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|ontology_enrichment_disease=DOID:305!1.83e-07!106
|ontology_enrichment_disease=DOID:305!1.83e-07!106
|ontology_enrichment_uberon=UBERON:0001004!1.39e-08!72;UBERON:0004119!1.84e-08!169;UBERON:0000925!1.84e-08!169;UBERON:0006595!1.84e-08!169;UBERON:0000065!3.62e-07!53
|ontology_enrichment_uberon=UBERON:0001004!1.39e-08!72;UBERON:0004119!1.84e-08!169;UBERON:0000925!1.84e-08!169;UBERON:0006595!1.84e-08!169;UBERON:0000065!3.62e-07!53
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}}
}}

Revision as of 18:00, 8 August 2012


Full id: C2101_adult_B_xeroderma_lymphoma_signet_appendix_tonsil



Phase1 CAGE Peaks

Hg19::chr11:119622609..119622621,+p@chr11:119622609..119622621
+
Hg19::chr11:119622634..119622668,+p@chr11:119622634..119622668
+
Hg19::chr17:39928110..39928152,-p5@JUP
Hg19::chr1:25255329..25255339,-p21@RUNX3


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


GO IDGO nameFDR corrected p-value
GO:0005916fascia adherens0.014008857951139
GO:0009898internal side of plasma membrane0.014008857951139
GO:0030057desmosome0.014008857951139
GO:0050680negative regulation of epithelial cell proliferation0.014008857951139
GO:0005913cell-cell adherens junction0.014008857951139
GO:0030018Z disc0.014008857951139
GO:0031674I band0.014580004135363
GO:0050678regulation of epithelial cell proliferation0.022007762260344
GO:0050673epithelial cell proliferation0.022007762260344
GO:0014704intercalated disc0.0249241607803606
GO:0030017sarcomere0.0249241607803606
GO:0030016myofibril0.0249241607803606
GO:0005912adherens junction0.0249241607803606
GO:0044449contractile fiber part0.0255973422701364
GO:0043292contractile fiber0.0255973422701364
GO:0043296apical junction complex0.0370325943749413
GO:0016327apicolateral plasma membrane0.0370325943749413



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>disease_data<br>


Cell Type
Ontology termp-valuen
lymphocyte of B lineage2.61e-1624
pro-B cell2.61e-1624
lymphocyte7.03e-1253
common lymphoid progenitor7.03e-1253
lymphoid lineage restricted progenitor cell1.73e-1152
epithelial cell2.06e-11254
endo-epithelial cell7.69e-1143
B cell2.64e-0914
respiratory epithelial cell5.73e-0713
endodermal cell6.87e-0759
Uber Anatomy
Ontology termp-valuen
respiratory system1.39e-0872
endoderm-derived structure1.84e-08169
endoderm1.84e-08169
presumptive endoderm1.84e-08169
respiratory tract3.62e-0753
Disease
Ontology termp-valuen
carcinoma1.83e-07106


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.