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Coexpression cluster:C4141: Difference between revisions

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|ontology_enrichment_disease=DOID:305!1.51e-13!106;DOID:1749!2.75e-08!14;DOID:0050687!2.28e-07!143
|ontology_enrichment_disease=DOID:305!1.51e-13!106;DOID:1749!2.75e-08!14;DOID:0050687!2.28e-07!143
|ontology_enrichment_uberon=UBERON:0004119!3.81e-18!169;UBERON:0000925!3.81e-18!169;UBERON:0006595!3.81e-18!169;UBERON:0001007!5.44e-15!155;UBERON:0001555!5.44e-15!155;UBERON:0007026!5.44e-15!155;UBERON:0001004!3.60e-13!72;UBERON:0004921!3.34e-10!129;UBERON:0004185!3.34e-10!129;UBERON:0000077!6.69e-10!130;UBERON:0000065!2.01e-09!53;UBERON:0000064!3.24e-08!219;UBERON:0000161!6.41e-08!35;UBERON:0000062!2.03e-07!511;UBERON:0008947!2.34e-07!38;UBERON:0003258!2.34e-07!38;UBERON:0007023!5.12e-07!115;UBERON:0000166!6.91e-07!21;UBERON:0000165!8.00e-07!28;UBERON:0000930!8.00e-07!28;UBERON:0000072!9.70e-07!46
|ontology_enrichment_uberon=UBERON:0004119!3.81e-18!169;UBERON:0000925!3.81e-18!169;UBERON:0006595!3.81e-18!169;UBERON:0001007!5.44e-15!155;UBERON:0001555!5.44e-15!155;UBERON:0007026!5.44e-15!155;UBERON:0001004!3.60e-13!72;UBERON:0004921!3.34e-10!129;UBERON:0004185!3.34e-10!129;UBERON:0000077!6.69e-10!130;UBERON:0000065!2.01e-09!53;UBERON:0000064!3.24e-08!219;UBERON:0000161!6.41e-08!35;UBERON:0000062!2.03e-07!511;UBERON:0008947!2.34e-07!38;UBERON:0003258!2.34e-07!38;UBERON:0007023!5.12e-07!115;UBERON:0000166!6.91e-07!21;UBERON:0000165!8.00e-07!28;UBERON:0000930!8.00e-07!28;UBERON:0000072!9.70e-07!46
|tf_chipseq_enrich=CTCF#10664;3:5.36025637307503:0.006492509252767:0.0280090534036818!E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0326144847080658!NRF1#4899;3:12.2102794477109:0.000549217240102001:0.00471863271956342!ZEB1#6935;3:16.8884320175439:0.000207548691732758:0.00243115498159236!ZNF263#10127;3:8.22184163701068:0.00179904392556587:0.01096273694744
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}}
}}

Revision as of 12:57, 5 September 2012


Full id: C4141_Mallassezderived_Urothelial_papillotubular_large_Prostate_serous_Keratinocyte



Phase1 CAGE Peaks

Hg19::chr2:166650594..166650630,-p5@GALNT3
Hg19::chr2:166650634..166650663,-p3@GALNT3
Hg19::chr2:166650700..166650816,-p1@GALNT3


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 cell2.54e-14254
endo-epithelial cell1.77e-1243
endodermal cell1.39e-0759
epithelial cell of alimentary canal2.05e-0721
Uber Anatomy
Ontology termp-valuen
endoderm-derived structure3.81e-18169
endoderm3.81e-18169
presumptive endoderm3.81e-18169
digestive system5.44e-15155
digestive tract5.44e-15155
primitive gut5.44e-15155
respiratory system3.60e-1372
subdivision of digestive tract3.34e-10129
endodermal part of digestive tract3.34e-10129
mixed endoderm/mesoderm-derived structure6.69e-10130
respiratory tract2.01e-0953
organ part3.24e-08219
orifice6.41e-0835
organ2.03e-07511
respiratory primordium2.34e-0738
endoderm of foregut2.34e-0738
adult organism5.12e-07115
oral opening6.91e-0721
mouth8.00e-0728
stomodeum8.00e-0728
segment of respiratory tract9.70e-0746
Disease
Ontology termp-valuen
carcinoma1.51e-13106
squamous cell carcinoma2.75e-0814
cell type cancer2.28e-07143


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#1066435.360256373075030.0064925092527670.0280090534036818
E2F1#186934.907389214879320.008460985347239390.0326144847080658
NRF1#4899312.21027944771090.0005492172401020010.00471863271956342
ZEB1#6935316.88843201754390.0002075486917327580.00243115498159236
ZNF263#1012738.221841637010680.001799043925565870.01096273694744



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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