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Coexpression cluster:C4387: Difference between revisions

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|id=C4387
|id=C4387
|ontology_enrichment_celltype=
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_disease=DOID:114!6.13e-07!2
|ontology_enrichment_uberon=UBERON:0007023!6.05e-33!115;UBERON:0001049!1.94e-09!57;UBERON:0005068!1.94e-09!57;UBERON:0006241!1.94e-09!57;UBERON:0007135!1.94e-09!57;UBERON:0003075!1.07e-07!86;UBERON:0007284!1.07e-07!86;UBERON:0003080!3.81e-07!42;UBERON:0002346!5.05e-07!90;UBERON:0002616!7.98e-07!59
|ontology_enrichment_uberon=UBERON:0007023!2.79e-46!114;UBERON:0002298!5.76e-15!6;UBERON:0001049!5.52e-11!56;UBERON:0005068!5.52e-11!56;UBERON:0006241!5.52e-11!56;UBERON:0007135!5.52e-11!56;UBERON:0003075!3.22e-10!82;UBERON:0007284!3.22e-10!82;UBERON:0004151!9.30e-10!3;UBERON:0003076!9.30e-10!15;UBERON:0003057!9.30e-10!15;UBERON:0003978!1.13e-09!3;UBERON:0009751!1.13e-09!3;UBERON:0000946!1.13e-09!3;UBERON:0002523!1.13e-09!3;UBERON:0005983!1.13e-09!3;UBERON:0002165!1.13e-09!3;UBERON:0002062!1.13e-09!3;UBERON:0007280!1.13e-09!3;UBERON:0010314!1.53e-09!132;UBERON:0002346!1.72e-09!86;UBERON:0000073!4.24e-09!53;UBERON:0002616!4.24e-09!53;UBERON:0001017!7.76e-09!81;UBERON:0010371!1.11e-08!104;UBERON:0001896!1.66e-08!3;UBERON:0005290!1.66e-08!3;UBERON:0010096!1.66e-08!3;UBERON:0000349!3.69e-08!5;UBERON:0000988!3.84e-08!3;UBERON:0000955!5.21e-08!68;UBERON:0006238!5.21e-08!68;UBERON:0003103!1.47e-07!68;UBERON:0001016!1.78e-07!89;UBERON:0007100!3.48e-07!27;UBERON:0004733!4.09e-07!12;UBERON:0002028!4.09e-07!12;UBERON:0007277!4.09e-07!12;UBERON:0002081!5.04e-07!2;UBERON:0010227!5.04e-07!2;UBERON:0002133!5.33e-07!2;UBERON:0002420!7.59e-07!9;UBERON:0007245!7.59e-07!9;UBERON:0010009!7.59e-07!9;UBERON:0010011!7.59e-07!9;UBERON:0000454!7.59e-07!9;UBERON:0000125!8.10e-07!9;UBERON:0002308!8.10e-07!9
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}}
}}

Revision as of 15:54, 19 October 2012


Full id: C4387_heart_left_mature_skeletal_umbilical_bladder_esophagus



Phase1 CAGE Peaks

Hg19::chr4:159762956..159762968,+p@chr4:159762956..159762968
+
Hg19::chr5:175084797..175084805,+p3@HRH2
Hg19::chr9:124072974..124072996,+p@chr9:124072974..124072996
+


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><br>uberon_data<br>disease_data<br>

Uber Anatomy
Ontology termp-valuen
adult organism2.79e-46114
brainstem5.76e-156
neural tube5.52e-1156
neural rod5.52e-1156
future spinal cord5.52e-1156
neural keel5.52e-1156
neural plate3.22e-1082
presumptive neural plate3.22e-1082
cardiac chamber9.30e-103
posterior neural tube9.30e-1015
chordal neural plate9.30e-1015
valve1.13e-093
cardiac mesenchyme1.13e-093
cardial valve1.13e-093
tunica intima1.13e-093
heart layer1.13e-093
endocardium1.13e-093
endocardial cushion1.13e-093
presumptive endocardium1.13e-093
structure with developmental contribution from neural crest1.53e-09132
neurectoderm1.72e-0986
regional part of nervous system4.24e-0953
regional part of brain4.24e-0953
central nervous system7.76e-0981
ecto-epithelium1.11e-08104
medulla oblongata1.66e-083
myelencephalon1.66e-083
future myelencephalon1.66e-083
limbic system3.69e-085
pons3.84e-083
brain5.21e-0868
future brain5.21e-0868
compound organ1.47e-0768
nervous system1.78e-0789
primary circulatory organ3.48e-0727
segmental subdivision of hindbrain4.09e-0712
hindbrain4.09e-0712
presumptive hindbrain4.09e-0712
cardiac atrium5.04e-072
future cardiac atrium5.04e-072
atrioventricular valve5.33e-072
basal ganglion7.59e-079
nuclear complex of neuraxis7.59e-079
aggregate regional part of brain7.59e-079
collection of basal ganglia7.59e-079
cerebral subcortex7.59e-079
neural nucleus8.10e-079
nucleus of brain8.10e-079
Disease
Ontology termp-valuen
heart disease6.13e-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

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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