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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C3897_Mesothelial_Multipotent_mesenchymal_Fibroblast_argyrophil_medial_leiomyoma
|full_id=C3897_Mesothelial_Multipotent_mesenchymal_Fibroblast_argyrophil_medial_leiomyoma
|id=C3897
|id=C3897

Revision as of 16:53, 12 September 2012


Full id: C3897_Mesothelial_Multipotent_mesenchymal_Fibroblast_argyrophil_medial_leiomyoma



Phase1 CAGE Peaks

Hg19::chr1:163038648..163038667,+p3@RGS4
Hg19::chr1:163038669..163038763,+p2@RGS4
Hg19::chr1:163039143..163039159,+p1@RGS4


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>disease_data<br>

Uber Anatomy
Ontology termp-valuen
cell layer5.76e-26312
vasculature1.10e-2579
vascular system1.10e-2579
tube3.07e-25194
epithelium6.71e-25309
splanchnic layer of lateral plate mesoderm3.68e-2484
blood vessel6.61e-2360
epithelial tube open at both ends6.61e-2360
blood vasculature6.61e-2360
vascular cord6.61e-2360
organism subdivision1.13e-22365
artery3.20e-2242
arterial blood vessel3.20e-2242
arterial system3.20e-2242
vessel7.21e-2269
anatomical conduit1.30e-21241
anatomical cluster7.64e-21286
somite3.89e-1983
paraxial mesoderm3.89e-1983
presomitic mesoderm3.89e-1983
presumptive segmental plate3.89e-1983
trunk paraxial mesoderm3.89e-1983
presumptive paraxial mesoderm3.89e-1983
cardiovascular system5.78e-19110
circulatory system2.00e-18113
multi-tissue structure2.12e-18347
dermomyotome3.02e-1870
skeletal muscle tissue6.77e-1861
striated muscle tissue6.77e-1861
myotome6.77e-1861
systemic artery1.13e-1733
systemic arterial system1.13e-1733
muscle tissue1.52e-1763
musculature1.52e-1763
musculature of body1.52e-1763
epithelial tube5.68e-17118
neural plate2.60e-1686
presumptive neural plate2.60e-1686
regional part of brain3.31e-1659
regional part of nervous system3.59e-1694
nervous system3.59e-1694
neurectoderm1.01e-1590
brain3.26e-1569
future brain3.26e-1569
central nervous system9.34e-1582
multi-cellular organism1.22e-14659
neural tube2.91e-1457
neural rod2.91e-1457
future spinal cord2.91e-1457
neural keel2.91e-1457
unilaminar epithelium1.10e-13138
regional part of forebrain3.50e-1341
forebrain3.50e-1341
future forebrain3.50e-1341
pre-chordal neural plate5.50e-1361
anterior neural tube6.96e-1342
trunk mesenchyme7.24e-13143
multilaminar epithelium1.11e-1282
head1.24e-12123
cerebral hemisphere1.57e-1232
telencephalon2.68e-1234
anatomical system3.53e-12625
gray matter3.66e-1234
brain grey matter3.66e-1234
anatomical group6.07e-12626
regional part of telencephalon1.11e-1133
anterior region of body1.58e-11129
craniocervical region1.58e-11129
aorta6.91e-1121
aortic system6.91e-1121
regional part of cerebral cortex9.06e-1122
ectoderm-derived structure9.18e-11169
ectoderm1.35e-10173
presumptive ectoderm1.35e-10173
cerebral cortex3.64e-1025
pallium3.64e-1025
neocortex3.75e-1020
embryo3.20e-09612
embryonic structure4.98e-09605
developing anatomical structure4.98e-09605
germ layer7.13e-09604
embryonic tissue7.13e-09604

Disease
Ontology termp-valuen


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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