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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C1223_Retinal_tubular_Endothelial_placenta_small_temporal_duodenum
|full_id=C1223_Retinal_tubular_Endothelial_placenta_small_temporal_duodenum
|id=C1223
|id=C1223

Revision as of 13:43, 12 September 2012


Full id: C1223_Retinal_tubular_Endothelial_placenta_small_temporal_duodenum



Phase1 CAGE Peaks

Hg19::chr16:82068830..82068841,+p6@HSD17B2
Hg19::chr16:82068851..82068864,+p4@HSD17B2
Hg19::chr16:82068873..82068889,+p3@HSD17B2
Hg19::chr16:82068905..82068918,+p7@HSD17B2
Hg19::chr16:82068920..82068953,+p2@HSD17B2
Hg19::chr16:82068960..82068995,+p1@HSD17B2
Hg19::chr16:82068997..82069008,+p5@HSD17B2


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>

Cell Type
Ontology termp-valuen
epithelial cell7.93e-20254
embryonic cell1.45e-17248
endodermal cell1.53e-1259
endothelial cell1.65e-1035
endothelial cell of vascular tree1.87e-1024
endo-epithelial cell7.09e-0843
metabolising cell2.89e-0712
endopolyploid cell2.89e-0712
parenchymal cell2.89e-0712
polyploid cell2.89e-0712
hepatocyte2.89e-0712
meso-epithelial cell8.79e-0744
Uber Anatomy
Ontology termp-valuen
endoderm-derived structure2.58e-19169
endoderm2.58e-19169
presumptive endoderm2.58e-19169
digestive system3.89e-17155
digestive tract3.89e-17155
primitive gut3.89e-17155
subdivision of digestive tract1.88e-16129
endodermal part of digestive tract1.88e-16129
gut epithelium1.38e-1454
endo-epithelium5.46e-1482
multi-tissue structure5.71e-14347
unilaminar epithelium1.74e-13138
gland1.70e-1159
exocrine gland2.38e-1131
exocrine system2.38e-1131
mixed endoderm/mesoderm-derived structure2.47e-11130
mesenchyme1.45e-10238
entire embryonic mesenchyme1.45e-10238
cell layer1.52e-10312
epithelium1.93e-10309
organism subdivision4.33e-10365
multi-cellular organism4.91e-10659
digestive tract diverticulum1.89e-0923
epithelium of foregut-midgut junction3.00e-0925
anatomical boundary3.00e-0925
hepatobiliary system3.00e-0925
foregut-midgut junction3.00e-0925
septum transversum3.00e-0925
hepatic diverticulum6.08e-0922
liver primordium6.08e-0922
sac6.12e-0926
vasculature1.81e-0879
vascular system1.81e-0879
epithelial sac1.90e-0825
anatomical cluster2.19e-08286
eye2.96e-0820
sense organ3.31e-0823
pigment epithelium of eye3.71e-0811
anatomical system4.23e-08625
anatomical group5.61e-08626
ectodermal placode5.84e-0829
liver6.46e-0819
digestive gland6.46e-0819
liver bud6.46e-0819
orifice7.27e-0835
subdivision of head8.94e-0848
camera-type eye1.18e-0719
simple eye1.18e-0719
ocular region1.18e-0719
optic cup1.18e-0719
eye primordium1.18e-0719
optic vesicle1.18e-0719
sensory system1.45e-0724
entire sense organ system1.45e-0724
visual system1.52e-0721
embryo1.65e-07612
trunk mesenchyme1.97e-07143
face2.69e-0721
foregut3.26e-0798
anatomical conduit3.55e-07241
hindgut6.09e-0719
germ layer6.17e-07604
embryonic tissue6.17e-07604
presumptive structure6.17e-07604
epiblast (generic)6.17e-07604
embryonic structure7.99e-07605
developing anatomical structure7.99e-07605
intestine8.86e-0727


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
ELF1#199774.258097958807543.93848941900192e-050.000735309074778588
EP300#203376.77394172622321.52695018318475e-065.86513976394382e-05
FOS#235378.99795530889442.09217725654467e-071.11881669480936e-05
FOSL2#2355716.93020060456172.50368126508949e-092.11897866810925e-07
FOXA1#3169711.08141974938554.86782131208363e-083.14598013621722e-06
POLR2A#543072.147453176558070.004747636447610280.02234412162372
SIN3A#2594275.408884726815147.3795239773719e-060.000211617272013384
SP1#666775.69838137814095.12280185510121e-060.000157266402982044



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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