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|ontology_enrichment_disease=
|ontology_enrichment_disease=
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}}

Revision as of 19:11, 8 August 2012


Full id: C3470_Smooth_Mesothelial_mesothelioma_Synoviocyte_Prostate_normal_mesenchymal



Phase1 CAGE Peaks

Hg19::chr14:96722152..96722166,+p4@BDKRB1
Hg19::chr14:96722171..96722185,+p3@BDKRB1
Hg19::chr14:96722201..96722212,+p5@BDKRB1


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
non-terminally differentiated cell4.81e-32180
smooth muscle cell2.17e-2542
smooth muscle myoblast2.17e-2542
muscle precursor cell8.62e-2557
myoblast8.62e-2557
multi-potent skeletal muscle stem cell8.62e-2557
muscle cell1.24e-2354
contractile cell1.35e-2059
electrically responsive cell4.73e-2060
electrically active cell4.73e-2060
vascular associated smooth muscle cell2.17e-1832
mesodermal cell3.71e-18119
multi fate stem cell4.79e-16430
somatic stem cell2.27e-15436
stem cell1.68e-14444
fibroblast2.77e-1375
aortic smooth muscle cell1.39e-1010
skin fibroblast3.54e-0923
stromal cell2.40e-0827
mesothelial cell4.80e-0819
somatic cell6.72e-08591
smooth muscle cell of the subclavian artery1.74e-075
GAG secreting cell3.57e-079
carbohydrate secreting cell3.57e-079
preadipocyte3.67e-0712
animal cell5.40e-07679
eukaryotic cell5.40e-07679
extracellular matrix secreting cell7.67e-0714
Uber Anatomy
Ontology termp-valuen
muscle tissue2.40e-2263
musculature2.40e-2263
musculature of body2.40e-2263
skeletal muscle tissue2.57e-2261
striated muscle tissue2.57e-2261
myotome2.57e-2261
dermomyotome4.20e-1970
somite4.81e-1783
paraxial mesoderm4.81e-1783
presomitic mesoderm4.81e-1783
presumptive segmental plate4.81e-1783
trunk paraxial mesoderm4.81e-1783
presumptive paraxial mesoderm4.81e-1783
multilaminar epithelium1.22e-1682
smooth muscle tissue1.03e-1315
artery1.25e-1342
arterial blood vessel1.25e-1342
arterial system1.25e-1342
systemic artery1.62e-1333
systemic arterial system1.62e-1333
trunk mesenchyme6.80e-13143
unilaminar epithelium1.34e-10138
blood vessel smooth muscle1.39e-1010
arterial system smooth muscle1.39e-1010
artery smooth muscle tissue1.39e-1010
aorta smooth muscle tissue1.39e-1010
musculoskeletal system5.66e-10167
blood vessel9.12e-1060
epithelial tube open at both ends9.12e-1060
blood vasculature9.12e-1060
vascular cord9.12e-1060
vasculature3.94e-0879
vascular system3.94e-0879
splanchnic layer of lateral plate mesoderm5.13e-0884
vessel1.67e-0769
thoracic segment blood vessel1.74e-075
subclavian artery1.74e-075
aorta5.26e-0721
aortic system5.26e-0721


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.