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Coexpression cluster:C2887: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0007023!6.63e-67!114;UBERON:0001049!5.43e-24!56;UBERON:0005068!5.43e-24!56;UBERON:0006241!5.43e-24!56;UBERON:0007135!5.43e-24!56;UBERON:0000073!2.38e-21!53;UBERON:0002616!2.38e-21!53;UBERON:0001017!4.52e-21!81;UBERON:0001016!1.32e-19!89;UBERON:0002780!5.04e-19!41;UBERON:0001890!5.04e-19!41;UBERON:0003080!5.04e-19!41;UBERON:0006240!5.04e-19!41;UBERON:0003075!5.40e-19!82;UBERON:0007284!5.40e-19!82;UBERON:0001893!1.11e-17!34;UBERON:0000955!1.54e-17!68;UBERON:0006238!1.54e-17!68;UBERON:0011216!1.60e-17!223;UBERON:0003528!2.09e-17!34;UBERON:0002020!2.09e-17!34;UBERON:0002346!2.18e-17!86;UBERON:0001869!2.59e-16!32;UBERON:0002791!3.82e-16!32;UBERON:0001950!5.36e-15!20;UBERON:0002619!8.40e-15!22;UBERON:0000956!1.58e-13!25;UBERON:0000203!1.58e-13!25;UBERON:0003056!2.96e-13!61;UBERON:0010371!1.21e-12!104;UBERON:0010314!4.32e-11!132;UBERON:0001737!5.19e-11!9;UBERON:0000477!9.20e-09!373;UBERON:0001557!1.26e-08!19;UBERON:0004121!9.39e-08!171;UBERON:0000924!9.39e-08!171;UBERON:0006601!9.39e-08!171;UBERON:0000064!9.59e-08!218;UBERON:0000200!6.44e-07!6
|ontology_enrichment_uberon=UBERON:0007023!6.63e-67!114;UBERON:0001049!5.43e-24!56;UBERON:0005068!5.43e-24!56;UBERON:0006241!5.43e-24!56;UBERON:0007135!5.43e-24!56;UBERON:0000073!2.38e-21!53;UBERON:0002616!2.38e-21!53;UBERON:0001017!4.52e-21!81;UBERON:0001016!1.32e-19!89;UBERON:0002780!5.04e-19!41;UBERON:0001890!5.04e-19!41;UBERON:0003080!5.04e-19!41;UBERON:0006240!5.04e-19!41;UBERON:0003075!5.40e-19!82;UBERON:0007284!5.40e-19!82;UBERON:0001893!1.11e-17!34;UBERON:0000955!1.54e-17!68;UBERON:0006238!1.54e-17!68;UBERON:0011216!1.60e-17!223;UBERON:0003528!2.09e-17!34;UBERON:0002020!2.09e-17!34;UBERON:0002346!2.18e-17!86;UBERON:0001869!2.59e-16!32;UBERON:0002791!3.82e-16!32;UBERON:0001950!5.36e-15!20;UBERON:0002619!8.40e-15!22;UBERON:0000956!1.58e-13!25;UBERON:0000203!1.58e-13!25;UBERON:0003056!2.96e-13!61;UBERON:0010371!1.21e-12!104;UBERON:0010314!4.32e-11!132;UBERON:0001737!5.19e-11!9;UBERON:0000477!9.20e-09!373;UBERON:0001557!1.26e-08!19;UBERON:0004121!9.39e-08!171;UBERON:0000924!9.39e-08!171;UBERON:0006601!9.39e-08!171;UBERON:0000064!9.59e-08!218;UBERON:0000200!6.44e-07!6
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}}
}}

Revision as of 15:47, 26 November 2012


Full id: C2887_mesodermal_Dendritic_acute_thymus_spinal_heart_seminal



Phase1 CAGE Peaks

Hg19::chr7:158937551..158937569,-p1@VIPR2
Hg19::chr7:158937577..158937594,-p4@VIPR2
Hg19::chr7:158937598..158937613,-p3@VIPR2
Hg19::chr7:158937633..158937652,-p2@VIPR2


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
adult organism6.63e-67114
neural tube5.43e-2456
neural rod5.43e-2456
future spinal cord5.43e-2456
neural keel5.43e-2456
regional part of nervous system2.38e-2153
regional part of brain2.38e-2153
central nervous system4.52e-2181
nervous system1.32e-1989
regional part of forebrain5.04e-1941
forebrain5.04e-1941
anterior neural tube5.04e-1941
future forebrain5.04e-1941
neural plate5.40e-1982
presumptive neural plate5.40e-1982
telencephalon1.11e-1734
brain1.54e-1768
future brain1.54e-1768
organ system subdivision1.60e-17223
brain grey matter2.09e-1734
gray matter2.09e-1734
neurectoderm2.18e-1786
cerebral hemisphere2.59e-1632
regional part of telencephalon3.82e-1632
neocortex5.36e-1520
regional part of cerebral cortex8.40e-1522
cerebral cortex1.58e-1325
pallium1.58e-1325
pre-chordal neural plate2.96e-1361
ecto-epithelium1.21e-12104
structure with developmental contribution from neural crest4.32e-11132
larynx5.19e-119
anatomical cluster9.20e-09373
upper respiratory tract1.26e-0819
ectoderm-derived structure9.39e-08171
ectoderm9.39e-08171
presumptive ectoderm9.39e-08171
organ part9.59e-08218
gyrus6.44e-076


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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