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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C619_squamous_bile_Small_Mammary_mucinous_Tracheal_giant
|full_id=C619_squamous_bile_Small_Mammary_mucinous_Tracheal_giant
|id=C619
|id=C619

Revision as of 18:15, 12 September 2012


Full id: C619_squamous_bile_Small_Mammary_mucinous_Tracheal_giant



Phase1 CAGE Peaks

Hg19::chr11:128376979..128377025,-p@chr11:128376979..128377025
-
Hg19::chr12:31910006..31910040,-p@chr12:31910006..31910040
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Hg19::chr20:10400351..10400358,-p@chr20:10400351..10400358
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Hg19::chr20:10400359..10400384,-p@chr20:10400359..10400384
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Hg19::chr20:10400400..10400411,-p@chr20:10400400..10400411
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Hg19::chr2:20133179..20133195,-p@chr2:20133179..20133195
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Hg19::chr2:20133198..20133223,-p@chr2:20133198..20133223
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Hg19::chr2:29353197..29353206,-p@chr2:29353197..29353206
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Hg19::chr2:29353207..29353220,-p@chr2:29353207..29353220
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Hg19::chr2:29353224..29353251,-p@chr2:29353224..29353251
-
Hg19::chr3:101957544..101957547,+p@chr3:101957544..101957547
+
Hg19::chr6:150813975..150813994,+p@chr6:150813975..150813994
+
Hg19::chr6:150813996..150814008,+p@chr6:150813996..150814008
+
Hg19::chr7:101917407..101917443,+p3@CUX1


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
endoderm-derived structure5.53e-22169
endoderm5.53e-22169
presumptive endoderm5.53e-22169
digestive system1.26e-18155
digestive tract1.26e-18155
primitive gut1.26e-18155
subdivision of digestive tract2.64e-13129
endodermal part of digestive tract2.64e-13129
mixed endoderm/mesoderm-derived structure5.97e-13130
endo-epithelium2.66e-1282
respiratory system4.87e-1272
respiratory tract1.74e-1153
respiratory primordium7.84e-1138
endoderm of foregut7.84e-1138
organ1.06e-10511
epithelial bud3.51e-1037
segment of respiratory tract5.94e-1046
foregut6.69e-1098
anatomical system1.24e-09625
anatomical group1.98e-09626
trunk region element7.61e-09107
multi-cellular organism3.33e-08659
thoracic cavity element4.59e-0834
thoracic cavity4.59e-0834
anatomical space4.62e-08104
immaterial anatomical entity8.11e-08126
urinary system structure1.16e-0744
renal system1.30e-0745
epithelial fold1.82e-0751
thoracic segment organ1.95e-0735
mesenchyme2.94e-07238
entire embryonic mesenchyme2.94e-07238
respiratory tract epithelium3.97e-0719
lung epithelium3.97e-0719
mesoderm4.51e-07448
mesoderm-derived structure4.51e-07448
presumptive mesoderm4.51e-07448
respiratory system epithelium8.63e-0728
Disease
Ontology termp-valuen
carcinoma6.78e-25106
cell type cancer1.01e-17143
disease of cellular proliferation7.82e-10239
cancer1.97e-09235
adenocarcinoma5.45e-0925
squamous cell carcinoma6.30e-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
BCL3#60237.402950600801070.006944266328473380.0293719516879731
CEBPB#105173.985573812912410.0007472043419239960.00588338919377264
EP300#2033104.838529804445142.76491461776768e-069.56808872647577e-05
FOS#235363.856266560954750.002556261076114450.0141450328774143
FOSL1#8061514.18342132727611.67209788666175e-050.00038550161409507
FOSL2#235556.046500215914890.0009158002195483010.00666424603744461
GATA3#262535.836396362258430.0132868415026020.0469885019534827
JUN#372565.362641082429860.0004446028323499080.004139229382046
JUND#3727104.996188529907882.04570531488249e-067.46771818878058e-05
MAFF#23764312.06757639070250.001758447738855720.0108074220795829
MAFK#797535.807299958106410.01346697296069050.0475723723673787
NFE2#4778316.54377013963480.0007099302705452480.0057051714008522
POLR2A#5430131.994063663946780.0003845688903765380.00377481112237173
STAT3#677486.011122855516711.1795981756812e-050.000298801973975184



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.