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Coexpression cluster:C2376: Difference between revisions

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|tf_chipseq_enrich=ESR1#2099;3:23.0764524721159:0.000133910524496857:0.0017576324328173!HNF4A#3172;3:17.3492177722153:0.000312564155748275:0.00321487963976699!HNF4G#3174;3:21.5650668948351:0.000163803242129261:0.00203611602055913!ZBTB7A#51341;3:5.51393198090692:0.00903835282108109:0.0342348141399517
|tf_chipseq_enrich=ESR1#2099;3:23.0764524721159:0.000133910524496857:0.0017576324328173!HNF4A#3172;3:17.3492177722153:0.000312564155748275:0.00321487963976699!HNF4G#3174;3:21.5650668948351:0.000163803242129261:0.00203611602055913!ZBTB7A#51341;3:5.51393198090692:0.00903835282108109:0.0342348141399517
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}}
}}

Revision as of 15:27, 26 November 2012


Full id: C2376_esophagus_amniotic_throat_tonsil_tongue_salivary_endometrioid



Phase1 CAGE Peaks

Hg19::chr16:4940321..4940338,-p@chr16:4940321..4940338
-
Hg19::chr16:4987129..4987156,-p1@PPL
Hg19::chr16:4987174..4987185,-p3@PPL
Hg19::chr16:4987202..4987221,-p2@PPL


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 cell2.08e-23253
endo-epithelial cell2.14e-1642
endodermal cell7.73e-1458
epithelial cell of alimentary canal2.96e-0920
Uber Anatomy
Ontology termp-valuen
endoderm-derived structure2.59e-19160
endoderm2.59e-19160
presumptive endoderm2.59e-19160
digestive system2.51e-17145
digestive tract2.51e-17145
primitive gut2.51e-17145
respiratory system1.17e-1674
organ part2.21e-15218
organ4.27e-15503
subdivision of digestive tract4.39e-14118
multi-tissue structure3.05e-13342
respiratory tract1.61e-1154
multi-cellular organism4.85e-11656
anatomical space5.91e-1195
foregut9.64e-1187
organ system subdivision2.40e-10223
immaterial anatomical entity3.24e-10117
thoracic segment organ3.51e-1035
thoracic cavity element6.66e-1034
thoracic cavity6.66e-1034
adult organism1.14e-09114
segment of respiratory tract4.18e-0947
trunk region element7.99e-09101
anatomical system1.33e-08624
primordium1.41e-08160
respiratory primordium1.62e-0838
endoderm of foregut1.62e-0838
anatomical group1.85e-08625
epithelial fold2.28e-0847
orifice2.66e-0836
oral opening3.89e-0822
anatomical cluster5.14e-08373
endo-epithelium6.12e-0882
organ segment8.09e-0898
embryo1.27e-07592
epithelial bud1.34e-0737
organism subdivision1.45e-07264
thoracic segment of trunk5.95e-0752
tracheobronchial tree9.24e-0715
lower respiratory tract9.24e-0715
Disease
Ontology termp-valuen
carcinoma3.59e-18106
cell type cancer9.62e-11143
adenocarcinoma9.65e-0825
squamous cell carcinoma9.29e-0714


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
ESR1#2099323.07645247211590.0001339105244968570.0017576324328173
HNF4A#3172317.34921777221530.0003125641557482750.00321487963976699
HNF4G#3174321.56506689483510.0001638032421292610.00203611602055913
ZBTB7A#5134135.513931980906920.009038352821081090.0342348141399517



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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