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Coexpression cluster:C3346: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0001986!5.07e-34!18;UBERON:0004638!5.07e-34!18;UBERON:0004852!5.07e-34!18;UBERON:0000487!9.03e-31!22;UBERON:0006914!1.54e-26!25;UBERON:0000055!4.50e-18!69;UBERON:0002049!2.54e-16!79;UBERON:0007798!2.54e-16!79;UBERON:0003915!2.29e-15!9;UBERON:0004700!2.29e-15!9;UBERON:0001917!2.29e-15!9;UBERON:0001473!3.85e-13!8;UBERON:0004536!3.85e-13!8;UBERON:0006558!3.85e-13!8;UBERON:0001981!4.02e-11!60;UBERON:0007500!4.02e-11!60;UBERON:0004537!4.02e-11!60;UBERON:0006965!4.02e-11!60;UBERON:0003914!1.71e-10!118;UBERON:0004111!2.11e-10!241;UBERON:0002465!2.42e-10!10;UBERON:0001915!3.22e-10!3;UBERON:0001982!3.22e-10!3;UBERON:0004535!7.19e-10!110;UBERON:0000477!1.38e-09!286;UBERON:0001009!1.93e-09!113;UBERON:0006562!5.14e-08!11;UBERON:0001638!5.66e-08!9;UBERON:0003920!5.66e-08!9;UBERON:0004582!5.66e-08!9;UBERON:0005800!9.61e-07!2;UBERON:0001515!9.61e-07!2
|ontology_enrichment_uberon=UBERON:0001986!5.07e-34!18;UBERON:0004638!5.07e-34!18;UBERON:0004852!5.07e-34!18;UBERON:0000487!9.03e-31!22;UBERON:0006914!1.54e-26!25;UBERON:0000055!4.50e-18!69;UBERON:0002049!2.54e-16!79;UBERON:0007798!2.54e-16!79;UBERON:0003915!2.29e-15!9;UBERON:0004700!2.29e-15!9;UBERON:0001917!2.29e-15!9;UBERON:0001473!3.85e-13!8;UBERON:0004536!3.85e-13!8;UBERON:0006558!3.85e-13!8;UBERON:0001981!4.02e-11!60;UBERON:0007500!4.02e-11!60;UBERON:0004537!4.02e-11!60;UBERON:0006965!4.02e-11!60;UBERON:0003914!1.71e-10!118;UBERON:0004111!2.11e-10!241;UBERON:0002465!2.42e-10!10;UBERON:0001915!3.22e-10!3;UBERON:0001982!3.22e-10!3;UBERON:0004535!7.19e-10!110;UBERON:0000477!1.38e-09!286;UBERON:0001009!1.93e-09!113;UBERON:0006562!5.14e-08!11;UBERON:0001638!5.66e-08!9;UBERON:0003920!5.66e-08!9;UBERON:0004582!5.66e-08!9;UBERON:0005800!9.61e-07!2;UBERON:0001515!9.61e-07!2
|tf_chipseq_enrich=EP300#2033;3:6.7739417262232:0.00321688050010379:0.0167098270441828!FOS#2353;3:8.9979553088944:0.00137249927241713:0.00895722374004703!GATA2#2624;3:12.744931733554:0.000482952770428379:0.00436324432446103!JUN#3725;3:12.5128291923363:0.000510331399272625:0.00443488941659458
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}}
}}

Revision as of 13:36, 5 September 2012


Full id: C3346_Endothelial_Renal_somatostatinoma_Lymphatic_Small_Fibroblast_Natural



Phase1 CAGE Peaks

Hg19::chr12:96028776..96028781,-p@chr12:96028776..96028781
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Hg19::chr5:106837869..106837878,-p@chr5:106837869..106837878
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Hg19::chr5:106837881..106837888,-p@chr5:106837881..106837888
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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><br>


Uber Anatomy
Ontology termp-valuen
endothelium5.07e-3418
blood vessel endothelium5.07e-3418
cardiovascular system endothelium5.07e-3418
simple squamous epithelium9.03e-3122
squamous epithelium1.54e-2625
vessel4.50e-1869
vasculature2.54e-1679
vascular system2.54e-1679
endothelial tube2.29e-159
arterial system endothelium2.29e-159
endothelium of artery2.29e-159
lymphatic vessel3.85e-138
lymph vasculature3.85e-138
lymphatic part of lymphoid system3.85e-138
blood vessel4.02e-1160
epithelial tube open at both ends4.02e-1160
blood vasculature4.02e-1160
vascular cord4.02e-1160
epithelial tube1.71e-10118
anatomical conduit2.11e-10241
lymphoid system2.42e-1010
endothelium of capillary3.22e-103
capillary3.22e-103
cardiovascular system7.19e-10110
anatomical cluster1.38e-09286
circulatory system1.93e-09113
pharynx5.14e-0811
vein5.66e-089
venous blood vessel5.66e-089
venous system5.66e-089
segment of aorta9.61e-072
thoracic aorta9.61e-072


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
EP300#203336.77394172622320.003216880500103790.0167098270441828
FOS#235338.99795530889440.001372499272417130.00895722374004703
GATA2#2624312.7449317335540.0004829527704283790.00436324432446103
JUN#3725312.51282919233630.0005103313992726250.00443488941659458



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.