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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C856_Endothelial_lung_diaphragm_left_kidney_heart_Hepatic
|full_id=C856_Endothelial_lung_diaphragm_left_kidney_heart_Hepatic
|id=C856
|id=C856

Revision as of 18:37, 12 September 2012


Full id: C856_Endothelial_lung_diaphragm_left_kidney_heart_Hepatic



Phase1 CAGE Peaks

Hg19::chr2:197226875..197226907,-p3@HECW2
Hg19::chr4:101439078..101439098,-p3@EMCN
Hg19::chr4:101439101..101439106,-p7@EMCN
Hg19::chr4:101439116..101439130,-p2@EMCN
Hg19::chr4:101439148..101439199,-p1@EMCN
Hg19::chr6:46922659..46922725,-p1@GPR116
Hg19::chr6:76203560..76203582,-p4@FILIP1
Hg19::chr6:76203624..76203635,-p7@FILIP1
Hg19::chr8:68864263..68864328,+p2@PREX2
Hg19::chrX:71299835..71299852,+p@chrX:71299835..71299852
+


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 organism1.67e-41115
tube5.43e-26194
anatomical conduit3.46e-23241
neural tube5.21e-2057
neural rod5.21e-2057
future spinal cord5.21e-2057
neural keel5.21e-2057
central nervous system5.87e-2082
regional part of brain2.02e-1959
anatomical cluster5.51e-19286
regional part of nervous system1.02e-1894
nervous system1.02e-1894
brain1.57e-1769
future brain1.57e-1769
anterior neural tube1.03e-1642
regional part of forebrain4.33e-1641
forebrain4.33e-1641
future forebrain4.33e-1641
neural plate8.23e-1686
presumptive neural plate8.23e-1686
vessel1.43e-1569
splanchnic layer of lateral plate mesoderm1.59e-1584
vasculature3.41e-1579
vascular system3.41e-1579
multi-cellular organism4.71e-15659
cell layer1.53e-14312
neurectoderm2.92e-1490
circulatory system3.80e-14113
blood vessel4.35e-1460
epithelial tube open at both ends4.35e-1460
blood vasculature4.35e-1460
vascular cord4.35e-1460
epithelium5.59e-14309
gray matter2.86e-1334
brain grey matter2.86e-1334
telencephalon3.64e-1334
cardiovascular system5.93e-13110
regional part of telencephalon8.00e-1333
anatomical system8.44e-13625
anatomical group1.36e-12626
cerebral hemisphere2.09e-1232
endothelium9.56e-1218
blood vessel endothelium9.56e-1218
cardiovascular system endothelium9.56e-1218
epithelial tube1.88e-11118
pre-chordal neural plate2.10e-1061
cerebral cortex8.01e-1025
pallium8.01e-1025
regional part of cerebral cortex1.08e-0922
simple squamous epithelium2.45e-0922
neocortex5.75e-0920
embryo3.93e-08612
squamous epithelium4.02e-0825
artery2.14e-0742
arterial blood vessel2.14e-0742
arterial system2.14e-0742
anterior region of body2.89e-07129
craniocervical region2.89e-07129
ectoderm-derived structure3.82e-07169
organism subdivision3.84e-07365
embryonic structure4.64e-07605
developing anatomical structure4.64e-07605
compound organ6.49e-0769
primary circulatory organ7.30e-0727
germ layer8.58e-07604
embryonic tissue8.58e-07604
presumptive structure8.58e-07604
epiblast (generic)8.58e-07604


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
GATA2#262456.3724658667770.0005348865075213680.00462289076125655
TRIM28#1015535.577157513578760.01403197805233580.04925009261352



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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