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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C2508_mature_skeletal_left_Endothelial_adipose_heart_gastric
|full_id=C2508_mature_skeletal_left_Endothelial_adipose_heart_gastric
|id=C2508
|id=C2508

Revision as of 15:15, 12 September 2012


Full id: C2508_mature_skeletal_left_Endothelial_adipose_heart_gastric



Phase1 CAGE Peaks

Hg19::chr1:100111421..100111448,+p5@PALMD
Hg19::chr1:100111479..100111490,+p8@PALMD
Hg19::chr1:100111546..100111567,+p3@PALMD
Hg19::chr1:100111580..100111773,+p1@PALMD


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
anatomical cluster3.11e-34286
anatomical conduit4.88e-31241
adult organism1.51e-28115
tube3.53e-26194
anatomical system1.78e-23625
anatomical group1.87e-23626
multi-cellular organism6.52e-22659
epithelium9.57e-22309
multi-tissue structure1.15e-21347
cell layer1.44e-21312
organism subdivision2.85e-18365
embryonic structure1.90e-15605
developing anatomical structure1.90e-15605
embryo1.99e-15612
germ layer3.98e-15604
embryonic tissue3.98e-15604
presumptive structure3.98e-15604
epiblast (generic)3.98e-15604
central nervous system1.40e-1382
vessel1.73e-1369
anterior region of body2.08e-13129
craniocervical region2.08e-13129
splanchnic layer of lateral plate mesoderm2.52e-1384
head3.31e-13123
epithelial tube4.33e-13118
neural plate4.54e-1386
presumptive neural plate4.54e-1386
neural tube7.22e-1357
neural rod7.22e-1357
future spinal cord7.22e-1357
neural keel7.22e-1357
vasculature1.45e-1279
vascular system1.45e-1279
ectoderm-derived structure1.52e-12169
regional part of nervous system1.60e-1294
nervous system1.60e-1294
brain3.35e-1269
future brain3.35e-1269
blood vessel4.71e-1260
epithelial tube open at both ends4.71e-1260
blood vasculature4.71e-1260
vascular cord4.71e-1260
endothelium8.52e-1218
blood vessel endothelium8.52e-1218
cardiovascular system endothelium8.52e-1218
regional part of brain1.28e-1159
ectoderm3.04e-11173
presumptive ectoderm3.04e-11173
neurectoderm3.74e-1190
circulatory system1.52e-10113
anterior neural tube1.73e-1042
organ2.39e-10511
organ part3.40e-10219
regional part of forebrain6.16e-1041
forebrain6.16e-1041
future forebrain6.16e-1041
simple squamous epithelium2.05e-0922
cardiovascular system2.18e-09110
pre-chordal neural plate6.26e-0961
unilaminar epithelium1.07e-08138
squamous epithelium1.17e-0825
mesenchyme3.64e-08238
entire embryonic mesenchyme3.64e-08238
primary circulatory organ4.91e-0827
gray matter6.37e-0834
brain grey matter6.37e-0834
telencephalon8.50e-0834
regional part of telencephalon1.23e-0733
primordium1.95e-07168
cerebral hemisphere2.28e-0732
compound organ3.50e-0769
endothelial tube3.93e-079
arterial system endothelium3.93e-079
endothelium of artery3.93e-079
artery4.36e-0742
arterial blood vessel4.36e-0742
arterial system4.36e-0742
regional part of cerebral cortex5.91e-0722
subdivision of digestive tract6.58e-07129
endodermal part of digestive tract6.58e-07129


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
FOXA1#3169411.08141974938556.62943068949433e-050.00107111867540238
FOXA2#3170424.63046375266522.71504128667089e-069.43614632075277e-05
GATA3#2625427.2365163572061.81561517799785e-066.77459927027214e-05
HEY1#2346244.040111043105710.00375304636917980.0186100280007012



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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