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|ontology_enrichment_disease=DOID:14566!7.15e-33!239;DOID:162!7.44e-33!235;DOID:2531!6.83e-19!51;DOID:0060083!6.83e-19!51;DOID:0050686!6.83e-17!137;DOID:1240!4.38e-15!39;DOID:0050687!6.12e-15!143;DOID:305!9.95e-14!106;DOID:8692!9.93e-13!31
|ontology_enrichment_disease=DOID:14566!7.15e-33!239;DOID:162!7.44e-33!235;DOID:2531!6.83e-19!51;DOID:0060083!6.83e-19!51;DOID:0050686!6.83e-17!137;DOID:1240!4.38e-15!39;DOID:0050687!6.12e-15!143;DOID:305!9.95e-14!106;DOID:8692!9.93e-13!31
|ontology_enrichment_uberon=UBERON:0003104!2.15e-11!238;UBERON:0009142!2.15e-11!238;UBERON:0002100!6.38e-08!216;UBERON:0000072!1.96e-07!46;UBERON:0008947!4.12e-07!38;UBERON:0003258!4.12e-07!38;UBERON:0001737!4.48e-07!9
|ontology_enrichment_uberon=UBERON:0003104!2.15e-11!238;UBERON:0009142!2.15e-11!238;UBERON:0002100!6.38e-08!216;UBERON:0000072!1.96e-07!46;UBERON:0008947!4.12e-07!38;UBERON:0003258!4.12e-07!38;UBERON:0001737!4.48e-07!9
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}}
}}

Revision as of 19:04, 8 August 2012


Full id: C3300_acute_lymphoma_chronic_giant_Fibroblast_hereditary_diffuse



Phase1 CAGE Peaks

Hg19::chr12:56498312..56498413,+p1@PA2G4
Hg19::chr1:19578280..19578334,+p1@MRTO4
Hg19::chr5:175815565..175815615,-p1@NOP16


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:0042254ribosome biogenesis and assembly0.000846401070932352
GO:0022613ribonucleoprotein complex biogenesis and assembly0.00208896775368931
GO:0004239methionyl aminopeptidase activity0.0188359938245719
GO:0050897cobalt ion binding0.0211886214040835
GO:0006996organelle organization and biogenesis0.0322637551551224
GO:0006364rRNA processing0.0488047959039513
GO:0016072rRNA metabolic process0.0488047959039513
GO:0004177aminopeptidase activity0.0488047959039513



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
epithelial cell7.29e-29254
animal cell2.55e-27679
eukaryotic cell2.55e-27679
embryonic cell1.35e-19248
native cell4.59e-16722
squamous epithelial cell1.26e-1162
somatic cell1.85e-08591
mesodermal cell3.74e-08119
non-terminally differentiated cell5.17e-07180
Uber Anatomy
Ontology termp-valuen
mesenchyme2.15e-11238
entire embryonic mesenchyme2.15e-11238
trunk6.38e-08216
segment of respiratory tract1.96e-0746
respiratory primordium4.12e-0738
endoderm of foregut4.12e-0738
larynx4.48e-079
Disease
Ontology termp-valuen
disease of cellular proliferation7.15e-33239
cancer7.44e-33235
hematologic cancer6.83e-1951
immune system cancer6.83e-1951
organ system cancer6.83e-17137
leukemia4.38e-1539
cell type cancer6.12e-15143
carcinoma9.95e-14106
myeloid leukemia9.93e-1331


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.