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Coexpression cluster:C4617: Difference between revisions

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|tf_chipseq_enrich=E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0327486509535758!MYC#4609;3:5.2222818716094:0.00702084375574015:0.0295891974095374!STAT3#6774;3:10.5194649971542:0.000858918453041531:0.00645356721706507!TFAP2C#7022;3:10.8092286098602:0.000791674657575313:0.00618643543303465!ZNF263#10127;3:8.22184163701068:0.00179904392556587:0.0110064055147428
|tf_chipseq_enrich=E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0327486509535758!MYC#4609;3:5.2222818716094:0.00702084375574015:0.0295891974095374!STAT3#6774;3:10.5194649971542:0.000858918453041531:0.00645356721706507!TFAP2C#7022;3:10.8092286098602:0.000791674657575313:0.00618643543303465!ZNF263#10127;3:8.22184163701068:0.00179904392556587:0.0110064055147428
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}}
}}

Revision as of 16:51, 26 November 2012


Full id: C4617_immature_malignant_squamous_oral_amniotic_Keratinocyte_epidermoid



Phase1 CAGE Peaks

Hg19::chr6:54711471..54711486,+p3@FAM83B
Hg19::chr6:54711509..54711522,+p2@FAM83B
Hg19::chr6:54711533..54711580,+p1@FAM83B


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 cell9.07e-32253
endo-epithelial cell4.90e-2542
endodermal cell3.08e-1858
epithelial cell of alimentary canal6.44e-1520
respiratory epithelial cell3.13e-1013
general ecto-epithelial cell4.51e-0814
Uber Anatomy
Ontology termp-valuen
endoderm-derived structure6.28e-25160
endoderm6.28e-25160
presumptive endoderm6.28e-25160
digestive system9.41e-20145
digestive tract9.41e-20145
primitive gut9.41e-20145
respiratory system1.21e-1774
subdivision of digestive tract2.49e-16118
respiratory tract8.76e-1554
segment of respiratory tract2.10e-1147
respiratory primordium4.51e-1138
endoderm of foregut4.51e-1138
foregut7.78e-1087
orifice2.64e-0936
epithelial bud1.27e-0737
upper respiratory tract1.34e-0719
endo-epithelium1.77e-0782
organ1.79e-07503
oral opening1.90e-0722
epithelial fold2.59e-0747
anatomical space2.96e-0795
extraembryonic membrane3.90e-0714
membranous layer3.90e-0714
mucosa5.97e-0720
organ part8.65e-07218
larynx9.90e-079
Disease
Ontology termp-valuen
carcinoma1.11e-25106
cell type cancer1.64e-17143
squamous cell carcinoma1.57e-1214
adenocarcinoma9.79e-1025


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)

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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
E2F1#186934.907389214879320.008460985347239390.0327486509535758
MYC#460935.22228187160940.007020843755740150.0295891974095374
STAT3#6774310.51946499715420.0008589184530415310.00645356721706507
TFAP2C#7022310.80922860986020.0007916746575753130.00618643543303465
ZNF263#1012738.221841637010680.001799043925565870.0110064055147428



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.