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Coexpression cluster:C2569: Difference between revisions

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|ontology_enrichment_disease=DOID:3095!7.16e-09!22;DOID:2994!7.16e-09!22;DOID:5093!8.71e-07!4;DOID:1612!8.71e-07!4
|ontology_enrichment_disease=DOID:3095!7.16e-09!22;DOID:2994!7.16e-09!22;DOID:5093!8.71e-07!4;DOID:1612!8.71e-07!4
|ontology_enrichment_uberon=UBERON:0003101!1.14e-10!22;UBERON:0000079!1.14e-10!22;UBERON:0000473!7.60e-10!8;UBERON:0003135!2.56e-09!11;UBERON:0002020!4.76e-08!34;UBERON:0003528!4.76e-08!34;UBERON:0007023!1.57e-07!115
|ontology_enrichment_uberon=UBERON:0003101!1.14e-10!22;UBERON:0000079!1.14e-10!22;UBERON:0000473!7.60e-10!8;UBERON:0003135!2.56e-09!11;UBERON:0002020!4.76e-08!34;UBERON:0003528!4.76e-08!34;UBERON:0007023!1.57e-07!115
|tf_chipseq_enrich=JUND#3727;3:5.24599795640327:0.0104343275174842:0.0386971603138572!MAX#4149;3:4.83941663175534:0.0131573713783684:0.046628527634388!SP1#6667;4:5.6983813781409:0.000948260606533398:0.00684655302355628!TBP#6908;4:3.70677068709639:0.00529637781478435:0.0244442265499254!USF1#7391;3:4.77112445790597:0.0137046588718802:0.048310691866213!USF2#7392;3:9.7441480388022:0.00171834184841007:0.0107224654541495
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}}
}}

Revision as of 12:01, 5 September 2012


Full id: C2569_small_MCF7_iPS_H9_hepatoblastoma_merkel_HES3GFP



Phase1 CAGE Peaks

Hg19::chr1:223203728..223203733,-p@chr1:223203728..223203733
-
Hg19::chr5:128795329..128795337,+p@chr5:128795329..128795337
+
Hg19::chr5:128795341..128795348,+p@chr5:128795341..128795348
+
Hg19::chr5:128795366..128795383,+p@chr5:128795366..128795383
+


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
embryonic stem cell5.07e-145
germ line cell4.12e-117
germ cell4.12e-117
Uber Anatomy
Ontology termp-valuen
male organism1.14e-1022
male reproductive system1.14e-1022
testis7.60e-108
male reproductive organ2.56e-0911
gray matter4.76e-0834
brain grey matter4.76e-0834
adult organism1.57e-07115
Disease
Ontology termp-valuen
germ cell and embryonal cancer7.16e-0922
germ cell cancer7.16e-0922
thoracic cancer8.71e-074
breast cancer8.71e-074


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
JUND#372735.245997956403270.01043432751748420.0386971603138572
MAX#414934.839416631755340.01315737137836840.046628527634388
SP1#666745.69838137814090.0009482606065333980.00684655302355628
TBP#690843.706770687096390.005296377814784350.0244442265499254
USF1#739134.771124457905970.01370465887188020.048310691866213
USF2#739239.74414803880220.001718341848410070.0107224654541495



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:C2569&oldid=2130821"