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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C3629_clear_serous_papillotubular_testicular_signet_breast_esophagus
|full_id=C3629_clear_serous_papillotubular_testicular_signet_breast_esophagus
|id=C3629
|id=C3629

Revision as of 16:35, 12 September 2012


Full id: C3629_clear_serous_papillotubular_testicular_signet_breast_esophagus



Phase1 CAGE Peaks

Hg19::chr17:37894179..37894202,+p3@GRB7
Hg19::chr17:37894206..37894222,+p2@GRB7
Hg19::chr17:37894570..37894614,+p1@GRB7


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>

Cell Type
Ontology termp-valuen
epithelial cell3.70e-37254
endodermal cell5.86e-1859
endo-epithelial cell1.20e-1543
epithelial cell of alimentary canal6.64e-0821
Uber Anatomy
Ontology termp-valuen
endoderm-derived structure1.41e-26169
endoderm1.41e-26169
presumptive endoderm1.41e-26169
digestive system4.89e-23155
digestive tract4.89e-23155
primitive gut4.89e-23155
subdivision of digestive tract1.22e-21129
endodermal part of digestive tract1.22e-21129
mixed endoderm/mesoderm-derived structure2.38e-20130
immaterial anatomical entity2.61e-18126
anatomical space4.33e-16104
foregut1.02e-1598
organ1.91e-15511
multi-tissue structure4.07e-14347
trunk region element1.30e-13107
primordium2.33e-12168
organ part6.45e-12219
respiratory system9.75e-1272
endo-epithelium1.35e-1182
anatomical cavity6.96e-1170
embryo3.62e-10612
renal system6.14e-1045
mesenchyme6.76e-10238
entire embryonic mesenchyme6.76e-10238
urinary system structure1.54e-0944
reproductive structure1.61e-0959
reproductive system1.61e-0959
respiratory tract1.77e-0953
subdivision of trunk1.98e-09113
multi-cellular organism2.27e-09659
body cavity precursor6.59e-0963
reproductive organ8.03e-0948
respiratory primordium2.33e-0838
endoderm of foregut2.33e-0838
embryonic structure4.11e-08605
developing anatomical structure4.11e-08605
epithelial bud5.94e-0837
gastrointestinal system6.61e-0835
germ layer6.73e-08604
embryonic tissue6.73e-08604
presumptive structure6.73e-08604
epiblast (generic)6.73e-08604
anatomical group8.61e-08626
anatomical system9.79e-08625
intestine1.25e-0727
abdomen element1.34e-0755
abdominal segment element1.34e-0755
organ segment1.42e-0797
internal genitalia2.25e-0725
organism subdivision2.56e-07365
orifice3.11e-0735
segment of respiratory tract4.54e-0746
duct5.73e-0726
adult organism6.67e-07115
female organism6.94e-0741
epithelial fold6.95e-0751
kidney9.75e-0727
kidney mesenchyme9.75e-0727
kidney rudiment9.75e-0727
kidney field9.75e-0727
Disease
Ontology termp-valuen
carcinoma2.57e-29106
cell type cancer1.45e-19143
adenocarcinoma1.79e-1025
squamous cell carcinoma9.70e-0814
cancer9.04e-07235


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
GATA3#2625327.2365163572064.94721007899563e-050.000850644836088615
HNF4A#3172215.42152690863580.005444210486686610.0246740105458715



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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