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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C2209_acute_testis_spinal_Endothelial_rectum_heart_substantia
|full_id=C2209_acute_testis_spinal_Endothelial_rectum_heart_substantia
|id=C2209
|id=C2209

Revision as of 14:54, 12 September 2012


Full id: C2209_acute_testis_spinal_Endothelial_rectum_heart_substantia



Phase1 CAGE Peaks

Hg19::chr12:49488535..49488546,-p3@DHH
Hg19::chr12:49488554..49488568,-p2@DHH
Hg19::chr12:49488573..49488590,-p1@DHH
Hg19::chr19:2247294..2247304,+p@chr19:2247294..2247304
+


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 organism1.17e-47115
endothelium5.43e-1718
blood vessel endothelium5.43e-1718
cardiovascular system endothelium5.43e-1718
neural tube1.04e-1657
neural rod1.04e-1657
future spinal cord1.04e-1657
neural keel1.04e-1657
anatomical conduit4.51e-16241
neural plate3.08e-1586
presumptive neural plate3.08e-1586
neurectoderm5.72e-1490
tube2.61e-13194
anatomical cluster4.17e-13286
simple squamous epithelium6.96e-1322
endothelial tube1.31e-129
arterial system endothelium1.31e-129
endothelium of artery1.31e-129
regional part of brain4.19e-1259
regional part of nervous system1.31e-1194
nervous system1.31e-1194
central nervous system3.66e-1182
squamous epithelium1.07e-1025
anterior neural tube2.04e-1042
brain3.57e-1069
future brain3.57e-1069
brainstem1.14e-098
regional part of forebrain1.22e-0941
forebrain1.22e-0941
future forebrain1.22e-0941
epithelium1.39e-08309
vessel2.59e-0869
cell layer2.72e-08312
posterior neural tube4.60e-0815
chordal neural plate4.60e-0815
pre-chordal neural plate3.11e-0761
anterior region of body5.94e-07129
craniocervical region5.94e-07129
blood vessel6.66e-0760
epithelial tube open at both ends6.66e-0760
blood vasculature6.66e-0760
vascular cord6.66e-0760


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
USF1#739134.771124457905970.01370465887188020.0482846158594033
ZBTB7A#5134135.513931980906920.009038352821081090.0342310897258808



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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