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Coexpression cluster:C3430: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C3430_Mesenchymal_Fibroblast_Pericytes_Cardiac_Nucleus_Meningeal_Placental
|full_id=C3430_Mesenchymal_Fibroblast_Pericytes_Cardiac_Nucleus_Meningeal_Placental
|id=C3430
|id=C3430

Revision as of 16:21, 12 September 2012


Full id: C3430_Mesenchymal_Fibroblast_Pericytes_Cardiac_Nucleus_Meningeal_Placental



Phase1 CAGE Peaks

Hg19::chr14:52535726..52535753,-p2@NID2
Hg19::chr14:52535757..52535831,-p1@NID2
Hg19::chr14:52535971..52535992,-p3@NID2


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
somite1.27e-2183
paraxial mesoderm1.27e-2183
presomitic mesoderm1.27e-2183
presumptive segmental plate1.27e-2183
trunk paraxial mesoderm1.27e-2183
presumptive paraxial mesoderm1.27e-2183
dermomyotome1.01e-2070
trunk mesenchyme2.04e-20143
splanchnic layer of lateral plate mesoderm2.44e-2084
skeletal muscle tissue5.55e-2061
striated muscle tissue5.55e-2061
myotome5.55e-2061
muscle tissue9.25e-2063
musculature9.25e-2063
musculature of body9.25e-2063
circulatory system8.19e-19113
cardiovascular system3.56e-18110
vasculature1.13e-1779
vascular system1.13e-1779
cell layer2.84e-17312
unilaminar epithelium6.59e-17138
epithelium3.44e-16309
epithelial tube4.85e-16118
multilaminar epithelium1.78e-1582
multi-cellular organism5.48e-15659
organism subdivision6.51e-15365
multi-tissue structure9.17e-14347
trunk3.88e-13216
vessel6.62e-1369
anatomical cluster7.93e-13286
blood vessel1.28e-1260
epithelial tube open at both ends1.28e-1260
blood vasculature1.28e-1260
vascular cord1.28e-1260
primary circulatory organ7.03e-1127
anatomical system7.72e-11625
anatomical group1.28e-10626
heart2.09e-1024
primitive heart tube2.09e-1024
primary heart field2.09e-1024
anterior lateral plate mesoderm2.09e-1024
heart tube2.09e-1024
heart primordium2.09e-1024
cardiac mesoderm2.09e-1024
cardiogenic plate2.09e-1024
heart rudiment2.09e-1024
artery1.21e-0942
arterial blood vessel1.21e-0942
arterial system1.21e-0942
anatomical conduit1.38e-09241
compound organ1.34e-0869
mesenchyme1.35e-08238
entire embryonic mesenchyme1.35e-08238
systemic artery5.18e-0833
systemic arterial system5.18e-0833
tube6.88e-08194
embryo1.03e-07612
embryonic structure4.06e-07605
developing anatomical structure4.06e-07605
mesoderm5.04e-07448
mesoderm-derived structure5.04e-07448
presumptive mesoderm5.04e-07448
germ layer5.93e-07604
embryonic tissue5.93e-07604
presumptive structure5.93e-07604
epiblast (generic)5.93e-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
SP1#666735.69838137814090.005403962701712170.024592987084584
TCF12#6938310.63446490218640.0008313523990202070.00628578970544207



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.