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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C1432_mesenchymal_Smooth_Lymphatic_Preadipocyte_Sebocyte_CD14_anaplastic
|full_id=C1432_mesenchymal_Smooth_Lymphatic_Preadipocyte_Sebocyte_CD14_anaplastic
|id=C1432
|id=C1432

Revision as of 13:59, 12 September 2012


Full id: C1432_mesenchymal_Smooth_Lymphatic_Preadipocyte_Sebocyte_CD14_anaplastic



Phase1 CAGE Peaks

Hg19::chr17:38171624..38171635,+p2@CSF3
Hg19::chr17:38171681..38171699,+p1@CSF3
Hg19::chr17:38171895..38171901,+p4@CSF3
Hg19::chr17:38172763..38172779,+p@chr17:38172763..38172779
+
Hg19::chr17:38172802..38172815,+p@chr17:38172802..38172815
+
Hg19::chr17:38173175..38173226,+p@chr17:38173175..38173226
+


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
vessel7.99e-2169
artery9.61e-1942
arterial blood vessel9.61e-1942
arterial system9.61e-1942
blood vessel1.63e-1860
epithelial tube open at both ends1.63e-1860
blood vasculature1.63e-1860
vascular cord1.63e-1860
multilaminar epithelium4.15e-1882
vasculature1.19e-1779
vascular system1.19e-1779
splanchnic layer of lateral plate mesoderm4.47e-1784
cell layer8.98e-17312
epithelium1.20e-16309
systemic artery1.42e-1633
systemic arterial system1.42e-1633
dermomyotome3.08e-1670
somite4.06e-1683
paraxial mesoderm4.06e-1683
presomitic mesoderm4.06e-1683
presumptive segmental plate4.06e-1683
trunk paraxial mesoderm4.06e-1683
presumptive paraxial mesoderm4.06e-1683
anatomical system3.71e-15625
anatomical group5.74e-15626
germ layer4.88e-14604
embryonic tissue4.88e-14604
presumptive structure4.88e-14604
epiblast (generic)4.88e-14604
embryonic structure7.43e-14605
developing anatomical structure7.43e-14605
multi-cellular organism8.13e-14659
anatomical conduit2.48e-13241
circulatory system2.57e-13113
embryo3.07e-13612
muscle tissue7.12e-1363
musculature7.12e-1363
musculature of body7.12e-1363
skeletal muscle tissue1.12e-1261
striated muscle tissue1.12e-1261
myotome1.12e-1261
cardiovascular system1.78e-12110
anatomical cluster9.54e-11286
tube1.40e-10194
multi-tissue structure1.55e-10347
unilaminar epithelium4.84e-09138
aorta5.82e-0921
aortic system5.82e-0921
epithelial tube6.91e-09118
organism subdivision1.12e-08365
smooth muscle tissue3.04e-0815
blood vessel smooth muscle5.15e-0810
arterial system smooth muscle5.15e-0810
artery smooth muscle tissue5.15e-0810
aorta smooth muscle tissue5.15e-0810
mesoderm1.19e-07448
mesoderm-derived structure1.19e-07448
presumptive mesoderm1.19e-07448
trunk mesenchyme1.38e-07143
adult organism1.91e-07115
Disease
Ontology termp-valuen
ovarian cancer5.08e-0714


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
POLR2A#543062.147453176558070.01019570676818780.0380255479471045
STAT3#677435.259732498577120.01377662058078550.0484727445620948
TCF7L2#693435.385088281568670.01290488779931040.0464093377250155



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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