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Coexpression cluster:C814

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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 cell1.07e-31253
mesothelial cell5.46e-1219
kidney cell1.51e-0717
kidney epithelial cell1.51e-0717
endo-epithelial cell2.07e-0742
squamous epithelial cell4.75e-0763
Uber Anatomy
Ontology termp-valuen
endoderm-derived structure2.55e-13160
endoderm2.55e-13160
presumptive endoderm2.55e-13160
digestive system7.03e-12145
digestive tract7.03e-12145
primitive gut7.03e-12145
urinary system structure2.16e-1147
subdivision of digestive tract6.01e-11118
renal system6.72e-1148
respiratory primordium1.09e-0938
endoderm of foregut1.09e-0938
endo-epithelium2.59e-0982
epithelial bud4.11e-0937
respiratory tract6.59e-0954
larynx7.56e-099
prostate gland1.01e-0811
male accessory sex gland1.01e-0811
embryonic cloacal epithelium1.01e-0811
epithelium of hindgut1.01e-0811
urogenital sinus epithelium1.01e-0811
prostate bud1.01e-0811
prostate field1.01e-0811
trunk3.80e-08199
cloaca4.96e-0814
anal region4.96e-0814
embryonic cloaca4.96e-0814
terminal part of digestive tract4.96e-0814
primitive urogenital sinus4.96e-0814
proctodeum4.96e-0814
sex gland1.18e-0712
male reproductive gland1.18e-0712
organism subdivision1.24e-07264
trunk region element1.54e-07101
genitourinary system3.42e-0715
intermediate mesoderm5.21e-0728
Disease
Ontology termp-valuen
carcinoma2.59e-25106
cell type cancer1.64e-18143
disease of cellular proliferation1.28e-11239
adenocarcinoma2.51e-1025
cancer3.65e-10235
squamous cell carcinoma6.77e-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
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.