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Coexpression cluster:C4317

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Full id: C4317_renal_squamous_bile_glassy_epidermoid_epithelioid_malignant



Phase1 CAGE Peaks

  Short description
Hg19::chr3:194040528..194040540,- p@chr3:194040528..194040540
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Hg19::chr3:194040578..194040593,- p@chr3:194040578..194040593
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Hg19::chr3:194040598..194040638,- p@chr3:194040598..194040638
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Enriched pathways on this co-expression clusterSummary:
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.
Analyst: Emmanuel Dimont

link to source dataset
data


No results for this coexpression

Enriched Gene Ontology terms on this co-expression clusterSummary: 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.
Analyst: Erik Arner

link to source dataset
data


No GOStat results

Enriched sample ontology terms on this co-expression clusterSummary: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. Analyst: Hideya Kawaji

links to source dataset

cell_data
uberon_data
disease_data


Cell Type
Ontology termp-valuen
epithelial cell5.07e-39253
endo-epithelial cell9.93e-1542
endodermal cell3.07e-1458
epithelial cell of alimentary canal2.26e-1120
squamous epithelial cell8.08e-0963
Uber Anatomy
Ontology termp-valuen
endoderm-derived structure6.18e-18160
endoderm6.18e-18160
presumptive endoderm6.18e-18160
digestive system1.11e-16145
digestive tract1.11e-16145
primitive gut1.11e-16145
larynx1.98e-149
subdivision of digestive tract3.71e-14118
foregut1.62e-1387
upper respiratory tract7.23e-1219
respiratory system1.16e-1074
segment of respiratory tract1.43e-1047
respiratory tract2.70e-1054
respiratory primordium2.96e-0938
endoderm of foregut2.96e-0938
biliary system1.42e-089
biliary tree1.42e-089
biliary bud1.42e-089
orifice2.36e-0736
viscus8.18e-0718
Disease
Ontology termp-valuen
carcinoma3.28e-50106
cell type cancer5.02e-37143
cancer3.06e-25235
disease of cellular proliferation3.26e-24239
adenocarcinoma1.75e-1725
squamous cell carcinoma6.35e-1614


Overrepresented TFBS (DNA) motifs on this co-expression clusterSummary: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. Analyst: Michiel de Hoon

link to source data
Novel motifs
data

Jaspar motifs
data


Novel motifs



JASPAR motifs

Motifs-log10(p-value)

{{{tfbs_overrepresentation_jaspar}}}



ENCODE TF ChIP-seq peak enrichment analysisSummary: 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.
Analyst: Erik Arner

link to source dataset

data


(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
CEBPB#105137.971147625824820.001974187055288560.0115547030860391
E2F1#186934.907389214879320.008460985347239390.03266632836791
EP300#203336.77394172622320.003216880500103790.0167967094565713
ESR1#2099330.76860329615453.43136389821584e-050.000678470681873843
FOS#235338.99795530889440.001372499272417130.00899996556237663
FOSL1#8061339.7135797163731.59554825631833e-050.000371875617812163
FOSL2#2355316.93020060456170.0002060162053171620.00243615562354156
GATA1#2623313.56030814380040.0004009615963782630.00388784961137772
GTF2F1#2962312.73966087675770.0004835525047438590.00435059786724189
JUN#3725312.51282919233630.0005103313992726250.00445378967231835
JUND#372736.994663941871030.002921845042734990.0157223233766912
MAX#414936.452555509007120.003721913834265510.018709711154065
MXI1#460139.96157162875930.001011470541259020.00721859859632028
MYC#460935.22228187160940.007020843755740150.0295427035054692
NR3C1#2908314.9730233311730.0002978331194675480.00309598817199873
SMARCC1#6599343.66335931963151.20046018043203e-050.000302108098275038
SMC3#9126315.04493284493280.0002935825420371870.00310024945478481
STAT3#6774310.51946499715420.0008589184530415310.0064438319314133
TFAP2A#7020316.5186343730450.0002218033880766340.0024895135999286
TFAP2C#7022310.80922860986020.0007916746575753130.00617534614702428
TRIM28#10155318.59052504526250.0001555969297255280.00197597127232543



Relative expression of the co-expression clusterSummary:Co-expression clusters are compared against FANTOM5 samples to obtain relative expression.
Analyst:NA

link to data source
data


This analysis result is provided for C0 - C305 clusters.