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{{Coexpression_clusters
 
{{Coexpression_clusters
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|full_id=C2731_optic_Endothelial_small_corpus_Prostate_medulla_Pericytes
 
|full_id=C2731_optic_Endothelial_small_corpus_Prostate_medulla_Pericytes
 
|id=C2731
 
|id=C2731

Revision as of 06:30, 12 September 2012


Full id: C2731_optic_Endothelial_small_corpus_Prostate_medulla_Pericytes



Phase1 CAGE Peaks

Hg19::chr3:170138971..170138982,+p11@CLDN11
Hg19::chr3:170138985..170138998,+p7@CLDN11
Hg19::chr3:170139006..170139041,+p3@CLDN11
Hg19::chr3:170139046..170139064,+p4@CLDN11


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
cell layer2.03e-34312
anatomical cluster9.32e-34286
epithelium7.93e-33309
anatomical conduit5.58e-32241
tube6.12e-29194
vasculature6.41e-2879
vascular system6.41e-2879
circulatory system1.62e-22113
cardiovascular system1.92e-22110
vessel2.31e-2269
organism subdivision2.38e-22365
splanchnic layer of lateral plate mesoderm3.63e-2284
neural plate5.24e-1986
presumptive neural plate5.24e-1986
regional part of brain2.04e-1859
neural tube4.30e-1857
neural rod4.30e-1857
future spinal cord4.30e-1857
neural keel4.30e-1857
blood vessel4.41e-1860
epithelial tube open at both ends4.41e-1860
blood vasculature4.41e-1860
vascular cord4.41e-1860
multi-tissue structure1.74e-17347
somite2.05e-1783
paraxial mesoderm2.05e-1783
presomitic mesoderm2.05e-1783
presumptive segmental plate2.05e-1783
trunk paraxial mesoderm2.05e-1783
presumptive paraxial mesoderm2.05e-1783
adult organism4.04e-17115
epithelial tube7.17e-17118
neurectoderm8.54e-1790
dermomyotome1.18e-1670
brain3.00e-1569
future brain3.00e-1569
unilaminar epithelium4.09e-15138
head8.85e-15123
skeletal muscle tissue2.51e-1461
striated muscle tissue2.51e-1461
myotome2.51e-1461
muscle tissue2.54e-1463
musculature2.54e-1463
musculature of body2.54e-1463
trunk mesenchyme2.78e-14143
anatomical system4.65e-14625
anterior region of body6.65e-14129
craniocervical region6.65e-14129
anatomical group7.35e-14626
multi-cellular organism9.66e-14659
central nervous system1.60e-1382
multilaminar epithelium5.26e-1382
artery7.87e-1342
arterial blood vessel7.87e-1342
arterial system7.87e-1342
pre-chordal neural plate9.84e-1361
regional part of nervous system4.86e-1294
nervous system4.86e-1294
anterior neural tube3.19e-1142
regional part of forebrain4.03e-1141
forebrain4.03e-1141
future forebrain4.03e-1141
systemic artery1.45e-1033
systemic arterial system1.45e-1033
endothelium1.83e-0918
blood vessel endothelium1.83e-0918
cardiovascular system endothelium1.83e-0918
telencephalon4.56e-0934
gray matter5.44e-0934
brain grey matter5.44e-0934
posterior neural tube1.15e-0815
chordal neural plate1.15e-0815
regional part of telencephalon1.29e-0833
embryonic structure1.33e-08605
developing anatomical structure1.33e-08605
ectoderm-derived structure1.35e-08169
embryo1.48e-08612
germ layer1.62e-08604


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.