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Coexpression cluster:C4078: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C4078_Mast_Endothelial_Lymphatic_Melanocyte_melanoma_Hep2_Hepatic
|full_id=C4078_Mast_Endothelial_Lymphatic_Melanocyte_melanoma_Hep2_Hepatic
|id=C4078
|id=C4078

Revision as of 17:07, 12 September 2012


Full id: C4078_Mast_Endothelial_Lymphatic_Melanocyte_melanoma_Hep2_Hepatic



Phase1 CAGE Peaks

Hg19::chr21:42540033..42540062,+p2@BACE2
Hg19::chr21:42540070..42540107,+p1@BACE2
Hg19::chr21:42540108..42540124,+p3@BACE2


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
vasculature1.08e-1779
vascular system1.08e-1779
vessel1.55e-1769
splanchnic layer of lateral plate mesoderm8.43e-1684
epithelial tube1.14e-15118
blood vessel2.02e-1560
epithelial tube open at both ends2.02e-1560
blood vasculature2.02e-1560
vascular cord2.02e-1560
anatomical cluster9.31e-14286
cardiovascular system4.98e-13110
circulatory system1.36e-12113
cell layer1.77e-12312
epithelium1.85e-12309
anatomical conduit1.67e-10241
artery1.88e-1042
arterial blood vessel1.88e-1042
arterial system1.88e-1042
endothelium3.41e-1018
blood vessel endothelium3.41e-1018
cardiovascular system endothelium3.41e-1018
mesenchyme4.69e-10238
entire embryonic mesenchyme4.69e-10238
multi-tissue structure1.32e-09347
systemic artery1.53e-0933
systemic arterial system1.53e-0933
multi-cellular organism3.90e-09659
primordium1.00e-08168
compound organ1.10e-0869
simple squamous epithelium2.16e-0822
unilaminar epithelium3.50e-08138
squamous epithelium5.22e-0825
trunk8.01e-08216
organ segment1.46e-0797
anatomical system2.21e-07625
larynx2.60e-079
anatomical group3.80e-07626
organ part4.26e-07219
tube4.70e-07194
organism subdivision9.58e-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#105137.971147625824820.001974187055288560.0115398288390486
CTCF#1066435.360256373075030.0064925092527670.0279974884945594
CTCFL#140690319.74647435897440.0001298372005551160.00172016584914066
E2F1#186934.907389214879320.008460985347239390.0325964384034946
GATA3#2625327.2365163572064.94721007899563e-050.000852469350668577
ZBTB7A#5134137.35190930787590.002516255860282270.0140479631042936
ZNF263#1012738.221841637010680.001799043925565870.0109601789968019



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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