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Coexpression cluster:C1649: Difference between revisions

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|ontology_enrichment_disease=DOID:305!4.67e-07!106
|ontology_enrichment_disease=DOID:305!4.67e-07!106
|ontology_enrichment_uberon=UBERON:0007023!6.63e-17!115;UBERON:0001049!3.15e-13!57;UBERON:0005068!3.15e-13!57;UBERON:0006241!3.15e-13!57;UBERON:0007135!3.15e-13!57;UBERON:0002020!1.77e-12!34;UBERON:0003528!1.77e-12!34;UBERON:0002619!9.44e-12!22;UBERON:0002791!1.08e-11!33;UBERON:0001950!1.42e-11!20;UBERON:0001893!3.31e-11!34;UBERON:0002616!2.75e-10!59;UBERON:0003075!4.92e-10!86;UBERON:0007284!4.92e-10!86;UBERON:0000033!5.31e-10!123;UBERON:0000956!6.38e-10!25;UBERON:0000203!6.38e-10!25;UBERON:0001871!1.50e-09!7;UBERON:0001869!1.62e-09!32;UBERON:0002780!1.89e-09!41;UBERON:0001890!1.89e-09!41;UBERON:0006240!1.89e-09!41;UBERON:0002346!3.29e-09!90;UBERON:0000955!3.38e-09!69;UBERON:0006238!3.38e-09!69;UBERON:0003080!4.17e-09!42;UBERON:0000153!4.76e-09!129;UBERON:0007811!4.76e-09!129;UBERON:0003135!6.01e-09!11;UBERON:0005743!7.00e-09!86;UBERON:0000477!1.88e-08!286;UBERON:0001017!3.56e-08!82;UBERON:0000073!2.59e-07!94;UBERON:0001016!2.59e-07!94;UBERON:0005904!2.91e-07!4;UBERON:0000064!5.31e-07!219;UBERON:0004111!7.90e-07!241;UBERON:0003056!8.56e-07!61
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}}
}}

Revision as of 17:30, 8 August 2012


Full id: C1649_gastric_small_Wilms_adrenal_rhabdomyosarcoma_cerebellum_mesothelioma



Phase1 CAGE Peaks

Hg19::chr11:90966303..90966313,-p@chr11:90966303..90966313
-
Hg19::chr12:89363898..89363911,+p@chr12:89363898..89363911
+
Hg19::chr4:139026744..139026753,+p2@ENST00000514752
Hg19::chr6:125541245..125541259,+p16@TPD52L1
Hg19::chr8:16860160..16860190,-p2@FGF20


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:0000086G2/M transition of mitotic cell cycle0.0350205981682738
GO:0048471perinuclear region of cytoplasm0.0432046934374315
GO:0051329interphase of mitotic cell cycle0.0432046934374315
GO:0051325interphase0.0432046934374315
GO:0046982protein heterodimerization activity0.0432046934374315



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><br>uberon_data<br>disease_data<br>


Uber Anatomy
Ontology termp-valuen
adult organism6.63e-17115
neural tube3.15e-1357
neural rod3.15e-1357
future spinal cord3.15e-1357
neural keel3.15e-1357
gray matter1.77e-1234
brain grey matter1.77e-1234
regional part of cerebral cortex9.44e-1222
regional part of telencephalon1.08e-1133
neocortex1.42e-1120
telencephalon3.31e-1134
regional part of brain2.75e-1059
neural plate4.92e-1086
presumptive neural plate4.92e-1086
head5.31e-10123
cerebral cortex6.38e-1025
pallium6.38e-1025
temporal lobe1.50e-097
cerebral hemisphere1.62e-0932
regional part of forebrain1.89e-0941
forebrain1.89e-0941
future forebrain1.89e-0941
neurectoderm3.29e-0990
brain3.38e-0969
future brain3.38e-0969
anterior neural tube4.17e-0942
anterior region of body4.76e-09129
craniocervical region4.76e-09129
male reproductive organ6.01e-0911
anatomical cluster1.88e-08286
central nervous system3.56e-0882
regional part of nervous system2.59e-0794
nervous system2.59e-0794
duct of male reproductive system2.91e-074
organ part5.31e-07219
anatomical conduit7.90e-07241
pre-chordal neural plate8.56e-0761
Disease
Ontology termp-valuen
carcinoma4.67e-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)

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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.