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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C2093_mesenchymal_mucinous_bile_Fibroblast_lung_Smooth_liposarcoma
|full_id=C2093_mesenchymal_mucinous_bile_Fibroblast_lung_Smooth_liposarcoma
|id=C2093
|id=C2093

Revision as of 14:46, 12 September 2012


Full id: C2093_mesenchymal_mucinous_bile_Fibroblast_lung_Smooth_liposarcoma



Phase1 CAGE Peaks

Hg19::chr11:108800197..108800208,+p6@DDX10
Hg19::chr11:108800225..108800254,+p4@DDX10
Hg19::chr11:108800264..108800294,+p3@DDX10
Hg19::chr11:108800302..108800338,+p2@DDX10


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
vasculature6.86e-1679
vascular system6.86e-1679
somite5.77e-1583
paraxial mesoderm5.77e-1583
presomitic mesoderm5.77e-1583
presumptive segmental plate5.77e-1583
trunk paraxial mesoderm5.77e-1583
presumptive paraxial mesoderm5.77e-1583
dermomyotome1.00e-1370
unilaminar epithelium4.76e-13138
artery6.36e-1342
arterial blood vessel6.36e-1342
arterial system6.36e-1342
systemic artery1.06e-1233
systemic arterial system1.06e-1233
trunk mesenchyme1.13e-12143
skeletal muscle tissue4.17e-1261
striated muscle tissue4.17e-1261
myotome4.17e-1261
blood vessel5.70e-1260
epithelial tube open at both ends5.70e-1260
blood vasculature5.70e-1260
vascular cord5.70e-1260
vessel6.90e-1269
multilaminar epithelium8.79e-1282
muscle tissue3.98e-1163
musculature3.98e-1163
musculature of body3.98e-1163
cardiovascular system8.24e-11110
splanchnic layer of lateral plate mesoderm2.62e-1084
epithelial tube3.55e-10118
circulatory system7.16e-10113
musculoskeletal system1.95e-09167
anatomical system2.70e-09625
anatomical group3.83e-09626
trunk5.67e-08216
multi-cellular organism7.02e-08659
surface structure1.03e-0795
aorta5.40e-0721
aortic system5.40e-0721
mesoderm5.69e-07448
mesoderm-derived structure5.69e-07448
presumptive mesoderm5.69e-07448
organism subdivision8.03e-07365


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
CEBPB#105147.971147625824820.0002476385788090830.00267485009124437
EP300#203346.77394172622320.0004748459821442640.00433500345534657
FOS#235348.99795530889440.0001525147711168630.00194558326379309
FOSL2#2355416.93020060456171.2165416097647e-050.000303087760453759
GATA2#2624412.7449317335543.78864877853583e-050.000719815699074957
JUN#3725412.51282919233634.07770316866756e-050.000741806725714111
JUND#372746.994663941871030.000417684217818580.00390987918120953
NR3C1#2908414.9730233311731.98868032687801e-050.000441905924805984
RAD21#5885410.35503389545638.6948481184721e-050.00129062143639157
STAT3#6774410.51946499715428.16377768286615e-050.00122873148497025
USF1#739134.771124457905970.01370465887188020.0482683326449362



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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