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Coexpression cluster:C2111: Difference between revisions

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|ontology_enrichment_disease=DOID:1749!4.14e-10!14
|ontology_enrichment_disease=DOID:1749!4.14e-10!14
|ontology_enrichment_uberon=UBERON:0007023!1.76e-27!115;UBERON:0001869!1.92e-22!32;UBERON:0003080!6.89e-22!42;UBERON:0001893!9.77e-22!34;UBERON:0002780!1.92e-21!41;UBERON:0001890!1.92e-21!41;UBERON:0006240!1.92e-21!41;UBERON:0002791!9.51e-21!33;UBERON:0002619!2.37e-20!22;UBERON:0001950!5.65e-19!20;UBERON:0002020!1.42e-18!34;UBERON:0003528!1.42e-18!34;UBERON:0000153!1.38e-17!129;UBERON:0007811!1.38e-17!129;UBERON:0000956!6.71e-17!25;UBERON:0000203!6.71e-17!25;UBERON:0000033!1.29e-16!123;UBERON:0003056!1.20e-15!61;UBERON:0004121!3.34e-15!169;UBERON:0001049!3.73e-15!57;UBERON:0005068!3.73e-15!57;UBERON:0006241!3.73e-15!57;UBERON:0007135!3.73e-15!57;UBERON:0001017!1.44e-14!82;UBERON:0000955!2.49e-14!69;UBERON:0006238!2.49e-14!69;UBERON:0000924!2.85e-14!173;UBERON:0006601!2.85e-14!173;UBERON:0005743!4.67e-14!86;UBERON:0002616!1.84e-13!59;UBERON:0000073!6.63e-12!94;UBERON:0001016!6.63e-12!94;UBERON:0003075!2.64e-10!86;UBERON:0007284!2.64e-10!86;UBERON:0004119!3.55e-10!169;UBERON:0000925!3.55e-10!169;UBERON:0006595!3.55e-10!169;UBERON:0000064!2.88e-09!219;UBERON:0002346!3.06e-09!90;UBERON:0000161!9.09e-09!35;UBERON:0001871!9.59e-09!7;UBERON:0001004!2.00e-08!72;UBERON:0000166!2.27e-08!21;UBERON:0001007!2.40e-08!155;UBERON:0001555!2.40e-08!155;UBERON:0007026!2.40e-08!155;UBERON:0000200!1.02e-07!6;UBERON:0004921!2.09e-07!129;UBERON:0004185!2.09e-07!129;UBERON:0002420!7.24e-07!9;UBERON:0007245!7.24e-07!9;UBERON:0010009!7.24e-07!9;UBERON:0010011!7.24e-07!9;UBERON:0000454!7.24e-07!9;UBERON:0000062!7.65e-07!511
|ontology_enrichment_uberon=UBERON:0007023!1.76e-27!115;UBERON:0001869!1.92e-22!32;UBERON:0003080!6.89e-22!42;UBERON:0001893!9.77e-22!34;UBERON:0002780!1.92e-21!41;UBERON:0001890!1.92e-21!41;UBERON:0006240!1.92e-21!41;UBERON:0002791!9.51e-21!33;UBERON:0002619!2.37e-20!22;UBERON:0001950!5.65e-19!20;UBERON:0002020!1.42e-18!34;UBERON:0003528!1.42e-18!34;UBERON:0000153!1.38e-17!129;UBERON:0007811!1.38e-17!129;UBERON:0000956!6.71e-17!25;UBERON:0000203!6.71e-17!25;UBERON:0000033!1.29e-16!123;UBERON:0003056!1.20e-15!61;UBERON:0004121!3.34e-15!169;UBERON:0001049!3.73e-15!57;UBERON:0005068!3.73e-15!57;UBERON:0006241!3.73e-15!57;UBERON:0007135!3.73e-15!57;UBERON:0001017!1.44e-14!82;UBERON:0000955!2.49e-14!69;UBERON:0006238!2.49e-14!69;UBERON:0000924!2.85e-14!173;UBERON:0006601!2.85e-14!173;UBERON:0005743!4.67e-14!86;UBERON:0002616!1.84e-13!59;UBERON:0000073!6.63e-12!94;UBERON:0001016!6.63e-12!94;UBERON:0003075!2.64e-10!86;UBERON:0007284!2.64e-10!86;UBERON:0004119!3.55e-10!169;UBERON:0000925!3.55e-10!169;UBERON:0006595!3.55e-10!169;UBERON:0000064!2.88e-09!219;UBERON:0002346!3.06e-09!90;UBERON:0000161!9.09e-09!35;UBERON:0001871!9.59e-09!7;UBERON:0001004!2.00e-08!72;UBERON:0000166!2.27e-08!21;UBERON:0001007!2.40e-08!155;UBERON:0001555!2.40e-08!155;UBERON:0007026!2.40e-08!155;UBERON:0000200!1.02e-07!6;UBERON:0004921!2.09e-07!129;UBERON:0004185!2.09e-07!129;UBERON:0002420!7.24e-07!9;UBERON:0007245!7.24e-07!9;UBERON:0010009!7.24e-07!9;UBERON:0010011!7.24e-07!9;UBERON:0000454!7.24e-07!9;UBERON:0000062!7.65e-07!511
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}}
}}

