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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C2097_amniotic_Urothelial_esophagus_trachea_Sebocyte_Small_Prostate
|full_id=C2097_amniotic_Urothelial_esophagus_trachea_Sebocyte_Small_Prostate
|id=C2097
|id=C2097

Revision as of 14:46, 12 September 2012


Full id: C2097_amniotic_Urothelial_esophagus_trachea_Sebocyte_Small_Prostate



Phase1 CAGE Peaks

Hg19::chr11:118134950..118134961,-p6@MPZL2
Hg19::chr11:118134962..118134971,-p5@MPZL2
Hg19::chr11:118134982..118134993,-p2@MPZL2
Hg19::chr11:118134997..118135052,-p1@MPZL2


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>

Uber Anatomy
Ontology termp-valuen
adult organism1.96e-21115
endoderm-derived structure2.83e-17169
endoderm2.83e-17169
presumptive endoderm2.83e-17169
anatomical conduit2.16e-14241
digestive system3.07e-13155
digestive tract3.07e-13155
primitive gut3.07e-13155
anatomical cluster7.73e-13286
anatomical group2.60e-12626
subdivision of digestive tract3.15e-12129
endodermal part of digestive tract3.15e-12129
anatomical system3.89e-12625
respiratory system6.11e-1272
mixed endoderm/mesoderm-derived structure3.09e-11130
embryo3.26e-11612
multi-cellular organism5.23e-11659
respiratory tract3.54e-1053
embryonic structure3.67e-10605
developing anatomical structure3.67e-10605
germ layer7.91e-10604
embryonic tissue7.91e-10604
presumptive structure7.91e-10604
epiblast (generic)7.91e-10604
organ1.14e-09511
organ part4.71e-09219
foregut6.39e-0998
endo-epithelium1.70e-0882
tube2.26e-08194
respiratory primordium9.35e-0838
endoderm of foregut9.35e-0838
renal system1.31e-0745
urinary system structure2.58e-0744
endothelium2.61e-0718
blood vessel endothelium2.61e-0718
cardiovascular system endothelium2.61e-0718
segment of respiratory tract6.29e-0746
simple squamous epithelium7.77e-0722
Disease
Ontology termp-valuen
carcinoma1.11e-13106
squamous cell carcinoma1.30e-0814


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
CEBPB#105147.971147625824820.0002476385788090830.00267540348942193
CTCF#1066445.360256373075030.001211145381643620.00815543600989544
E2F1#186944.907389214879320.001724022357361790.0106246044126104
FOSL2#2355416.93020060456171.2165416097647e-050.000303160079174936
GATA3#2625427.2365163572061.81561517799785e-066.74807948665185e-05
GTF2F1#2962412.73966087675773.79492332235515e-050.000716575658765956
HEY1#2346244.040111043105710.00375304636917980.018550137707088
RAD21#5885410.35503389545638.6948481184721e-050.00129080489359646
SMARCB1#6598418.25271578115749.00423392720929e-060.000240694442570722
SMC3#9126415.04493284493281.95092670935632e-050.000437050267263974
TAF1#687243.343046285745290.008005664898701650.0321195357979141
TBP#690843.706770687096390.005296377814784350.0243463205368954
ZNF263#1012748.221841637010680.0002187871180958320.00248071955561943



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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