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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C1586_choriocarcinoma_serous_maxillary_colon_small_Prostate_H9
|full_id=C1586_choriocarcinoma_serous_maxillary_colon_small_Prostate_H9
|id=C1586
|id=C1586

Revision as of 14:10, 12 September 2012


Full id: C1586_choriocarcinoma_serous_maxillary_colon_small_Prostate_H9



Phase1 CAGE Peaks

Hg19::chr10:54783268..54783282,-p@chr10:54783268..54783282
-
Hg19::chr4:53617723..53617731,-p5@ERVMER34-1
Hg19::chr4:53617739..53617760,-p4@ERVMER34-1
Hg19::chr4:53617761..53617784,-p1@uc003gzr.2
p1@uc003gzs.2
Hg19::chr4:53617798..53617813,-p2@ERVMER34-1


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 cell2.69e-24254
endo-epithelial cell3.00e-1443
endodermal cell6.82e-1059
epithelial cell of alimentary canal8.15e-0821
general ecto-epithelial cell1.87e-0713
Uber Anatomy
Ontology termp-valuen
organ part1.48e-15219
organ5.72e-13511
endoderm-derived structure9.08e-13169
endoderm9.08e-13169
presumptive endoderm9.08e-13169
ectoderm-derived structure3.43e-11169
ectoderm1.04e-10173
presumptive ectoderm1.04e-10173
multi-tissue structure1.71e-10347
adult organism2.46e-10115
embryo2.96e-10612
cell layer6.40e-10312
epithelium7.29e-10309
anterior region of body1.94e-09129
craniocervical region1.94e-09129
anatomical space2.82e-09104
head2.85e-09123
digestive system3.95e-09155
digestive tract3.95e-09155
primitive gut3.95e-09155
multi-cellular organism1.51e-08659
renal system1.54e-0845
embryonic structure2.33e-08605
developing anatomical structure2.33e-08605
organism subdivision2.51e-08365
subdivision of digestive tract2.58e-08129
endodermal part of digestive tract2.58e-08129
urinary system structure3.94e-0844
germ layer3.96e-08604
embryonic tissue3.96e-08604
presumptive structure3.96e-08604
epiblast (generic)3.96e-08604
epithelial bud5.21e-0837
neural plate9.55e-0886
presumptive neural plate9.55e-0886
pre-chordal neural plate1.08e-0761
immaterial anatomical entity1.11e-07126
anatomical system1.26e-07625
anatomical group1.64e-07626
epithelial fold1.81e-0751
neurectoderm3.58e-0790
endo-epithelium4.97e-0782
orifice7.12e-0735
reproductive structure8.89e-0759
reproductive system8.89e-0759
Disease
Ontology termp-valuen
carcinoma4.47e-12106
cell type cancer7.09e-10143
squamous cell carcinoma7.92e-0814


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
MAX#414945.16204440720570.002526309009485180.0139948648300866
MYC#460944.177825497287520.005691969036823440.0256665754603343



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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