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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C1394_large_bronchioalveolar_prostate_nonsmall_papillary_small_Alveolar
|full_id=C1394_large_bronchioalveolar_prostate_nonsmall_papillary_small_Alveolar
|id=C1394
|id=C1394

Revision as of 13:56, 12 September 2012


Full id: C1394_large_bronchioalveolar_prostate_nonsmall_papillary_small_Alveolar



Phase1 CAGE Peaks

Hg19::chr14:36989336..36989354,-p5@NKX2-1
Hg19::chr14:36989358..36989378,-p3@NKX2-1
Hg19::chr14:36989379..36989390,-p8@NKX2-1
Hg19::chr14:36989407..36989410,-p15@NKX2-1
Hg19::chr14:36989412..36989423,-p12@NKX2-1
Hg19::chr14:36989427..36989442,-p1@NKX2-1


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
endo-epithelial cell1.50e-1343
respiratory epithelial cell2.16e-1113
endodermal cell4.64e-1059
epithelial cell1.36e-08254
epithelial cell of lung1.60e-0819
Uber Anatomy
Ontology termp-valuen
respiratory primordium3.88e-2338
endoderm of foregut3.88e-2338
respiratory tract4.86e-2253
respiratory system1.54e-1772
regional part of forebrain5.85e-1541
forebrain5.85e-1541
future forebrain5.85e-1541
anterior neural tube1.89e-1442
larynx5.49e-149
segment of respiratory tract5.60e-1446
regional part of telencephalon3.44e-1333
telencephalon1.18e-1234
cerebral hemisphere2.07e-1232
lung2.47e-1222
respiratory tube2.47e-1222
respiration organ2.47e-1222
pair of lungs2.47e-1222
lung primordium2.47e-1222
lung bud2.47e-1222
endoderm-derived structure6.79e-12169
endoderm6.79e-12169
presumptive endoderm6.79e-12169
thoracic cavity element1.57e-1134
thoracic cavity1.57e-1134
gray matter2.11e-1134
brain grey matter2.11e-1134
thoracic segment organ4.69e-1135
digestive system6.08e-11155
digestive tract6.08e-11155
primitive gut6.08e-11155
neural tube7.11e-1057
neural rod7.11e-1057
future spinal cord7.11e-1057
neural keel7.11e-1057
foregut8.85e-1098
organ part1.40e-09219
subdivision of digestive tract1.77e-09129
endodermal part of digestive tract1.77e-09129
regional part of brain2.50e-0959
mixed endoderm/mesoderm-derived structure7.18e-09130
brain1.24e-0869
future brain1.24e-0869
respiratory tract epithelium1.60e-0819
lung epithelium1.60e-0819
pre-chordal neural plate4.77e-0861
epithelial bud4.89e-0837
telencephalic nucleus7.50e-087
central nervous system1.05e-0782
cerebral cortex2.55e-0725
pallium2.55e-0725
corpus striatum5.07e-074
striatum5.07e-074
ventral part of telencephalon5.07e-074
future corpus striatum5.07e-074
Disease
Ontology termp-valuen
carcinoma9.08e-17106
cell type cancer3.07e-15143
cancer1.30e-11235
disease of cellular proliferation5.00e-11239
squamous cell carcinoma1.95e-0914


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
CTBP2#1488662.71700033932811.6349770986689e-111.98783903618022e-09
CTCF#1066465.360256373075034.21437267579784e-050.000755094986940557
SUZ12#23512650.11578091106296.2866744827465e-116.97740697453307e-09



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.