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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C2773_mesodermal_basal_bone_Multipotent_osteoclastoma_Fibroblast_amniotic
|full_id=C2773_mesodermal_basal_bone_Multipotent_osteoclastoma_Fibroblast_amniotic
|id=C2773
|id=C2773

Revision as of 15:33, 12 September 2012


Full id: C2773_mesodermal_basal_bone_Multipotent_osteoclastoma_Fibroblast_amniotic



Phase1 CAGE Peaks

Hg19::chr4:115286059..115286076,-p@chr4:115286059..115286076
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Hg19::chr4:115286085..115286091,-p@chr4:115286085..115286091
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Hg19::chr4:115286093..115286110,-p@chr4:115286093..115286110
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Hg19::chr6:132455433..132455444,+p4@ENST00000443303


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
somite2.24e-2283
paraxial mesoderm2.24e-2283
presomitic mesoderm2.24e-2283
presumptive segmental plate2.24e-2283
trunk paraxial mesoderm2.24e-2283
presumptive paraxial mesoderm2.24e-2283
dermomyotome1.97e-1870
skeletal muscle tissue5.35e-1861
striated muscle tissue5.35e-1861
myotome5.35e-1861
muscle tissue1.40e-1763
musculature1.40e-1763
musculature of body1.40e-1763
multilaminar epithelium1.65e-1782
trunk mesenchyme1.93e-16143
splanchnic layer of lateral plate mesoderm3.63e-1584
artery1.48e-1242
arterial blood vessel1.48e-1242
arterial system1.48e-1242
vasculature1.66e-1279
vascular system1.66e-1279
circulatory system1.32e-11113
blood vessel1.75e-1160
epithelial tube open at both ends1.75e-1160
blood vasculature1.75e-1160
vascular cord1.75e-1160
unilaminar epithelium6.57e-11138
vessel1.08e-1069
systemic artery1.25e-1033
systemic arterial system1.25e-1033
cardiovascular system1.28e-10110
smooth muscle tissue3.53e-0915
epithelial tube3.78e-09118
trunk9.74e-09216
blood vessel smooth muscle1.18e-0810
arterial system smooth muscle1.18e-0810
artery smooth muscle tissue1.18e-0810
aorta smooth muscle tissue1.18e-0810
aorta1.50e-0821
aortic system1.50e-0821
primary circulatory organ2.10e-0827
organism subdivision5.56e-08365
organ component layer6.44e-0857
heart3.67e-0724
primitive heart tube3.67e-0724
primary heart field3.67e-0724
anterior lateral plate mesoderm3.67e-0724
heart tube3.67e-0724
heart primordium3.67e-0724
cardiac mesoderm3.67e-0724
cardiogenic plate3.67e-0724
heart rudiment3.67e-0724
cell layer3.89e-07312
multi-tissue structure4.18e-07347
skin of body5.47e-0740
mesenchyme8.46e-07238
entire embryonic mesenchyme8.46e-07238


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.

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