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Difference between revisions of "Coexpression cluster:C670"

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{{Coexpression_clusters
 
{{Coexpression_clusters
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|full_id=C670_putamen_parietal_pineal_caudate_middle_occipital_cerebellum
 
|full_id=C670_putamen_parietal_pineal_caudate_middle_occipital_cerebellum
 
|id=C670
 
|id=C670

Revision as of 09:20, 12 September 2012


Full id: C670_putamen_parietal_pineal_caudate_middle_occipital_cerebellum



Phase1 CAGE Peaks

Hg19::chr4:21115074..21115079,-p@chr4:21115074..21115079
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Hg19::chr4:21326759..21326765,-p@chr4:21326759..21326765
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Hg19::chr4:21385117..21385122,-p@chr4:21385117..21385122
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Hg19::chr4:21490941..21490944,-p@chr4:21490941..21490944
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Hg19::chr4:21617919..21617938,-p@chr4:21617919..21617938
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Hg19::chr4:21635843..21635847,-p@chr4:21635843..21635847
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Hg19::chr4:21698935..21698940,-p@chr4:21698935..21698940
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Hg19::chr4:21767439..21767443,-p@chr4:21767439..21767443
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Hg19::chr4:21792588..21792593,-p@chr4:21792588..21792593
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Hg19::chr4:21833284..21833287,-p@chr4:21833284..21833287
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Hg19::chr4:21923515..21923532,-p@chr4:21923515..21923532
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Hg19::chr4:21931695..21931698,-p@chr4:21931695..21931698
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Hg19::chr4:21937276..21937287,-p@chr4:21937276..21937287
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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><br>uberon_data<br><br>


Uber Anatomy
Ontology termp-valuen
central nervous system6.16e-5082
neural tube4.40e-4957
neural rod4.40e-4957
future spinal cord4.40e-4957
neural keel4.40e-4957
regional part of nervous system6.17e-4794
nervous system6.17e-4794
brain1.77e-4369
future brain1.77e-4369
regional part of forebrain4.37e-4141
forebrain4.37e-4141
future forebrain4.37e-4141
regional part of brain7.80e-4159
anterior neural tube1.06e-3942
neural plate3.08e-3986
presumptive neural plate3.08e-3986
neurectoderm7.64e-3890
gray matter8.20e-3434
brain grey matter8.20e-3434
telencephalon8.83e-3434
regional part of telencephalon1.02e-3233
cerebral hemisphere3.43e-3232
adult organism3.77e-32115
pre-chordal neural plate8.20e-3261
anterior region of body3.89e-25129
craniocervical region3.89e-25129
head4.79e-25123
cerebral cortex8.35e-2525
pallium8.35e-2525
ectoderm-derived structure3.64e-23169
regional part of cerebral cortex4.07e-2322
ectoderm7.78e-23173
presumptive ectoderm7.78e-23173
neocortex5.00e-2120
basal ganglion9.57e-119
nuclear complex of neuraxis9.57e-119
aggregate regional part of brain9.57e-119
collection of basal ganglia9.57e-119
cerebral subcortex9.57e-119
posterior neural tube1.84e-1015
chordal neural plate1.84e-1015
nucleus of brain2.20e-109
neural nucleus2.20e-109
tube6.54e-10194
segmental subdivision of nervous system4.65e-0913
diencephalon1.29e-087
future diencephalon1.29e-087
telencephalic nucleus1.39e-087
segmental subdivision of hindbrain3.32e-0812
hindbrain3.32e-0812
presumptive hindbrain3.32e-0812
gyrus5.17e-086
temporal lobe1.27e-077
anatomical conduit3.69e-07241
limbic system6.81e-075
parietal lobe7.99e-075


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.