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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C3008_choriocarcinoma_Small_testicular_Amniotic_oral_pancreatic_medulloblastoma
|full_id=C3008_choriocarcinoma_Small_testicular_Amniotic_oral_pancreatic_medulloblastoma
|id=C3008
|id=C3008

Revision as of 15:51, 12 September 2012


Full id: C3008_choriocarcinoma_Small_testicular_Amniotic_oral_pancreatic_medulloblastoma



Phase1 CAGE Peaks

Hg19::chr10:24544249..24544276,+p3@KIAA1217
Hg19::chr10:24544284..24544304,+p6@KIAA1217
Hg19::chr10:24544308..24544313,+p18@KIAA1217


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 cell2.05e-25254
endo-epithelial cell1.65e-1643
endodermal cell6.30e-1159
epithelial cell of alimentary canal7.40e-1021
respiratory epithelial cell6.91e-0913
germ line cell4.04e-087
germ cell4.04e-087
ecto-epithelial cell4.55e-0833
Uber Anatomy
Ontology termp-valuen
anatomical space1.94e-14104
respiratory system7.62e-1172
immaterial anatomical entity6.56e-10126
endoderm-derived structure9.67e-10169
endoderm9.67e-10169
presumptive endoderm9.67e-10169
anatomical cavity5.42e-0970
oral opening1.12e-0821
extraembryonic membrane1.46e-0814
membranous layer1.46e-0814
orifice4.51e-0835
subdivision of head1.42e-0748
reproductive organ5.15e-0748
chorion6.47e-077
Disease
Ontology termp-valuen
squamous cell carcinoma5.77e-1014


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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