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|ontology_enrichment_disease=DOID:1749!5.46e-07!14
|ontology_enrichment_disease=DOID:1749!5.46e-07!14
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|ontology_enrichment_uberon=UBERON:0001049!3.04e-17!57;UBERON:0005068!3.04e-17!57;UBERON:0006241!3.04e-17!57;UBERON:0007135!3.04e-17!57;UBERON:0001893!2.82e-14!34;UBERON:0002020!4.39e-14!34;UBERON:0003528!4.39e-14!34;UBERON:0001017!5.34e-14!82;UBERON:0002791!8.90e-14!33;UBERON:0001869!1.08e-13!32;UBERON:0000064!1.25e-13!219;UBERON:0002780!2.25e-13!41;UBERON:0001890!2.25e-13!41;UBERON:0006240!2.25e-13!41;UBERON:0002616!4.07e-13!59;UBERON:0007023!6.12e-13!115;UBERON:0005743!8.77e-13!86;UBERON:0003080!9.96e-13!42;UBERON:0004121!3.97e-12!169;UBERON:0000924!6.43e-12!173;UBERON:0006601!6.43e-12!173;UBERON:0000955!9.74e-12!69;UBERON:0006238!9.74e-12!69;UBERON:0000956!2.69e-11!25;UBERON:0000203!2.69e-11!25;UBERON:0003075!2.95e-11!86;UBERON:0007284!2.95e-11!86;UBERON:0002619!6.05e-11!22;UBERON:0000153!6.86e-11!129;UBERON:0007811!6.86e-11!129;UBERON:0002346!7.59e-11!90;UBERON:0000033!1.38e-10!123;UBERON:0001950!3.77e-10!20;UBERON:0000073!1.07e-09!94;UBERON:0001016!1.07e-09!94;UBERON:0003056!3.35e-08!61
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}}

Revision as of 17:05, 8 August 2012


Full id: C1269_serous_Urothelial_clear_Gingival_Renal_choriocarcinoma_Corneal



Phase1 CAGE Peaks

Hg19::chr3:13859846..13859848,-p@chr3:13859846..13859848
-
Hg19::chr3:13921427..13921439,-p5@WNT7A
Hg19::chr3:13921455..13921496,-p2@WNT7A
Hg19::chr3:13921498..13921503,-p6@WNT7A
Hg19::chr3:13921557..13921575,-p1@WNT7A
Hg19::chr3:13921578..13921591,-p3@WNT7A
Hg19::chr3:13921594..13921601,-p4@WNT7A


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>disease_data<br>


Cell Type
Ontology termp-valuen
endo-epithelial cell2.69e-1343
epithelial cell7.01e-10254
endodermal cell1.80e-0959
mature alpha-beta T cell4.03e-0918
alpha-beta T cell4.03e-0918
immature T cell4.03e-0918
mature T cell4.03e-0918
immature alpha-beta T cell4.03e-0918
general ecto-epithelial cell1.53e-0813
respiratory epithelial cell6.15e-0713
Uber Anatomy
Ontology termp-valuen
neural tube3.04e-1757
neural rod3.04e-1757
future spinal cord3.04e-1757
neural keel3.04e-1757
telencephalon2.82e-1434
gray matter4.39e-1434
brain grey matter4.39e-1434
central nervous system5.34e-1482
regional part of telencephalon8.90e-1433
cerebral hemisphere1.08e-1332
organ part1.25e-13219
regional part of forebrain2.25e-1341
forebrain2.25e-1341
future forebrain2.25e-1341
regional part of brain4.07e-1359
adult organism6.12e-13115
anterior neural tube9.96e-1342
ectoderm-derived structure3.97e-12169
ectoderm6.43e-12173
presumptive ectoderm6.43e-12173
brain9.74e-1269
future brain9.74e-1269
cerebral cortex2.69e-1125
pallium2.69e-1125
neural plate2.95e-1186
presumptive neural plate2.95e-1186
regional part of cerebral cortex6.05e-1122
anterior region of body6.86e-11129
craniocervical region6.86e-11129
neurectoderm7.59e-1190
head1.38e-10123
neocortex3.77e-1020
regional part of nervous system1.07e-0994
nervous system1.07e-0994
pre-chordal neural plate3.35e-0861
Disease
Ontology termp-valuen
squamous cell carcinoma5.46e-0714


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.