Revision as of 18:00, 8 August 2012


Full id: C2111_retinoblastoma_insula_medial_occipital_parietal_brain_temporal



Phase1 CAGE Peaks

Hg19::chr11:128894012..128894023,-p11@ARHGAP32
Hg19::chr11:128894024..128894050,-p3@ARHGAP32
Hg19::chr19:35633194..35633212,+p@chr19:35633194..35633212
+
Hg19::chr22:43820905..43820917,+p10@MPPED1


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 cell1.02e-1143
endodermal cell8.23e-0859
epithelial cell of alimentary canal1.52e-0721
Uber Anatomy
Ontology termp-valuen
adult organism1.76e-27115
cerebral hemisphere1.92e-2232
anterior neural tube6.89e-2242
telencephalon9.77e-2234
regional part of forebrain1.92e-2141
forebrain1.92e-2141
future forebrain1.92e-2141
regional part of telencephalon9.51e-2133
regional part of cerebral cortex2.37e-2022
neocortex5.65e-1920
gray matter1.42e-1834
brain grey matter1.42e-1834
anterior region of body1.38e-17129
craniocervical region1.38e-17129
cerebral cortex6.71e-1725
pallium6.71e-1725
head1.29e-16123
pre-chordal neural plate1.20e-1561
ectoderm-derived structure3.34e-15169
neural tube3.73e-1557
neural rod3.73e-1557
future spinal cord3.73e-1557
neural keel3.73e-1557
central nervous system1.44e-1482
brain2.49e-1469
future brain2.49e-1469
ectoderm2.85e-14173
presumptive ectoderm2.85e-14173
regional part of brain1.84e-1359
regional part of nervous system6.63e-1294
nervous system6.63e-1294
neural plate2.64e-1086
presumptive neural plate2.64e-1086
endoderm-derived structure3.55e-10169
endoderm3.55e-10169
presumptive endoderm3.55e-10169
organ part2.88e-09219
neurectoderm3.06e-0990
orifice9.09e-0935
temporal lobe9.59e-097
respiratory system2.00e-0872
oral opening2.27e-0821
digestive system2.40e-08155
digestive tract2.40e-08155
primitive gut2.40e-08155
gyrus1.02e-076
subdivision of digestive tract2.09e-07129
endodermal part of digestive tract2.09e-07129
basal ganglion7.24e-079
nuclear complex of neuraxis7.24e-079
aggregate regional part of brain7.24e-079
collection of basal ganglia7.24e-079
cerebral subcortex7.24e-079
organ7.65e-07511
Disease
Ontology termp-valuen
squamous cell carcinoma4.14e-1014


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.