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|full_id=C3633_testicular_large_melanoma_papillary_osteosarcoma_Trabecular_gastric
|full_id=C3633_testicular_large_melanoma_papillary_osteosarcoma_Trabecular_gastric
|id=C3633
|id=C3633
|ontology_enrichment_celltype=CL:0000066!1.17e-35!254;CL:0002321!5.12e-27!248;CL:0000220!4.06e-26!246;CL:0000548!3.73e-15!679;CL:0000004!3.73e-15!679;CL:0000255!3.73e-15!679;CL:0000012!2.51e-14!682;CL:0000222!5.39e-12!119;CL:0000076!2.93e-10!62;CL:0000223!1.06e-09!59;CL:0000071!1.67e-09!18;CL:0002546!1.67e-09!18;CL:0002139!1.95e-08!24;CL:0002078!5.10e-08!44;CL:0000055!1.20e-07!180;CL:0000115!2.12e-07!35;CL:0000003!2.15e-07!722;CL:0002076!3.61e-07!43;CL:0000213!5.92e-07!57;CL:0000215!5.92e-07!57
|ontology_enrichment_disease=DOID:305!1.94e-11!106;DOID:0050687!5.00e-10!143;DOID:14566!1.11e-09!239;DOID:162!1.86e-09!235
|ontology_enrichment_uberon=UBERON:0003914!9.75e-17!118;UBERON:0000490!2.55e-15!138;UBERON:0003104!1.52e-14!238;UBERON:0009142!1.52e-14!238;UBERON:0000119!2.24e-14!312;UBERON:0000483!1.39e-13!309;UBERON:0002049!2.89e-12!79;UBERON:0007798!2.89e-12!79;UBERON:0005256!4.24e-12!143;UBERON:0002100!9.19e-12!216;UBERON:0004119!9.28e-12!169;UBERON:0000925!9.28e-12!169;UBERON:0006595!9.28e-12!169;UBERON:0000481!1.06e-11!347;UBERON:0000055!1.61e-11!69;UBERON:0001048!3.03e-11!168;UBERON:0001981!7.88e-11!60;UBERON:0007500!7.88e-11!60;UBERON:0004537!7.88e-11!60;UBERON:0006965!7.88e-11!60;UBERON:0000466!3.87e-10!126;UBERON:0004872!6.44e-10!84;UBERON:0001637!1.62e-09!42;UBERON:0003509!1.62e-09!42;UBERON:0004572!1.62e-09!42;UBERON:0001986!1.67e-09!18;UBERON:0004638!1.67e-09!18;UBERON:0004852!1.67e-09!18;UBERON:0001007!3.66e-09!155;UBERON:0001555!3.66e-09!155;UBERON:0007026!3.66e-09!155;UBERON:0000487!3.93e-09!22;UBERON:0000077!4.71e-09!130;UBERON:0004111!1.06e-08!241;UBERON:0000477!1.18e-08!286;UBERON:0006914!2.74e-08!25;UBERON:0000464!6.12e-08!104;UBERON:0005911!8.29e-08!82;UBERON:0000486!1.04e-07!82;UBERON:0005177!1.40e-07!107;UBERON:0004535!1.46e-07!110;UBERON:0000475!2.14e-07!365;UBERON:0004573!6.46e-07!33;UBERON:0004571!6.46e-07!33;UBERON:0001009!6.86e-07!113
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Revision as of 14:38, 21 May 2012


Full id: C3633_testicular_large_melanoma_papillary_osteosarcoma_Trabecular_gastric



Phase1 CAGE Peaks

Hg19::chr17:41622834..41622883,-p6@ETV4
Hg19::chr17:41622901..41622913,-p16@ETV4
Hg19::chr17:41622925..41622976,-p3@ETV4


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
epithelial tube9.75e-17118
unilaminar epithelium2.55e-15138
mesenchyme1.52e-14238
entire embryonic mesenchyme1.52e-14238
cell layer2.24e-14312
epithelium1.39e-13309
vasculature2.89e-1279
vascular system2.89e-1279
trunk mesenchyme4.24e-12143
trunk9.19e-12216
endoderm-derived structure9.28e-12169
endoderm9.28e-12169
presumptive endoderm9.28e-12169
multi-tissue structure1.06e-11347
vessel1.61e-1169
primordium3.03e-11168
blood vessel7.88e-1160
epithelial tube open at both ends7.88e-1160
blood vasculature7.88e-1160
vascular cord7.88e-1160
immaterial anatomical entity3.87e-10126
splanchnic layer of lateral plate mesoderm6.44e-1084
artery1.62e-0942
arterial blood vessel1.62e-0942
arterial system1.62e-0942
endothelium1.67e-0918
blood vessel endothelium1.67e-0918
cardiovascular system endothelium1.67e-0918
digestive system3.66e-09155
digestive tract3.66e-09155
primitive gut3.66e-09155
simple squamous epithelium3.93e-0922
mixed endoderm/mesoderm-derived structure4.71e-09130
anatomical conduit1.06e-08241
anatomical cluster1.18e-08286
squamous epithelium2.74e-0825
anatomical space6.12e-08104
endo-epithelium8.29e-0882
multilaminar epithelium1.04e-0782
trunk region element1.40e-07107
cardiovascular system1.46e-07110
organism subdivision2.14e-07365
systemic artery6.46e-0733
systemic arterial system6.46e-0733
circulatory system6.86e-07113
Disease
Ontology termp-valuen
carcinoma1.94e-11106
cell type cancer5.00e-10143
disease of cellular proliferation1.11e-09239
cancer1.86e-09235


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


No analysis results for this cluster

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.