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Coexpression cluster:C4568: Difference between revisions

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|tf_chipseq_enrich=CTCF#10664;3:5.36025637307503:0.006492509252767:0.0281065771543931!FOXA1#3169;3:11.0814197493855:0.00073475527569867:0.00583640905374911!HNF4A#3172;2:15.4215269086358:0.00544421048668661:0.0246890099443796
|tf_chipseq_enrich=CTCF#10664;3:5.36025637307503:0.006492509252767:0.0281065771543931!FOXA1#3169;3:11.0814197493855:0.00073475527569867:0.00583640905374911!HNF4A#3172;2:15.4215269086358:0.00544421048668661:0.0246890099443796
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}}
}}

Revision as of 16:49, 26 November 2012


Full id: C4568_liposarcoma_lung_Endothelial_mesothelioma_placenta_hepatocellular_adrenal



Phase1 CAGE Peaks

Hg19::chr6:142622791..142622804,+p6@GPR126
Hg19::chr6:142623063..142623261,+p1@GPR126
Hg19::chr6:142623429..142623443,+p16@GPR126


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><br>

Cell Type
Ontology termp-valuen
epithelial cell2.33e-18253
lining cell4.71e-1358
barrier cell4.71e-1358
mesothelial cell7.45e-1219
embryonic cell1.05e-07250
squamous epithelial cell1.09e-0763
vein endothelial cell6.28e-076
Uber Anatomy
Ontology termp-valuen
anatomical cluster3.82e-14373
endoderm-derived structure4.11e-14160
endoderm4.11e-14160
presumptive endoderm4.11e-14160
subdivision of digestive tract6.67e-14118
digestive system1.45e-12145
digestive tract1.45e-12145
primitive gut1.45e-12145
abdomen element2.60e-1254
abdominal segment element2.60e-1254
trunk region element5.89e-12101
endo-epithelium1.22e-1082
multi-tissue structure2.22e-10342
abdominal segment of trunk7.83e-1060
abdomen7.83e-1060
gastrointestinal system1.46e-0925
subdivision of trunk1.86e-09112
gut epithelium3.49e-0954
organism subdivision3.84e-09264
cortex6.85e-0915
epithelium1.15e-08306
cell layer2.73e-08309
intestine5.32e-0817
intermediate mesoderm7.91e-0828
organ system subdivision8.39e-08223
vein8.78e-089
venous blood vessel8.78e-089
venous system8.78e-089
multi-cellular organism1.30e-07656
foregut2.65e-0787
urinary system structure4.21e-0747
excretory tube4.68e-0716
kidney epithelium4.68e-0716
organ part4.99e-07218
trunk5.89e-07199
sac6.27e-0726
cavitated compound organ6.58e-0731
endocrine gland6.79e-0735
parenchyma8.20e-0715
renal system8.84e-0748
epithelial tube9.69e-07117
mesenchyme9.93e-07160
entire embryonic mesenchyme9.93e-07160


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
CTCF#1066435.360256373075030.0064925092527670.0281065771543931
FOXA1#3169311.08141974938550.000734755275698670.00583640905374911
HNF4A#3172215.42152690863580.005444210486686610.0246890099443796



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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