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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0003081!3.80e-21!216;UBERON:0004535!4.91e-14!110;UBERON:0001009!4.02e-13!113;UBERON:0000055!8.40e-12!69;UBERON:0004872!2.24e-11!84;UBERON:0001981!5.24e-11!60;UBERON:0007500!5.24e-11!60;UBERON:0004537!5.24e-11!60;UBERON:0006965!5.24e-11!60;UBERON:0002049!1.11e-10!79;UBERON:0007798!1.11e-10!79;UBERON:0001637!1.13e-10!42;UBERON:0003509!1.13e-10!42;UBERON:0004572!1.13e-10!42;UBERON:0003914!2.21e-10!118;UBERON:0000926!4.01e-09!448;UBERON:0004120!4.01e-09!448;UBERON:0006603!4.01e-09!448;UBERON:0004211!2.75e-07!16;UBERON:0001285!2.75e-07!16;UBERON:0007684!2.75e-07!16;UBERON:0003220!2.75e-07!16;UBERON:0004208!2.75e-07!16
|ontology_enrichment_uberon=UBERON:0003081!3.80e-21!216;UBERON:0004535!4.91e-14!110;UBERON:0001009!4.02e-13!113;UBERON:0000055!8.40e-12!69;UBERON:0004872!2.24e-11!84;UBERON:0001981!5.24e-11!60;UBERON:0007500!5.24e-11!60;UBERON:0004537!5.24e-11!60;UBERON:0006965!5.24e-11!60;UBERON:0002049!1.11e-10!79;UBERON:0007798!1.11e-10!79;UBERON:0001637!1.13e-10!42;UBERON:0003509!1.13e-10!42;UBERON:0004572!1.13e-10!42;UBERON:0003914!2.21e-10!118;UBERON:0000926!4.01e-09!448;UBERON:0004120!4.01e-09!448;UBERON:0006603!4.01e-09!448;UBERON:0004211!2.75e-07!16;UBERON:0001285!2.75e-07!16;UBERON:0007684!2.75e-07!16;UBERON:0003220!2.75e-07!16;UBERON:0004208!2.75e-07!16
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}}
}}

Revision as of 19:31, 8 August 2012


Full id: C3888_Alveolar_Whole_Neutrophils_Eosinophils_mesothelioma_Renal_Bronchial



Phase1 CAGE Peaks

Hg19::chr1:159895266..159895275,-p2@TAGLN2
Hg19::chr1:159895286..159895305,-p1@CCDC19
p1@TAGLN2
Hg19::chr8:107710288..107710306,-p1@TAGLN2P1


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
animal cell8.48e-39679
eukaryotic cell8.48e-39679
native cell1.39e-37722
somatic cell1.06e-33591
mesodermal cell3.83e-14119
squamous epithelial cell1.98e-1062
epithelial cell2.90e-10254
embryonic cell4.34e-10248
lining cell1.45e-0957
barrier cell1.45e-0957
somatic stem cell2.05e-09436
multi fate stem cell1.14e-08430
stem cell1.57e-08444
CD14-positive, CD16-negative classical monocyte1.03e-0742
kidney cell2.14e-0718
kidney epithelial cell2.14e-0718
epithelial cell of nephron2.75e-0716
vascular associated smooth muscle cell4.15e-0732
Uber Anatomy
Ontology termp-valuen
lateral plate mesoderm3.80e-21216
cardiovascular system4.91e-14110
circulatory system4.02e-13113
vessel8.40e-1269
splanchnic layer of lateral plate mesoderm2.24e-1184
blood vessel5.24e-1160
epithelial tube open at both ends5.24e-1160
blood vasculature5.24e-1160
vascular cord5.24e-1160
vasculature1.11e-1079
vascular system1.11e-1079
artery1.13e-1042
arterial blood vessel1.13e-1042
arterial system1.13e-1042
epithelial tube2.21e-10118
mesoderm4.01e-09448
mesoderm-derived structure4.01e-09448
presumptive mesoderm4.01e-09448
nephron epithelium2.75e-0716
nephron2.75e-0716
uriniferous tubule2.75e-0716
metanephric mesenchyme2.75e-0716
nephrogenic mesenchyme2.75e-0716


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)

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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.