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|ontology_enrichment_disease=
|ontology_enrichment_disease=
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|ontology_enrichment_uberon=UBERON:0003081!2.23e-20!216;UBERON:0000055!3.62e-18!69;UBERON:0001981!1.77e-16!60;UBERON:0007500!1.77e-16!60;UBERON:0004537!1.77e-16!60;UBERON:0006965!1.77e-16!60;UBERON:0004872!2.17e-15!84;UBERON:0002049!1.35e-13!79;UBERON:0007798!1.35e-13!79;UBERON:0001009!1.58e-13!113;UBERON:0003914!1.74e-13!118;UBERON:0004535!8.89e-13!110;UBERON:0001637!1.21e-12!42;UBERON:0003509!1.21e-12!42;UBERON:0004572!1.21e-12!42;UBERON:0001986!4.09e-11!18;UBERON:0004638!4.09e-11!18;UBERON:0004852!4.09e-11!18;UBERON:0000487!6.21e-11!22;UBERON:0004573!5.52e-10!33;UBERON:0004571!5.52e-10!33;UBERON:0002193!1.10e-09!112;UBERON:0006914!3.03e-08!25;UBERON:0002390!7.54e-08!102;UBERON:0003061!7.54e-08!102;UBERON:0002405!2.43e-07!115;UBERON:0000947!5.56e-07!21;UBERON:0010191!5.56e-07!21;UBERON:0002371!5.87e-07!80;UBERON:0003915!8.98e-07!9;UBERON:0004700!8.98e-07!9;UBERON:0001917!8.98e-07!9
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}}
}}

Revision as of 19:47, 8 August 2012


Full id: C4171_CD14_meningioma_Endothelial_adult_immature_mesothelioma_b



Phase1 CAGE Peaks

Hg19::chr2:201994042..201994070,+p10@CFLAR
Hg19::chr2:201994073..201994085,+p21@CFLAR
Hg19::chr2:201994091..201994109,+p20@CFLAR


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
CD14-positive, CD16-negative classical monocyte4.38e-1742
classical monocyte2.65e-1445
endothelial cell of vascular tree2.87e-1424
lining cell2.91e-1357
barrier cell2.91e-1357
endothelial cell8.41e-1235
blood vessel endothelial cell4.09e-1118
embryonic blood vessel endothelial progenitor cell4.09e-1118
meso-epithelial cell4.45e-1144
macrophage dendritic cell progenitor5.11e-1165
mesodermal cell1.57e-10119
monopoietic cell4.39e-1063
monocyte4.39e-1063
monoblast4.39e-1063
promonocyte4.39e-1063
nongranular leukocyte7.00e-10119
leukocyte1.11e-09140
granulocyte monocyte progenitor cell1.87e-0971
hematopoietic lineage restricted progenitor cell2.25e-09124
myeloid leukocyte5.46e-0976
myeloid lineage restricted progenitor cell4.02e-0870
hematopoietic oligopotent progenitor cell4.74e-08165
hematopoietic multipotent progenitor cell4.74e-08165
hematopoietic cell5.18e-07182
hematopoietic stem cell6.00e-07172
angioblastic mesenchymal cell6.00e-07172
endothelial cell of artery8.98e-079
Uber Anatomy
Ontology termp-valuen
lateral plate mesoderm2.23e-20216
vessel3.62e-1869
blood vessel1.77e-1660
epithelial tube open at both ends1.77e-1660
blood vasculature1.77e-1660
vascular cord1.77e-1660
splanchnic layer of lateral plate mesoderm2.17e-1584
vasculature1.35e-1379
vascular system1.35e-1379
circulatory system1.58e-13113
epithelial tube1.74e-13118
cardiovascular system8.89e-13110
artery1.21e-1242
arterial blood vessel1.21e-1242
arterial system1.21e-1242
endothelium4.09e-1118
blood vessel endothelium4.09e-1118
cardiovascular system endothelium4.09e-1118
simple squamous epithelium6.21e-1122
systemic artery5.52e-1033
systemic arterial system5.52e-1033
hemolymphoid system1.10e-09112
squamous epithelium3.03e-0825
hematopoietic system7.54e-08102
blood island7.54e-08102
immune system2.43e-07115
aorta5.56e-0721
aortic system5.56e-0721
bone marrow5.87e-0780
endothelial tube8.98e-079
arterial system endothelium8.98e-079
endothelium of artery8.98e-079


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.