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Coexpression cluster:C2498: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0001016!6.76e-44!89;UBERON:0001017!4.43e-42!81;UBERON:0001049!6.61e-36!56;UBERON:0005068!6.61e-36!56;UBERON:0006241!6.61e-36!56;UBERON:0007135!6.61e-36!56;UBERON:0000073!1.60e-32!53;UBERON:0002616!1.60e-32!53;UBERON:0000955!1.51e-31!68;UBERON:0006238!1.51e-31!68;UBERON:0001893!8.83e-30!34;UBERON:0003528!1.58e-29!34;UBERON:0002020!1.58e-29!34;UBERON:0002346!2.43e-28!86;UBERON:0001950!1.65e-27!20;UBERON:0001869!2.21e-27!32;UBERON:0002619!2.94e-27!22;UBERON:0002791!3.24e-27!32;UBERON:0002780!4.92e-27!41;UBERON:0001890!4.92e-27!41;UBERON:0003080!4.92e-27!41;UBERON:0006240!4.92e-27!41;UBERON:0003075!2.27e-26!82;UBERON:0007284!2.27e-26!82;UBERON:0004121!1.76e-23!171;UBERON:0000924!1.76e-23!171;UBERON:0006601!1.76e-23!171;UBERON:0007023!2.84e-23!114;UBERON:0000956!3.35e-23!25;UBERON:0000203!3.35e-23!25;UBERON:0010371!1.57e-20!104;UBERON:0011216!1.99e-20!223;UBERON:0003056!2.18e-18!61;UBERON:0010314!5.61e-17!132;UBERON:0000477!2.24e-11!373;UBERON:0000200!4.64e-10!6;UBERON:0003076!6.97e-10!15;UBERON:0003057!6.97e-10!15;UBERON:0001872!6.75e-09!5;UBERON:0000025!1.01e-08!192;UBERON:0002298!1.38e-08!6;UBERON:0001871!3.34e-08!6;UBERON:0002021!3.53e-08!5;UBERON:0002420!3.94e-08!9;UBERON:0007245!3.94e-08!9;UBERON:0010009!3.94e-08!9;UBERON:0010011!3.94e-08!9;UBERON:0000454!3.94e-08!9;UBERON:0000064!6.10e-08!218;UBERON:0000125!9.06e-08!9;UBERON:0002308!9.06e-08!9;UBERON:0004733!8.75e-07!12;UBERON:0002028!8.75e-07!12;UBERON:0007277!8.75e-07!12
|ontology_enrichment_uberon=UBERON:0001016!6.76e-44!89;UBERON:0001017!4.43e-42!81;UBERON:0001049!6.61e-36!56;UBERON:0005068!6.61e-36!56;UBERON:0006241!6.61e-36!56;UBERON:0007135!6.61e-36!56;UBERON:0000073!1.60e-32!53;UBERON:0002616!1.60e-32!53;UBERON:0000955!1.51e-31!68;UBERON:0006238!1.51e-31!68;UBERON:0001893!8.83e-30!34;UBERON:0003528!1.58e-29!34;UBERON:0002020!1.58e-29!34;UBERON:0002346!2.43e-28!86;UBERON:0001950!1.65e-27!20;UBERON:0001869!2.21e-27!32;UBERON:0002619!2.94e-27!22;UBERON:0002791!3.24e-27!32;UBERON:0002780!4.92e-27!41;UBERON:0001890!4.92e-27!41;UBERON:0003080!4.92e-27!41;UBERON:0006240!4.92e-27!41;UBERON:0003075!2.27e-26!82;UBERON:0007284!2.27e-26!82;UBERON:0004121!1.76e-23!171;UBERON:0000924!1.76e-23!171;UBERON:0006601!1.76e-23!171;UBERON:0007023!2.84e-23!114;UBERON:0000956!3.35e-23!25;UBERON:0000203!3.35e-23!25;UBERON:0010371!1.57e-20!104;UBERON:0011216!1.99e-20!223;UBERON:0003056!2.18e-18!61;UBERON:0010314!5.61e-17!132;UBERON:0000477!2.24e-11!373;UBERON:0000200!4.64e-10!6;UBERON:0003076!6.97e-10!15;UBERON:0003057!6.97e-10!15;UBERON:0001872!6.75e-09!5;UBERON:0000025!1.01e-08!192;UBERON:0002298!1.38e-08!6;UBERON:0001871!3.34e-08!6;UBERON:0002021!3.53e-08!5;UBERON:0002420!3.94e-08!9;UBERON:0007245!3.94e-08!9;UBERON:0010009!3.94e-08!9;UBERON:0010011!3.94e-08!9;UBERON:0000454!3.94e-08!9;UBERON:0000064!6.10e-08!218;UBERON:0000125!9.06e-08!9;UBERON:0002308!9.06e-08!9;UBERON:0004733!8.75e-07!12;UBERON:0002028!8.75e-07!12;UBERON:0007277!8.75e-07!12
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}}
}}

Revision as of 15:32, 26 November 2012


Full id: C2498_brain_postcentral_temporal_cerebellum_paracentral_frontal_occipital



Phase1 CAGE Peaks

Hg19::chr19:51191299..51191310,-p@chr19:51191299..51191310
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Hg19::chr22:32352289..32352331,-p@chr22:32352289..32352331
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Hg19::chr7:86274120..86274137,+p8@GRM3
Hg19::chr9:137987772..137987842,-p@chr9:137987772..137987842
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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
neuron4.96e-096
neuroblast4.96e-096
electrically signaling cell4.96e-096
Uber Anatomy
Ontology termp-valuen
nervous system6.76e-4489
central nervous system4.43e-4281
neural tube6.61e-3656
neural rod6.61e-3656
future spinal cord6.61e-3656
neural keel6.61e-3656
regional part of nervous system1.60e-3253
regional part of brain1.60e-3253
brain1.51e-3168
future brain1.51e-3168
telencephalon8.83e-3034
brain grey matter1.58e-2934
gray matter1.58e-2934
neurectoderm2.43e-2886
neocortex1.65e-2720
cerebral hemisphere2.21e-2732
regional part of cerebral cortex2.94e-2722
regional part of telencephalon3.24e-2732
regional part of forebrain4.92e-2741
forebrain4.92e-2741
anterior neural tube4.92e-2741
future forebrain4.92e-2741
neural plate2.27e-2682
presumptive neural plate2.27e-2682
ectoderm-derived structure1.76e-23171
ectoderm1.76e-23171
presumptive ectoderm1.76e-23171
adult organism2.84e-23114
cerebral cortex3.35e-2325
pallium3.35e-2325
ecto-epithelium1.57e-20104
organ system subdivision1.99e-20223
pre-chordal neural plate2.18e-1861
structure with developmental contribution from neural crest5.61e-17132
anatomical cluster2.24e-11373
gyrus4.64e-106
posterior neural tube6.97e-1015
chordal neural plate6.97e-1015
parietal lobe6.75e-095
tube1.01e-08192
brainstem1.38e-086
temporal lobe3.34e-086
occipital lobe3.53e-085
basal ganglion3.94e-089
nuclear complex of neuraxis3.94e-089
aggregate regional part of brain3.94e-089
collection of basal ganglia3.94e-089
cerebral subcortex3.94e-089
organ part6.10e-08218
neural nucleus9.06e-089
nucleus of brain9.06e-089
segmental subdivision of hindbrain8.75e-0712
hindbrain8.75e-0712
presumptive hindbrain8.75e-0712
Disease
Ontology termp-valuen
neuroectodermal tumor5.60e-0710


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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