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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C1127_cerebellum_substantia_spinal_thalamus_medulla_occipital_globus
|full_id=C1127_cerebellum_substantia_spinal_thalamus_medulla_occipital_globus
|id=C1127
|id=C1127

Revision as of 13:36, 12 September 2012


Full id: C1127_cerebellum_substantia_spinal_thalamus_medulla_occipital_globus



Phase1 CAGE Peaks

Hg19::chr11:105948129..105948161,-p2@KBTBD3
Hg19::chr17:36729056..36729072,-p8@SRCIN1
Hg19::chr17:66201593..66201646,+p@chr17:66201593..66201646
+
Hg19::chr1:171911363..171911369,+p@chr1:171911363..171911369
+
Hg19::chr3:129407466..129407477,-p19@TMCC1
Hg19::chr3:129407485..129407505,-p5@TMCC1
Hg19::chr3:129407535..129407543,-p21@TMCC1


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>


Uber Anatomy
Ontology termp-valuen
adult organism6.86e-34115
neural tube8.61e-3257
neural rod8.61e-3257
future spinal cord8.61e-3257
neural keel8.61e-3257
regional part of nervous system6.62e-3194
nervous system6.62e-3194
central nervous system2.51e-3082
anterior neural tube2.55e-2542
regional part of brain3.22e-2559
brain4.14e-2569
future brain4.14e-2569
regional part of forebrain4.51e-2541
forebrain4.51e-2541
future forebrain4.51e-2541
neurectoderm5.84e-2390
neural plate7.49e-2386
presumptive neural plate7.49e-2386
gray matter1.11e-2034
brain grey matter1.11e-2034
telencephalon1.21e-2034
regional part of telencephalon5.00e-2033
cerebral hemisphere2.70e-1932
pre-chordal neural plate2.07e-1761
cerebral cortex5.76e-1525
pallium5.76e-1525
regional part of cerebral cortex2.80e-1422
anterior region of body5.59e-14129
craniocervical region5.59e-14129
ectoderm5.96e-14173
presumptive ectoderm5.96e-14173
ectoderm-derived structure1.29e-13169
neocortex4.61e-1320
head1.94e-12123
posterior neural tube1.14e-0715
chordal neural plate1.14e-0715
nucleus of brain3.25e-079
neural nucleus3.25e-079
basal ganglion4.11e-079
nuclear complex of neuraxis4.11e-079
aggregate regional part of brain4.11e-079
collection of basal ganglia4.11e-079
cerebral subcortex4.11e-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)

{{{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


(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
FOXA1#316946.332239856791690.001854681016920170.0109423246371102
HEY1#2346252.885793602218360.01231366941853030.0446196419541282
NANOG#79923312.53347649186260.001261052189503470.00846801450649734
NRF1#489946.977302541549090.00128531428862220.00861874407636685



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.