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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C2814_Smooth_mesenchymal_alveolar_Preadipocyte_pancreas_leiomyoma_Mast
|full_id=C2814_Smooth_mesenchymal_alveolar_Preadipocyte_pancreas_leiomyoma_Mast
|id=C2814
|id=C2814

Revision as of 15:36, 12 September 2012


Full id: C2814_Smooth_mesenchymal_alveolar_Preadipocyte_pancreas_leiomyoma_Mast



Phase1 CAGE Peaks

Hg19::chr5:150157847..150157859,+p6@C5orf62
Hg19::chr5:150157860..150157883,+p4@C5orf62
Hg19::chr5:150157886..150157917,+p3@C5orf62
Hg19::chr5:150157924..150157963,+p2@C5orf62


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
tube3.68e-15194
skeletal muscle tissue4.06e-1361
striated muscle tissue4.06e-1361
myotome4.06e-1361
muscle tissue5.98e-1363
musculature5.98e-1363
musculature of body5.98e-1363
epithelium2.02e-12309
neural tube5.78e-1257
neural rod5.78e-1257
future spinal cord5.78e-1257
neural keel5.78e-1257
cell layer7.61e-12312
adult organism1.72e-11115
dermomyotome2.04e-1170
anatomical conduit2.18e-11241
brain1.13e-1069
future brain1.13e-1069
artery1.67e-1042
arterial blood vessel1.67e-1042
arterial system1.67e-1042
neural plate4.70e-1086
presumptive neural plate4.70e-1086
regional part of brain7.39e-1059
anterior neural tube9.46e-1042
central nervous system1.73e-0982
regional part of forebrain1.87e-0941
forebrain1.87e-0941
future forebrain1.87e-0941
splanchnic layer of lateral plate mesoderm2.01e-0984
gray matter2.57e-0934
brain grey matter2.57e-0934
telencephalon3.41e-0934
anatomical cluster4.91e-09286
primary circulatory organ6.75e-0927
regional part of telencephalon7.47e-0933
systemic artery8.09e-0933
systemic arterial system8.09e-0933
neurectoderm8.98e-0990
multilaminar epithelium1.14e-0882
multi-tissue structure1.16e-08347
cerebral hemisphere1.63e-0832
organism subdivision1.90e-08365
epithelial tube2.39e-08118
somite3.35e-0883
paraxial mesoderm3.35e-0883
presomitic mesoderm3.35e-0883
presumptive segmental plate3.35e-0883
trunk paraxial mesoderm3.35e-0883
presumptive paraxial mesoderm3.35e-0883
heart6.47e-0824
primitive heart tube6.47e-0824
primary heart field6.47e-0824
anterior lateral plate mesoderm6.47e-0824
heart tube6.47e-0824
heart primordium6.47e-0824
cardiac mesoderm6.47e-0824
cardiogenic plate6.47e-0824
heart rudiment6.47e-0824
regional part of nervous system7.60e-0894
nervous system7.60e-0894
pre-chordal neural plate2.63e-0761
regional part of cerebral cortex3.04e-0722
blood vessel3.16e-0760
epithelial tube open at both ends3.16e-0760
blood vasculature3.16e-0760
vascular cord3.16e-0760


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#2624412.7449317335543.78864877853583e-050.000724030539398909



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.