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Coexpression cluster:C3553: Difference between revisions

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|tf_chipseq_enrich=ESR1#2099;3:30.7686032961545:3.43136389821584e-05:0.000675274569748943!MYC#4609;3:5.2222818716094:0.00702084375574015:0.0294029152700997!ZNF263#10127;3:8.22184163701068:0.00179904392556587:0.0109232224023123
|tf_chipseq_enrich=ESR1#2099;3:30.7686032961545:3.43136389821584e-05:0.000675274569748943!MYC#4609;3:5.2222818716094:0.00702084375574015:0.0294029152700997!ZNF263#10127;3:8.22184163701068:0.00179904392556587:0.0109232224023123
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}}
}}

Revision as of 16:12, 26 November 2012


Full id: C3553_serous_pharyngeal_Intestinal_Prostate_papillotubular_rectal_Alveolar



Phase1 CAGE Peaks

Hg19::chr16:2907894..2907914,-p4@PRSS22
Hg19::chr16:2907916..2907972,-p2@PRSS22
Hg19::chr16:2908163..2908178,-p1@PRSS22


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 cell1.85e-20253
endo-epithelial cell2.90e-1942
endodermal cell2.22e-1358
epithelial cell of alimentary canal8.20e-1020
germ line cell8.29e-087
germ cell8.29e-087
respiratory epithelial cell1.53e-0713
Uber Anatomy
Ontology termp-valuen
endoderm-derived structure4.72e-18160
endoderm4.72e-18160
presumptive endoderm4.72e-18160
digestive system2.80e-14145
digestive tract2.80e-14145
primitive gut2.80e-14145
anatomical space4.00e-1395
epithelial bud5.20e-1237
respiratory system1.51e-1174
subdivision of digestive tract2.15e-11118
orifice2.99e-1136
endo-epithelium3.90e-1182
immaterial anatomical entity2.61e-10117
reproductive structure2.77e-1059
reproductive system2.77e-1059
renal system9.08e-1048
epithelial fold1.26e-0947
urinary system structure3.41e-0947
thoracic cavity element1.21e-0834
thoracic cavity1.21e-0834
reproductive organ2.71e-0848
thoracic segment organ3.11e-0835
respiratory tract4.26e-0854
mucosa1.02e-0720
lung1.12e-0722
respiratory tube1.12e-0722
respiration organ1.12e-0722
pair of lungs1.12e-0722
lung primordium1.12e-0722
lung bud1.12e-0722
trunk region element2.74e-07101
oral opening2.77e-0722
male organism3.95e-0722
male reproductive system3.95e-0722
female organism6.45e-0741
Disease
Ontology termp-valuen
carcinoma1.08e-17106
squamous cell carcinoma9.68e-1314
cell type cancer1.20e-11143
adenocarcinoma3.93e-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
ESR1#2099330.76860329615453.43136389821584e-050.000675274569748943
MYC#460935.22228187160940.007020843755740150.0294029152700997
ZNF263#1012738.221841637010680.001799043925565870.0109232224023123



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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