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|ontology_enrichment_disease=DOID:162!1.76e-24!235;DOID:14566!1.89e-24!239;DOID:0050687!7.92e-14!143;DOID:0050686!2.21e-11!137;DOID:2531!7.77e-11!51;DOID:0060083!7.77e-11!51;DOID:305!5.47e-10!106;DOID:1240!6.53e-09!39;DOID:8692!4.67e-07!31
|ontology_enrichment_disease=DOID:162!1.76e-24!235;DOID:14566!1.89e-24!239;DOID:0050687!7.92e-14!143;DOID:0050686!2.21e-11!137;DOID:2531!7.77e-11!51;DOID:0060083!7.77e-11!51;DOID:305!5.47e-10!106;DOID:1240!6.53e-09!39;DOID:8692!4.67e-07!31
|ontology_enrichment_uberon=UBERON:0003104!1.52e-09!238;UBERON:0009142!1.52e-09!238;UBERON:0000072!1.61e-07!46;UBERON:0002100!2.38e-07!216;UBERON:0004211!2.58e-07!16;UBERON:0001285!2.58e-07!16;UBERON:0007684!2.58e-07!16;UBERON:0003220!2.58e-07!16;UBERON:0004208!2.58e-07!16;UBERON:0005256!4.18e-07!143;UBERON:0000119!4.81e-07!312;UBERON:0008947!7.16e-07!38;UBERON:0003258!7.16e-07!38
|ontology_enrichment_uberon=UBERON:0003104!1.52e-09!238;UBERON:0009142!1.52e-09!238;UBERON:0000072!1.61e-07!46;UBERON:0002100!2.38e-07!216;UBERON:0004211!2.58e-07!16;UBERON:0001285!2.58e-07!16;UBERON:0007684!2.58e-07!16;UBERON:0003220!2.58e-07!16;UBERON:0004208!2.58e-07!16;UBERON:0005256!4.18e-07!143;UBERON:0000119!4.81e-07!312;UBERON:0008947!7.16e-07!38;UBERON:0003258!7.16e-07!38
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}}
}}

Revision as of 19:25, 8 August 2012


Full id: C3766_Alveolar_Renal_chronic_Placental_nonsmall_acute_carcinoid



Phase1 CAGE Peaks

Hg19::chr19:18433875..18433909,-p1@LSM4
Hg19::chr19:18433910..18433944,-p2@LSM4
Hg19::chr7:100303728..100303787,+p1@POP7


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:0005688snRNP U60.00312021664900506
GO:0006396RNA processing0.00445686189516397
GO:0030681multimeric ribonuclease P complex0.00445686189516397
GO:0005655nucleolar ribonuclease P complex0.00445686189516397
GO:0030677ribonuclease P complex0.00445686189516397
GO:0005684U2-dependent spliceosome0.00445686189516397
GO:0004526ribonuclease P activity0.00445686189516397
GO:0004549tRNA-specific ribonuclease activity0.00584920069324615
GO:0044428nuclear part0.0059422257858873
GO:0030529ribonucleoprotein complex0.0059422257858873
GO:0030532small nuclear ribonucleoprotein complex0.00708889649082795
GO:0016891endoribonuclease activity, producing 5'-phosphomonoesters0.00983488969882731
GO:0044452nucleolar part0.00983488969882731
GO:0016893endonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters0.0122482513790345
GO:0004521endoribonuclease activity0.0149613887740454
GO:0008033tRNA processing0.0179172156272548
GO:0004540ribonuclease activity0.0183274711924229
GO:0005681spliceosome0.0240460659124371
GO:0004519endonuclease activity0.0247427641746072
GO:0005730nucleolus0.0256796512216183
GO:0006399tRNA metabolic process0.0293575749978811
GO:0032991macromolecular complex0.0293575749978811
GO:0008380RNA splicing0.0293575749978811
GO:0004518nuclease activity0.0293575749978811
GO:0044446intracellular organelle part0.0293575749978811
GO:0044422organelle part0.0293575749978811
GO:0016070RNA metabolic process0.0293575749978811
GO:0006397mRNA processing0.0303003199967942
GO:0016071mRNA metabolic process0.0366123538767712
GO:0010467gene expression0.0455277092838167



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 cell1.49e-27254
embryonic cell3.07e-21248
animal cell1.16e-18679
eukaryotic cell1.16e-18679
mesodermal cell3.38e-09119
native cell2.20e-08722
ectodermal cell1.08e-0771
squamous epithelial cell1.13e-0762
epithelial cell of nephron2.58e-0716
kidney cell9.47e-0718
kidney epithelial cell9.47e-0718
Uber Anatomy
Ontology termp-valuen
mesenchyme1.52e-09238
entire embryonic mesenchyme1.52e-09238
segment of respiratory tract1.61e-0746
trunk2.38e-07216
nephron epithelium2.58e-0716
nephron2.58e-0716
uriniferous tubule2.58e-0716
metanephric mesenchyme2.58e-0716
nephrogenic mesenchyme2.58e-0716
trunk mesenchyme4.18e-07143
cell layer4.81e-07312
respiratory primordium7.16e-0738
endoderm of foregut7.16e-0738
Disease
Ontology termp-valuen
cancer1.76e-24235
disease of cellular proliferation1.89e-24239
cell type cancer7.92e-14143
organ system cancer2.21e-11137
hematologic cancer7.77e-1151
immune system cancer7.77e-1151
carcinoma5.47e-10106
leukemia6.53e-0939
myeloid leukemia4.67e-0731


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.