends4.85e-1160
blood vasculature4.85e-1160
vascular cord4.85e-1160
multi-cellular organism5.37e-11659
anatomical cluster8.48e-11286
trunk1.02e-10216
unilaminar epithelium1.42e-10138
multi-tissue structure3.74e-10347
organism subdivision1.13e-09365
dermomyotome1.46e-0970
multilaminar epithelium2.07e-0982
somite2.34e-0983
paraxial mesoderm2.34e-0983
presomitic mesoderm2.34e-0983
presumptive segmental plate2.34e-0983
trunk paraxial mesoderm2.34e-0983
presumptive paraxial mesoderm2.34e-0983
urogenital ridge3.18e-0920
excretory tube8.18e-0917
mesonephric epithelium8.18e-0917
mesonephric tubule8.18e-0917
nephric duct8.18e-0917
kidney epithelium8.18e-0917
renal duct8.18e-0917
mesonephric duct8.18e-0917
pronephric duct8.18e-0917
compound organ8.34e-0969
nephron epithelium8.89e-0916
nephron8.89e-0916
uriniferous tubule8.89e-0916
metanephric mesenchyme8.89e-0916
nephrogenic mesenchyme8.89e-0916
mesonephros8.89e-0918
pronephros8.89e-0918
nephrogenic cord8.89e-0918
pronephric mesoderm8.89e-0918
rostral part of nephrogenic cord8.89e-0918
presumptive pronephric mesoderm8.89e-0918
mesenchyme9.55e-09238
entire embryonic mesenchyme9.55e-09238
parenchyma2.04e-0817
intraembryonic coelom2.37e-0821
anatomical conduit3.80e-08241
intermediate mesoderm4.65e-0837
artery1.56e-0742
arterial blood vessel1.56e-0742
arterial system1.56e-0742
body cavity precursor3.47e-0763
cortex of kidney4.38e-0713
renal parenchyma4.38e-0713
anatomical system5.81e-07625
anatomical group8.80e-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

No analysis results for this cluster

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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