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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C2896_Mallassezderived_Mammary_Keratinocyte_mesodermal_Sebocyte_Gingival_Tracheal
|full_id=C2896_Mallassezderived_Mammary_Keratinocyte_mesodermal_Sebocyte_Gingival_Tracheal
|id=C2896
|id=C2896

Revision as of 15:41, 12 September 2012


Full id: C2896_Mallassezderived_Mammary_Keratinocyte_mesodermal_Sebocyte_Gingival_Tracheal



Phase1 CAGE Peaks

Hg19::chr7:40855224..40855239,+p@chr7:40855224..40855239
+
Hg19::chr7:40855246..40855275,+p@chr7:40855246..40855275
+
Hg19::chr7:40855279..40855286,+p@chr7:40855279..40855286
+
Hg19::chr7:40855299..40855321,+p@chr7:40855299..40855321
+


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
somite3.45e-2883
paraxial mesoderm3.45e-2883
presomitic mesoderm3.45e-2883
presumptive segmental plate3.45e-2883
trunk paraxial mesoderm3.45e-2883
presumptive paraxial mesoderm3.45e-2883
multilaminar epithelium3.44e-2682
dermomyotome4.30e-2270
surface structure1.44e-1895
trunk mesenchyme3.16e-18143
skeletal muscle tissue5.76e-1861
striated muscle tissue5.76e-1861
myotome5.76e-1861
muscle tissue1.01e-1663
musculature1.01e-1663
musculature of body1.01e-1663
artery8.50e-1442
arterial blood vessel8.50e-1442
arterial system8.50e-1442
trunk1.47e-13216
organism subdivision9.24e-13365
systemic artery2.24e-1133
systemic arterial system2.24e-1133
integument1.48e-1045
integumental system1.48e-1045
splanchnic layer of lateral plate mesoderm1.81e-1084
skin of body7.16e-1040
blood vessel9.54e-1060
epithelial tube open at both ends9.54e-1060
blood vasculature9.54e-1060
vascular cord9.54e-1060
vasculature1.43e-0979
vascular system1.43e-0979
mesenchyme2.53e-09238
entire embryonic mesenchyme2.53e-09238
vessel1.81e-0869
cell layer6.36e-08312
unilaminar epithelium6.81e-08138
epithelium1.37e-07309
blood vessel smooth muscle2.19e-0710
arterial system smooth muscle2.19e-0710
artery smooth muscle tissue2.19e-0710
aorta smooth muscle tissue2.19e-0710
subdivision of skeletal system2.75e-0713
skeleton2.75e-0713
sclerotome2.75e-0713
epithelial tube3.66e-07118
cardiovascular system9.53e-07110


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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