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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C3730_colon_stomach_pancreas_salivary_parotid_rectum_small
|full_id=C3730_colon_stomach_pancreas_salivary_parotid_rectum_small
|id=C3730
|id=C3730

Revision as of 16:42, 12 September 2012


Full id: C3730_colon_stomach_pancreas_salivary_parotid_rectum_small



Phase1 CAGE Peaks

Hg19::chr18:55470320..55470331,-p6@ATP8B1
Hg19::chr18:55470341..55470410,-p2@ATP8B1
Hg19::chr18:55470413..55470441,-p3@ATP8B1


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>

Cell Type
Ontology termp-valuen
epithelial cell6.97e-16254
endo-epithelial cell1.68e-0843
endodermal cell5.55e-0859
squamous epithelial cell2.40e-0762
Uber Anatomy
Ontology termp-valuen
endoderm-derived structure1.31e-19169
endoderm1.31e-19169
presumptive endoderm1.31e-19169
multi-cellular organism5.62e-19659
digestive system5.78e-16155
digestive tract5.78e-16155
primitive gut5.78e-16155
anatomical system1.80e-14625
anatomical group2.27e-14626
organism subdivision1.29e-13365
anatomical conduit1.64e-13241
multi-tissue structure4.80e-13347
anatomical cluster2.01e-12286
trunk4.63e-12216
mesenchyme1.03e-11238
entire embryonic mesenchyme1.03e-11238
surface structure3.16e-1195
orifice1.32e-1035
mixed endoderm/mesoderm-derived structure3.35e-10130
epithelium3.39e-10309
subdivision of digestive tract4.40e-10129
endodermal part of digestive tract4.40e-10129
cell layer6.31e-10312
embryo3.20e-09612
immaterial anatomical entity5.58e-09126
embryonic structure6.56e-09605
developing anatomical structure6.56e-09605
anatomical space1.10e-08104
germ layer1.25e-08604
embryonic tissue1.25e-08604
presumptive structure1.25e-08604
epiblast (generic)1.25e-08604
endo-epithelium1.47e-0882
organ component layer1.84e-0857
epithelial tube1.95e-08118
organ2.86e-08511
mouth4.67e-0828
stomodeum4.67e-0828
organ part6.21e-08219
trunk mesenchyme6.79e-08143
reproductive structure1.40e-0759
reproductive system1.40e-0759
respiratory system1.40e-0772
oral opening1.74e-0721
thoracic segment of trunk1.79e-0752
unilaminar epithelium1.83e-07138
subdivision of trunk5.75e-07113
splanchnic layer of lateral plate mesoderm8.19e-0784


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
E2F1#186934.907389214879320.008460985347239390.0325148783412567
EP300#203336.77394172622320.003216880500103790.0167406339404225
FOXA1#3169311.08141974938550.000734755275698670.00581077587753243
MYC#460935.22228187160940.007020843755740150.0294336023203976
NR3C1#2908314.9730233311730.0002978331194675480.00308830353098404
SUZ12#23512350.11578091106297.93834897779404e-060.000222212068853345



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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