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Coexpression cluster:C2661: Difference between revisions

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|ontology_enrichment_disease=DOID:305!3.18e-08!106
|ontology_enrichment_disease=DOID:305!3.18e-08!106
|ontology_enrichment_uberon=UBERON:0000475!1.16e-11!365;UBERON:0004121!6.02e-11!169;UBERON:0003102!6.25e-11!95;UBERON:0000924!5.83e-10!173;UBERON:0006601!5.83e-10!173;UBERON:0000033!2.54e-09!123;UBERON:0000153!2.58e-09!129;UBERON:0007811!2.58e-09!129;UBERON:0002097!1.17e-08!40;UBERON:0000064!1.23e-08!219;UBERON:0001444!2.01e-08!48;UBERON:0004119!4.43e-08!169;UBERON:0000925!4.43e-08!169;UBERON:0006595!4.43e-08!169;UBERON:0005085!1.98e-07!29;UBERON:0007023!2.46e-07!115;UBERON:0000062!3.58e-07!511;UBERON:0001007!9.76e-07!155;UBERON:0001555!9.76e-07!155;UBERON:0007026!9.76e-07!155
|ontology_enrichment_uberon=UBERON:0000475!1.16e-11!365;UBERON:0004121!6.02e-11!169;UBERON:0003102!6.25e-11!95;UBERON:0000924!5.83e-10!173;UBERON:0006601!5.83e-10!173;UBERON:0000033!2.54e-09!123;UBERON:0000153!2.58e-09!129;UBERON:0007811!2.58e-09!129;UBERON:0002097!1.17e-08!40;UBERON:0000064!1.23e-08!219;UBERON:0001444!2.01e-08!48;UBERON:0004119!4.43e-08!169;UBERON:0000925!4.43e-08!169;UBERON:0006595!4.43e-08!169;UBERON:0005085!1.98e-07!29;UBERON:0007023!2.46e-07!115;UBERON:0000062!3.58e-07!511;UBERON:0001007!9.76e-07!155;UBERON:0001555!9.76e-07!155;UBERON:0007026!9.76e-07!155
|tf_chipseq_enrich=CTCF#10664;4:5.36025637307503:0.00121114538164362:0.00818287052099096!RAD21#5885;4:10.3550338954563:8.6948481184721e-05:0.00129596295510933!ZEB1#6935;4:16.8884320175439:1.22862303393937e-05:0.000304644256983841
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}}
}}

Revision as of 13:59, 5 September 2012


Full id: C2661_amniotic_endometrioid_squamous_Olfactory_rectal_stomach_bronchogenic



Phase1 CAGE Peaks

Hg19::chr2:149895207..149895230,+p1@LYPD6B
Hg19::chr2:149895239..149895245,+p8@LYPD6B
Hg19::chr2:149895246..149895261,+p2@LYPD6B
Hg19::chr2:149895265..149895271,+p7@LYPD6B


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 cell9.12e-12254
endo-epithelial cell2.55e-0843
ecto-epithelial cell3.18e-0833
Uber Anatomy
Ontology termp-valuen
organism subdivision1.16e-11365
ectoderm-derived structure6.02e-11169
surface structure6.25e-1195
ectoderm5.83e-10173
presumptive ectoderm5.83e-10173
head2.54e-09123
anterior region of body2.58e-09129
craniocervical region2.58e-09129
skin of body1.17e-0840
organ part1.23e-08219
subdivision of head2.01e-0848
endoderm-derived structure4.43e-08169
endoderm4.43e-08169
presumptive endoderm4.43e-08169
ectodermal placode1.98e-0729
adult organism2.46e-07115
organ3.58e-07511
digestive system9.76e-07155
digestive tract9.76e-07155
primitive gut9.76e-07155
Disease
Ontology termp-valuen
carcinoma3.18e-08106


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
CTCF#1066445.360256373075030.001211145381643620.00818287052099096
RAD21#5885410.35503389545638.6948481184721e-050.00129596295510933
ZEB1#6935416.88843201754391.22862303393937e-050.000304644256983841



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.

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=Coexpression_cluster:C2661&oldid=2132842"