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Coexpression cluster:C2183: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0001016!1.79e-35!89;UBERON:0001017!3.25e-34!81;UBERON:0001049!1.95e-31!56;UBERON:0005068!1.95e-31!56;UBERON:0006241!1.95e-31!56;UBERON:0007135!1.95e-31!56;UBERON:0000073!1.09e-30!53;UBERON:0002616!1.09e-30!53;UBERON:0000955!2.22e-29!68;UBERON:0006238!2.22e-29!68;UBERON:0002780!1.62e-28!41;UBERON:0001890!1.62e-28!41;UBERON:0003080!1.62e-28!41;UBERON:0006240!1.62e-28!41;UBERON:0002346!1.49e-23!86;UBERON:0003075!1.63e-23!82;UBERON:0007284!1.63e-23!82;UBERON:0003528!6.17e-23!34;UBERON:0002020!6.17e-23!34;UBERON:0001893!9.34e-23!34;UBERON:0001869!2.84e-21!32;UBERON:0002791!2.98e-21!32;UBERON:0003056!9.23e-21!61;UBERON:0002619!2.65e-19!22;UBERON:0010371!5.03e-19!104;UBERON:0000956!1.56e-17!25;UBERON:0000203!1.56e-17!25;UBERON:0001950!2.12e-17!20;UBERON:0004121!4.41e-17!171;UBERON:0000924!4.41e-17!171;UBERON:0006601!4.41e-17!171;UBERON:0007023!1.25e-13!114;UBERON:0011216!3.87e-13!223;UBERON:0010314!3.49e-12!132;UBERON:0000025!2.21e-07!192;UBERON:0001894!3.03e-07!7;UBERON:0006222!3.03e-07!7;UBERON:0002420!5.42e-07!9;UBERON:0007245!5.42e-07!9;UBERON:0010009!5.42e-07!9;UBERON:0010011!5.42e-07!9;UBERON:0000454!5.42e-07!9;UBERON:0000125!7.55e-07!9;UBERON:0002308!7.55e-07!9
|ontology_enrichment_uberon=UBERON:0001016!1.79e-35!89;UBERON:0001017!3.25e-34!81;UBERON:0001049!1.95e-31!56;UBERON:0005068!1.95e-31!56;UBERON:0006241!1.95e-31!56;UBERON:0007135!1.95e-31!56;UBERON:0000073!1.09e-30!53;UBERON:0002616!1.09e-30!53;UBERON:0000955!2.22e-29!68;UBERON:0006238!2.22e-29!68;UBERON:0002780!1.62e-28!41;UBERON:0001890!1.62e-28!41;UBERON:0003080!1.62e-28!41;UBERON:0006240!1.62e-28!41;UBERON:0002346!1.49e-23!86;UBERON:0003075!1.63e-23!82;UBERON:0007284!1.63e-23!82;UBERON:0003528!6.17e-23!34;UBERON:0002020!6.17e-23!34;UBERON:0001893!9.34e-23!34;UBERON:0001869!2.84e-21!32;UBERON:0002791!2.98e-21!32;UBERON:0003056!9.23e-21!61;UBERON:0002619!2.65e-19!22;UBERON:0010371!5.03e-19!104;UBERON:0000956!1.56e-17!25;UBERON:0000203!1.56e-17!25;UBERON:0001950!2.12e-17!20;UBERON:0004121!4.41e-17!171;UBERON:0000924!4.41e-17!171;UBERON:0006601!4.41e-17!171;UBERON:0007023!1.25e-13!114;UBERON:0011216!3.87e-13!223;UBERON:0010314!3.49e-12!132;UBERON:0000025!2.21e-07!192;UBERON:0001894!3.03e-07!7;UBERON:0006222!3.03e-07!7;UBERON:0002420!5.42e-07!9;UBERON:0007245!5.42e-07!9;UBERON:0010009!5.42e-07!9;UBERON:0010011!5.42e-07!9;UBERON:0000454!5.42e-07!9;UBERON:0000125!7.55e-07!9;UBERON:0002308!7.55e-07!9
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}}
}}

Revision as of 15:20, 26 November 2012


Full id: C2183_pineal_parietal_temporal_cerebellum_hippocampus_middle_Cardiac



Phase1 CAGE Peaks

Hg19::chr12:109293077..109293088,-p@chr12:109293077..109293088
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Hg19::chr16:67210038..67210055,-p@chr16:67210038..67210055
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Hg19::chr16:67210067..67210086,-p@chr16:67210067..67210086
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Hg19::chr1:57889939..57889948,-p13@DAB1


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><br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
nervous system1.79e-3589
central nervous system3.25e-3481
neural tube1.95e-3156
neural rod1.95e-3156
future spinal cord1.95e-3156
neural keel1.95e-3156
regional part of nervous system1.09e-3053
regional part of brain1.09e-3053
brain2.22e-2968
future brain2.22e-2968
regional part of forebrain1.62e-2841
forebrain1.62e-2841
anterior neural tube1.62e-2841
future forebrain1.62e-2841
neurectoderm1.49e-2386
neural plate1.63e-2382
presumptive neural plate1.63e-2382
brain grey matter6.17e-2334
gray matter6.17e-2334
telencephalon9.34e-2334
cerebral hemisphere2.84e-2132
regional part of telencephalon2.98e-2132
pre-chordal neural plate9.23e-2161
regional part of cerebral cortex2.65e-1922
ecto-epithelium5.03e-19104
cerebral cortex1.56e-1725
pallium1.56e-1725
neocortex2.12e-1720
ectoderm-derived structure4.41e-17171
ectoderm4.41e-17171
presumptive ectoderm4.41e-17171
adult organism1.25e-13114
organ system subdivision3.87e-13223
structure with developmental contribution from neural crest3.49e-12132
tube2.21e-07192
diencephalon3.03e-077
future diencephalon3.03e-077
basal ganglion5.42e-079
nuclear complex of neuraxis5.42e-079
aggregate regional part of brain5.42e-079
collection of basal ganglia5.42e-079
cerebral subcortex5.42e-079
neural nucleus7.55e-079
nucleus of brain7.55e-079


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.

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