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Coexpression cluster:C2261: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!8.31e-65!115;UBERON:0001049!1.21e-23!57;UBERON:0005068!1.21e-23!57;UBERON:0006241!1.21e-23!57;UBERON:0007135!1.21e-23!57;UBERON:0002616!9.91e-21!59;UBERON:0001017!1.82e-19!82;UBERON:0004111!4.02e-19!241;UBERON:0005743!8.50e-19!86;UBERON:0000955!9.84e-19!69;UBERON:0006238!9.84e-19!69;UBERON:0003080!9.95e-19!42;UBERON:0000477!4.20e-18!286;UBERON:0002780!6.60e-18!41;UBERON:0001890!6.60e-18!41;UBERON:0006240!6.60e-18!41;UBERON:0000025!1.73e-17!194;UBERON:0003075!2.93e-17!86;UBERON:0007284!2.93e-17!86;UBERON:0000073!9.47e-17!94;UBERON:0001016!9.47e-17!94;UBERON:0002346!2.63e-16!90;UBERON:0001893!1.57e-13!34;UBERON:0002020!1.80e-13!34;UBERON:0003528!1.80e-13!34;UBERON:0002619!2.83e-13!22;UBERON:0002791!6.69e-13!33;UBERON:0001869!2.03e-12!32;UBERON:0001950!3.20e-12!20;UBERON:0000483!6.86e-12!309;UBERON:0000119!1.89e-11!312;UBERON:0000468!4.03e-11!659;UBERON:0000153!4.49e-11!129;UBERON:0007811!4.49e-11!129;UBERON:0000956!7.06e-11!25;UBERON:0000203!7.06e-11!25;UBERON:0000467!1.01e-10!625;UBERON:0000480!1.31e-10!626;UBERON:0003056!4.03e-10!61;UBERON:0000033!1.59e-09!123;UBERON:0004121!1.90e-08!169;UBERON:0000922!2.67e-08!612;UBERON:0000481!3.05e-08!347;UBERON:0000924!3.75e-08!173;UBERON:0006601!3.75e-08!173;UBERON:0002050!7.73e-08!605;UBERON:0005423!7.73e-08!605;UBERON:0000923!1.68e-07!604;UBERON:0005291!1.68e-07!604;UBERON:0006598!1.68e-07!604;UBERON:0002532!1.68e-07!604;UBERON:0002298!7.93e-07!8
|ontology_enrichment_uberon=UBERON:0007023!8.31e-65!115;UBERON:0001049!1.21e-23!57;UBERON:0005068!1.21e-23!57;UBERON:0006241!1.21e-23!57;UBERON:0007135!1.21e-23!57;UBERON:0002616!9.91e-21!59;UBERON:0001017!1.82e-19!82;UBERON:0004111!4.02e-19!241;UBERON:0005743!8.50e-19!86;UBERON:0000955!9.84e-19!69;UBERON:0006238!9.84e-19!69;UBERON:0003080!9.95e-19!42;UBERON:0000477!4.20e-18!286;UBERON:0002780!6.60e-18!41;UBERON:0001890!6.60e-18!41;UBERON:0006240!6.60e-18!41;UBERON:0000025!1.73e-17!194;UBERON:0003075!2.93e-17!86;UBERON:0007284!2.93e-17!86;UBERON:0000073!9.47e-17!94;UBERON:0001016!9.47e-17!94;UBERON:0002346!2.63e-16!90;UBERON:0001893!1.57e-13!34;UBERON:0002020!1.80e-13!34;UBERON:0003528!1.80e-13!34;UBERON:0002619!2.83e-13!22;UBERON:0002791!6.69e-13!33;UBERON:0001869!2.03e-12!32;UBERON:0001950!3.20e-12!20;UBERON:0000483!6.86e-12!309;UBERON:0000119!1.89e-11!312;UBERON:0000468!4.03e-11!659;UBERON:0000153!4.49e-11!129;UBERON:0007811!4.49e-11!129;UBERON:0000956!7.06e-11!25;UBERON:0000203!7.06e-11!25;UBERON:0000467!1.01e-10!625;UBERON:0000480!1.31e-10!626;UBERON:0003056!4.03e-10!61;UBERON:0000033!1.59e-09!123;UBERON:0004121!1.90e-08!169;UBERON:0000922!2.67e-08!612;UBERON:0000481!3.05e-08!347;UBERON:0000924!3.75e-08!173;UBERON:0006601!3.75e-08!173;UBERON:0002050!7.73e-08!605;UBERON:0005423!7.73e-08!605;UBERON:0000923!1.68e-07!604;UBERON:0005291!1.68e-07!604;UBERON:0006598!1.68e-07!604;UBERON:0002532!1.68e-07!604;UBERON:0002298!7.93e-07!8
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}}
}}

Revision as of 18:08, 8 August 2012


Full id: C2261_lung_smooth_aorta_bladder_heart_adipose_penis



Phase1 CAGE Peaks

Hg19::chr13:32828284..32828380,+p5@FRY
Hg19::chr13:32828389..32828409,+p13@FRY
Hg19::chr13:32828411..32828428,+p19@FRY
Hg19::chr6:76203532..76203548,-p3@FILIP1


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><br>


Cell Type
Ontology termp-valuen
endothelial cell of vascular tree9.88e-1024
Uber Anatomy
Ontology termp-valuen
adult organism8.31e-65115
neural tube1.21e-2357
neural rod1.21e-2357
future spinal cord1.21e-2357
neural keel1.21e-2357
regional part of brain9.91e-2159
central nervous system1.82e-1982
anatomical conduit4.02e-19241
brain9.84e-1969
future brain9.84e-1969
anterior neural tube9.95e-1942
anatomical cluster4.20e-18286
regional part of forebrain6.60e-1841
forebrain6.60e-1841
future forebrain6.60e-1841
tube1.73e-17194
neural plate2.93e-1786
presumptive neural plate2.93e-1786
regional part of nervous system9.47e-1794
nervous system9.47e-1794
neurectoderm2.63e-1690
telencephalon1.57e-1334
gray matter1.80e-1334
brain grey matter1.80e-1334
regional part of cerebral cortex2.83e-1322
regional part of telencephalon6.69e-1333
cerebral hemisphere2.03e-1232
neocortex3.20e-1220
epithelium6.86e-12309
cell layer1.89e-11312
multi-cellular organism4.03e-11659
anterior region of body4.49e-11129
craniocervical region4.49e-11129
cerebral cortex7.06e-1125
pallium7.06e-1125
anatomical system1.01e-10625
anatomical group1.31e-10626
pre-chordal neural plate4.03e-1061
head1.59e-09123
ectoderm-derived structure1.90e-08169
embryo2.67e-08612
multi-tissue structure3.05e-08347
ectoderm3.75e-08173
presumptive ectoderm3.75e-08173
embryonic structure7.73e-08605
developing anatomical structure7.73e-08605
germ layer1.68e-07604
embryonic tissue1.68e-07604
presumptive structure1.68e-07604
epiblast (generic)1.68e-07604
brainstem7.93e-078


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.