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Coexpression cluster:C2898

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Full id: C2898_oral_giant_large_epidermoid_squamous_embryonic_renal



Phase1 CAGE Peaks

Hg19::chr7:55053219..55053226,+p@chr7:55053219..55053226
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Hg19::chr7:55053266..55053282,+p@chr7:55053266..55053282
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Hg19::chr7:55053327..55053342,+p@chr7:55053327..55053342
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Hg19::chr7:55053540..55053550,+p@chr7:55053540..55053550
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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 cell3.54e-13254
endo-epithelial cell2.17e-0943
endodermal cell7.31e-0859
Uber Anatomy
Ontology termp-valuen
endoderm-derived structure6.66e-11169
endoderm6.66e-11169
presumptive endoderm6.66e-11169
mucosa of oral region7.14e-114
respiratory system mucosa7.14e-114
mouth mucosa1.11e-085
digestive system1.35e-08155
digestive tract1.35e-08155
primitive gut1.35e-08155
respiratory system1.39e-0772
mucosa3.41e-0712
respiratory tract6.32e-0753
mixed endoderm/mesoderm-derived structure7.06e-07130
Disease
Ontology termp-valuen
squamous cell carcinoma3.48e-2114
carcinoma2.34e-18106
cell type cancer3.24e-16143
disease of cellular proliferation8.69e-11239
cancer1.51e-10235
disease of anatomical entity9.87e-0739


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
CEBPB#105147.971147625824820.0002476385788090830.00268707797737577
EP300#203346.77394172622320.0004748459821442640.0043544156228962
FOS#235348.99795530889440.0001525147711168630.00195489570209549
FOSL2#2355416.93020060456171.2165416097647e-050.000304394799190742
FOXA1#3169411.08141974938556.62943068949433e-050.00107361003532346
GATA2#2624412.7449317335543.78864877853583e-050.000724693571028395
JUN#3725412.51282919233634.07770316866756e-050.000745181524466266
JUND#372746.994663941871030.000417684217818580.00392641962419034
RAD21#5885410.35503389545638.6948481184721e-050.00129967259574225
STAT3#6774410.51946499715428.16377768286615e-050.00123531842570394
TBP#690843.706770687096390.005296377814784350.0245070401222038
TFAP2C#7022410.80922860986027.32289634782688e-050.00114903240936102



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.