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Coexpression cluster:C1679: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0007023!3.10e-15!114;UBERON:0001473!2.84e-12!8;UBERON:0004536!2.84e-12!8;UBERON:0006558!2.84e-12!8;UBERON:0004638!5.58e-10!18;UBERON:0001986!5.58e-10!18;UBERON:0004852!5.58e-10!18;UBERON:0002465!9.52e-10!10;UBERON:0000341!1.54e-08!2;UBERON:0003127!2.60e-08!2;UBERON:0000055!3.09e-08!68;UBERON:0000487!5.67e-08!22;UBERON:0002066!6.92e-08!5;UBERON:0001638!2.31e-07!9;UBERON:0003920!2.31e-07!9;UBERON:0004582!2.31e-07!9;UBERON:0000477!5.33e-07!373;UBERON:0006914!6.85e-07!25;UBERON:0002049!8.56e-07!78;UBERON:0007798!8.56e-07!78
|ontology_enrichment_uberon=UBERON:0007023!3.10e-15!114;UBERON:0001473!2.84e-12!8;UBERON:0004536!2.84e-12!8;UBERON:0006558!2.84e-12!8;UBERON:0004638!5.58e-10!18;UBERON:0001986!5.58e-10!18;UBERON:0004852!5.58e-10!18;UBERON:0002465!9.52e-10!10;UBERON:0000341!1.54e-08!2;UBERON:0003127!2.60e-08!2;UBERON:0000055!3.09e-08!68;UBERON:0000487!5.67e-08!22;UBERON:0002066!6.92e-08!5;UBERON:0001638!2.31e-07!9;UBERON:0003920!2.31e-07!9;UBERON:0004582!2.31e-07!9;UBERON:0000477!5.33e-07!373;UBERON:0006914!6.85e-07!25;UBERON:0002049!8.56e-07!78;UBERON:0007798!8.56e-07!78
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}}
}}

Revision as of 15:02, 26 November 2012


Full id: C1679_Endothelial_retina_Hepatic_lung_Renal_kidney_gall



Phase1 CAGE Peaks

Hg19::chr12:6025654..6025658,-p@chr12:6025654..6025658
-
Hg19::chr6:142729306..142729321,+p@chr6:142729306..142729321
+
Hg19::chr6:46922535..46922542,-p9@GPR116
Hg19::chr7:10196589..10196595,-p@chr7:10196589..10196595
-
Hg19::chr7:47988099..47988115,-p2@PKD1L1


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
adult organism3.10e-15114
lymphatic vessel2.84e-128
lymph vasculature2.84e-128
lymphatic part of lymphoid system2.84e-128
blood vessel endothelium5.58e-1018
endothelium5.58e-1018
cardiovascular system endothelium5.58e-1018
lymphoid system9.52e-1010
throat1.54e-082
open tracheal system trachea2.60e-082
vessel3.09e-0868
simple squamous epithelium5.67e-0822
umbilical vein6.92e-085
vein2.31e-079
venous blood vessel2.31e-079
venous system2.31e-079
anatomical cluster5.33e-07373
squamous epithelium6.85e-0725
vasculature8.56e-0778
vascular system8.56e-0778


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.

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