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Coexpression cluster:C4027: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000055!1.98e-25!69;UBERON:0002049!3.69e-25!79;UBERON:0007798!3.69e-25!79;UBERON:0001981!7.40e-23!60;UBERON:0007500!7.40e-23!60;UBERON:0004537!7.40e-23!60;UBERON:0006965!7.40e-23!60;UBERON:0004872!8.43e-23!84;UBERON:0003914!1.99e-21!118;UBERON:0002100!1.22e-16!216;UBERON:0000468!1.82e-16!659;UBERON:0004535!7.01e-16!110;UBERON:0001009!1.47e-15!113;UBERON:0000486!2.89e-15!82;UBERON:0000490!3.91e-15!138;UBERON:0001637!6.65e-15!42;UBERON:0003509!6.65e-15!42;UBERON:0004572!6.65e-15!42;UBERON:0000467!2.27e-14!625;UBERON:0000480!4.91e-14!626;UBERON:0000926!6.77e-14!448;UBERON:0004120!6.77e-14!448;UBERON:0006603!6.77e-14!448;UBERON:0006914!1.49e-13!25;UBERON:0000914!1.88e-13!83;UBERON:0002329!1.88e-13!83;UBERON:0003077!1.88e-13!83;UBERON:0003059!1.88e-13!83;UBERON:0007282!1.88e-13!83;UBERON:0009618!1.88e-13!83;UBERON:0007285!1.88e-13!83;UBERON:0004290!2.37e-13!70;UBERON:0005256!3.75e-13!143;UBERON:0000487!4.00e-13!22;UBERON:0001986!4.27e-13!18;UBERON:0004638!4.27e-13!18;UBERON:0004852!4.27e-13!18;UBERON:0000119!7.42e-13!312;UBERON:0001134!8.30e-13!61;UBERON:0002036!8.30e-13!61;UBERON:0003082!8.30e-13!61;UBERON:0004573!1.05e-12!33;UBERON:0004571!1.05e-12!33;UBERON:0000483!1.12e-12!309;UBERON:0002385!1.15e-12!63;UBERON:0001015!1.15e-12!63;UBERON:0000383!1.15e-12!63;UBERON:0003104!1.88e-12!238;UBERON:0009142!1.88e-12!238;UBERON:0000922!7.70e-11!612;UBERON:0002050!1.60e-10!605;UBERON:0005423!1.60e-10!605;UBERON:0000923!2.00e-10!604;UBERON:0005291!2.00e-10!604;UBERON:0006598!2.00e-10!604;UBERON:0002532!2.00e-10!604;UBERON:0000475!1.99e-09!365;UBERON:0000481!4.88e-09!347;UBERON:0000947!5.56e-09!21;UBERON:0010191!5.56e-09!21;UBERON:0003103!5.68e-09!69;UBERON:0003886!7.38e-09!63;UBERON:0004111!9.77e-09!241;UBERON:0000464!1.32e-08!104;UBERON:0000477!6.75e-08!286;UBERON:0002553!1.45e-07!70;UBERON:0003915!1.55e-07!9;UBERON:0004700!1.55e-07!9;UBERON:0001917!1.55e-07!9;UBERON:0009569!8.00e-07!113
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}}
}}

Revision as of 19:40, 8 August 2012


Full id: C4027_Wilms_Endothelial_mesothelioma_Renal_mesenchymal_leiomyoma_Fibroblast



Phase1 CAGE Peaks

Hg19::chr20:33759838..33759845,+p5@PROCR
Hg19::chr20:33759854..33759916,+p1@PROCR
Hg19::chr20:33759924..33759940,+p6@PROCR


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
mesodermal cell3.23e-26119
embryonic cell5.45e-21248
non-terminally differentiated cell3.96e-17180
endothelial cell of vascular tree1.46e-1524
meso-epithelial cell2.20e-1544
endothelial cell2.82e-1535
lining cell6.49e-1457
barrier cell6.49e-1457
blood vessel endothelial cell4.27e-1318
embryonic blood vessel endothelial progenitor cell4.27e-1318
contractile cell4.41e-1359
muscle precursor cell1.94e-1257
myoblast1.94e-1257
multi-potent skeletal muscle stem cell1.94e-1257
muscle cell4.03e-1254
smooth muscle cell2.10e-1042
smooth muscle myoblast2.10e-1042
epithelial cell2.66e-10254
electrically responsive cell8.63e-1060
electrically active cell8.63e-1060
squamous epithelial cell1.42e-0962
vascular associated smooth muscle cell2.60e-0832
fibroblast3.15e-0875
endothelial cell of artery1.55e-079
somatic cell3.74e-07591
kidney cell7.85e-0718
kidney epithelial cell7.85e-0718
Uber Anatomy
Ontology termp-valuen
vessel1.98e-2569
vasculature3.69e-2579
vascular system3.69e-2579
blood vessel7.40e-2360
epithelial tube open at both ends7.40e-2360
blood vasculature7.40e-2360
vascular cord7.40e-2360
splanchnic layer of lateral plate mesoderm8.43e-2384
epithelial tube1.99e-21118
trunk1.22e-16216
multi-cellular organism1.82e-16659
cardiovascular system7.01e-16110
circulatory system1.47e-15113
multilaminar epithelium2.89e-1582
unilaminar epithelium3.91e-15138
artery6.65e-1542
arterial blood vessel6.65e-1542
arterial system6.65e-1542
anatomical system2.27e-14625
anatomical group4.91e-14626
mesoderm6.77e-14448
mesoderm-derived structure6.77e-14448
presumptive mesoderm6.77e-14448
squamous epithelium1.49e-1325
somite1.88e-1383
paraxial mesoderm1.88e-1383
presomitic mesoderm1.88e-1383
presumptive segmental plate1.88e-1383
trunk paraxial mesoderm1.88e-1383
presumptive paraxial mesoderm1.88e-1383
dermomyotome2.37e-1370
trunk mesenchyme3.75e-13143
simple squamous epithelium4.00e-1322
endothelium4.27e-1318
blood vessel endothelium4.27e-1318
cardiovascular system endothelium4.27e-1318
cell layer7.42e-13312
skeletal muscle tissue8.30e-1361
striated muscle tissue8.30e-1361
myotome8.30e-1361
systemic artery1.05e-1233
systemic arterial system1.05e-1233
epithelium1.12e-12309
muscle tissue1.15e-1263
musculature1.15e-1263
musculature of body1.15e-1263
mesenchyme1.88e-12238
entire embryonic mesenchyme1.88e-12238
embryo7.70e-11612
embryonic structure1.60e-10605
developing anatomical structure1.60e-10605
germ layer2.00e-10604
embryonic tissue2.00e-10604
presumptive structure2.00e-10604
epiblast (generic)2.00e-10604
organism subdivision1.99e-09365
multi-tissue structure4.88e-09347
aorta5.56e-0921
aortic system5.56e-0921
compound organ5.68e-0969
body cavity precursor7.38e-0963
anatomical conduit9.77e-09241
anatomical space1.32e-08104
anatomical cluster6.75e-08286
anatomical cavity1.45e-0770
endothelial tube1.55e-079
arterial system endothelium1.55e-079
endothelium of artery1.55e-079
subdivision of trunk8.00e-07113


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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