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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C4678_Smooth_Mesothelial_glioma_mesenchymal_Renal_liposarcoma_Hepatic
|full_id=C4678_Smooth_Mesothelial_glioma_mesenchymal_Renal_liposarcoma_Hepatic
|id=C4678
|id=C4678

Revision as of 17:47, 12 September 2012


Full id: C4678_Smooth_Mesothelial_glioma_mesenchymal_Renal_liposarcoma_Hepatic



Phase1 CAGE Peaks

Hg19::chr7:27157834..27157879,-p@chr7:27157834..27157879
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Hg19::chr7:27157924..27157950,-p@chr7:27157924..27157950
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Hg19::chr7:27157970..27157995,-p@chr7:27157970..27157995
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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
epithelial tube5.57e-22118
trunk4.60e-16216
tube5.03e-16194
subdivision of trunk1.50e-15113
anatomical conduit5.14e-14241
trunk mesenchyme6.46e-14143
mesonephros1.43e-1318
pronephros1.43e-1318
nephrogenic cord1.43e-1318
pronephric mesoderm1.43e-1318
rostral part of nephrogenic cord1.43e-1318
presumptive pronephric mesoderm1.43e-1318
intraembryonic coelom2.85e-1321
body cavity precursor5.09e-1363
excretory tube5.85e-1317
mesonephric epithelium5.85e-1317
mesonephric tubule5.85e-1317
nephric duct5.85e-1317
kidney epithelium5.85e-1317
renal duct5.85e-1317
mesonephric duct5.85e-1317
pronephric duct5.85e-1317
renal tubule7.52e-1312
nephron tubule7.52e-1312
nephron tubule epithelium7.52e-1312
anatomical cluster8.47e-13286
cavitated compound organ1.11e-1232
epithelium1.30e-12309
abdominal segment of trunk2.24e-1261
abdomen2.24e-1261
anatomical space2.76e-12104
nephron epithelium2.98e-1216
nephron2.98e-1216
uriniferous tubule2.98e-1216
metanephric mesenchyme2.98e-1216
nephrogenic mesenchyme2.98e-1216
cell layer3.32e-12312
immaterial anatomical entity3.66e-12126
compound organ4.62e-1269
muscle tissue9.97e-1263
musculature9.97e-1263
musculature of body9.97e-1263
urogenital ridge1.19e-1120
duct1.23e-1126
blood vessel1.54e-1160
epithelial tube open at both ends1.54e-1160
blood vasculature1.54e-1160
vascular cord1.54e-1160
vessel2.63e-1169
unilaminar epithelium2.76e-11138
trunk region element3.28e-11107
mesenchyme3.75e-11238
entire embryonic mesenchyme3.75e-11238
kidney5.40e-1127
kidney mesenchyme5.40e-1127
kidney rudiment5.40e-1127
kidney field5.40e-1127
systemic artery6.59e-1133
systemic arterial system6.59e-1133
splanchnic layer of lateral plate mesoderm8.32e-1184
skeletal muscle tissue1.09e-1061
striated muscle tissue1.09e-1061
myotome1.09e-1061
smooth muscle tissue1.22e-1015
anatomical cavity1.45e-1070
multi-tissue structure2.37e-10347
artery2.58e-1042
arterial blood vessel2.58e-1042
arterial system2.58e-1042
vasculature8.54e-1079
vascular system8.54e-1079
abdomen element1.58e-0955
abdominal segment element1.58e-0955
intermediate mesoderm3.38e-0937
cortex of kidney3.41e-0913
renal parenchyma3.41e-0913
renal system6.18e-0945
mesoderm1.22e-08448
mesoderm-derived structure1.22e-08448
presumptive mesoderm1.22e-08448


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
SUZ12#23512233.41052060737530.00117826764536030.0080031929379412
USF1#739136.361499277207960.00388404057290560.0191152779507887



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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