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Coexpression cluster:C1323: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
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}}
}}

Revision as of 17:09, 8 August 2012


Full id: C1323_heart_Lymphatic_left_mesenchymal_skeletal_bone_Adipocyte



Phase1 CAGE Peaks

Hg19::chr10:92672040..92672054,-p@chr10:92672040..92672054
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Hg19::chr10:92675596..92675615,-p@chr10:92675596..92675615
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Hg19::chr10:92679951..92679969,-p@chr10:92679951..92679969
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Hg19::chr10:92679988..92680056,-p@chr10:92679988..92680056
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Hg19::chr10:92680062..92680080,-p@chr10:92680062..92680080
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Hg19::chr10:92680836..92680853,-p1@ANKRD1


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>


Cell Type
Ontology termp-valuen
mesodermal cell5.98e-30119
lining cell5.36e-1857
barrier cell5.36e-1857
embryonic cell1.01e-16248
non-terminally differentiated cell2.60e-16180
endothelial cell of vascular tree1.77e-1424
meso-epithelial cell1.48e-1244
endothelial cell5.24e-1235
muscle precursor cell2.01e-1157
myoblast2.01e-1157
multi-potent skeletal muscle stem cell2.01e-1157
contractile cell4.91e-1159
blood vessel endothelial cell1.00e-1018
embryonic blood vessel endothelial progenitor cell1.00e-1018
epithelial cell1.57e-10254
muscle cell5.33e-1054
electrically responsive cell5.72e-0960
electrically active cell5.72e-0960
vascular associated smooth muscle cell5.67e-0832
mesothelial cell1.01e-0719
squamous epithelial cell1.58e-0762
fibroblast4.25e-0775
smooth muscle cell4.34e-0742
smooth muscle myoblast4.34e-0742
Uber Anatomy
Ontology termp-valuen
epithelial tube4.94e-28118
vasculature6.55e-2579
vascular system6.55e-2579
unilaminar epithelium1.75e-23138
vessel2.73e-2369
splanchnic layer of lateral plate mesoderm4.87e-2384
circulatory system2.37e-20113
blood vessel3.40e-2060
epithelial tube open at both ends3.40e-2060
blood vasculature3.40e-2060
vascular cord3.40e-2060
cardiovascular system8.60e-19110
trunk mesenchyme2.38e-18143
mesenchyme5.16e-18238
entire embryonic mesenchyme5.16e-18238
trunk1.45e-17216
cell layer4.58e-16312
epithelium1.28e-15309
multi-cellular organism2.10e-14659
skeletal muscle tissue3.89e-1361
striated muscle tissue3.89e-1361
myotome3.89e-1361
mesoderm5.04e-13448
mesoderm-derived structure5.04e-13448
presumptive mesoderm5.04e-13448
dermomyotome5.36e-1370
muscle tissue2.78e-1263
musculature2.78e-1263
musculature of body2.78e-1263
multi-tissue structure5.31e-12347
artery6.26e-1242
arterial blood vessel6.26e-1242
arterial system6.26e-1242
anatomical cluster7.48e-12286
compound organ1.81e-1169
anatomical conduit2.86e-11241
multilaminar epithelium3.12e-1182
somite4.23e-1183
paraxial mesoderm4.23e-1183
presomitic mesoderm4.23e-1183
presumptive segmental plate4.23e-1183
trunk paraxial mesoderm4.23e-1183
presumptive paraxial mesoderm4.23e-1183
endothelium1.00e-1018
blood vessel endothelium1.00e-1018
cardiovascular system endothelium1.00e-1018
simple squamous epithelium1.26e-1022
anatomical system1.96e-10625
anatomical group3.29e-10626
organism subdivision5.03e-10365
squamous epithelium5.59e-1025
tube1.27e-09194
primary circulatory organ2.29e-0927
abdominal segment of trunk2.05e-0861
abdomen2.05e-0861
systemic artery3.67e-0833
systemic arterial system3.67e-0833
subdivision of trunk6.25e-08113
heart1.07e-0724
primitive heart tube1.07e-0724
primary heart field1.07e-0724
anterior lateral plate mesoderm1.07e-0724
heart tube1.07e-0724
heart primordium1.07e-0724
cardiac mesoderm1.07e-0724
cardiogenic plate1.07e-0724
heart rudiment1.07e-0724


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.