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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C814_Alveolar_mesothelioma_bile_Renal_papillotubular_papillary_serous
|full_id=C814_Alveolar_mesothelioma_bile_Renal_papillotubular_papillary_serous
|gostat_on_coexpression_clusters=GO:0008067!metabotropic glutamate, GABA-B-like receptor activity!0.0259448957965383!9052$GO:0008066!glutamate receptor activity!0.0259448957965383!9052$GO:0030659!cytoplasmic vesicle membrane!0.0259448957965383!9052$GO:0044433!cytoplasmic vesicle part!0.0259448957965383!9052$GO:0012506!vesicle membrane!0.0259448957965383!9052
|gostat_on_coexpression_clusters=GO:0008067!metabotropic glutamate, GABA-B-like receptor activity!0.0259448957965383!9052$GO:0008066!glutamate receptor activity!0.0259448957965383!9052$GO:0030659!cytoplasmic vesicle membrane!0.0259448957965383!9052$GO:0044433!cytoplasmic vesicle part!0.0259448957965383!9052$GO:0012506!vesicle membrane!0.0259448957965383!9052

Revision as of 18:33, 12 September 2012


Full id: C814_Alveolar_mesothelioma_bile_Renal_papillotubular_papillary_serous



Phase1 CAGE Peaks

Hg19::chr12:13044488..13044506,+p1@GPRC5A
Hg19::chr12:13061554..13061566,+p7@GPRC5A
Hg19::chr12:13061590..13061609,+p12@GPRC5A
Hg19::chr12:13061810..13061833,+p5@GPRC5A
Hg19::chr12:13061894..13061915,+p2@GPRC5A
Hg19::chr12:13065023..13065045,+p@chr12:13065023..13065045
+
Hg19::chr12:13065626..13065659,+p@chr12:13065626..13065659
+
Hg19::chr12:13065686..13065702,+p@chr12:13065686..13065702
+
Hg19::chr12:13065994..13066009,+p@chr12:13065994..13066009
+
Hg19::chr12:13068454..13068484,+p1@MIR614


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

GO IDGO nameFDR corrected p-value
GO:0008067metabotropic glutamate, GABA-B-like receptor activity0.0259448957965383
GO:0008066glutamate receptor activity0.0259448957965383
GO:0030659cytoplasmic vesicle membrane0.0259448957965383
GO:0044433cytoplasmic vesicle part0.0259448957965383
GO:0012506vesicle membrane0.0259448957965383



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 cell6.99e-34254
embryonic cell2.12e-11248
mesothelial cell1.82e-1019
mesodermal cell2.47e-10119
squamous epithelial cell7.26e-0962
endo-epithelial cell1.44e-0743
Uber Anatomy
Ontology termp-valuen
endoderm-derived structure1.17e-18169
endoderm1.17e-18169
presumptive endoderm1.17e-18169
mesenchyme6.06e-18238
entire embryonic mesenchyme6.06e-18238
digestive system1.56e-15155
digestive tract1.56e-15155
primitive gut1.56e-15155
multi-tissue structure1.72e-15347
trunk6.05e-14216
subdivision of digestive tract1.95e-13129
endodermal part of digestive tract1.95e-13129
multi-cellular organism4.10e-13659
organ1.95e-12511
mixed endoderm/mesoderm-derived structure8.79e-12130
anatomical system2.37e-11625
anatomical group3.73e-11626
mesoderm8.09e-11448
mesoderm-derived structure8.09e-11448
presumptive mesoderm8.09e-11448
primordium9.41e-11168
renal system9.98e-1145
urinary system structure1.36e-1044
intermediate mesoderm1.74e-1037
respiratory primordium1.51e-0938
endoderm of foregut1.51e-0938
anatomical space1.86e-09104
respiratory tract2.07e-0953
endo-epithelium3.76e-0982
unilaminar epithelium5.46e-09138
reproductive structure6.26e-0959
reproductive system6.26e-0959
trunk mesenchyme6.48e-09143
embryonic structure6.95e-09605
developing anatomical structure6.95e-09605
immaterial anatomical entity7.77e-09126
germ layer8.41e-09604
embryonic tissue8.41e-09604
presumptive structure8.41e-09604
epiblast (generic)8.41e-09604
embryo1.13e-08612
trunk region element1.26e-08107
anatomical cluster1.46e-08286
epithelial bud2.36e-0837
epithelial tube3.25e-08118
subdivision of trunk4.87e-08113
organ segment6.62e-0897
organism subdivision8.88e-08365
epithelial fold1.18e-0751
respiratory system1.20e-0772
organ part1.59e-07219
cell layer2.29e-07312
duct2.43e-0726
genitourinary system2.61e-0715
segment of respiratory tract3.98e-0746
body cavity precursor5.57e-0763
cloaca5.86e-0714
anal region5.86e-0714
embryonic cloaca5.86e-0714
terminal part of digestive tract5.86e-0714
primitive urogenital sinus5.86e-0714
proctodeum5.86e-0714
foregut6.58e-0798
thoracic segment of trunk7.09e-0752
epithelium7.36e-07309
compound organ8.30e-0769
Disease
Ontology termp-valuen
carcinoma3.79e-18106
cell type cancer1.45e-13143
adenocarcinoma6.96e-0825
squamous cell carcinoma7.47e-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
POLR2A#5430102.147453176558070.0004793377491637920.00436570639094072



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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