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{{Coexpression_clusters
 
{{Coexpression_clusters
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|full_id=C3443_amygdala_putamen_caudate_Dendritic_medulloblastoma_occipital_medial
 
|full_id=C3443_amygdala_putamen_caudate_Dendritic_medulloblastoma_occipital_medial
 
|id=C3443
 
|id=C3443

Revision as of 07:22, 12 September 2012


Full id: C3443_amygdala_putamen_caudate_Dendritic_medulloblastoma_occipital_medial



Phase1 CAGE Peaks

Hg19::chr14:64932162..64932175,+p4@AKAP5
Hg19::chr14:64932186..64932205,+p2@AKAP5
Hg19::chr14:64932210..64932226,+p1@AKAP5


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>


Cell Type
Ontology termp-valuen
neural cell2.85e-0725
Uber Anatomy
Ontology termp-valuen
central nervous system6.77e-3082
regional part of nervous system2.83e-2794
nervous system2.83e-2794
brain3.22e-2569
future brain3.22e-2569
anterior neural tube1.71e-2342
regional part of forebrain2.66e-2341
forebrain2.66e-2341
future forebrain2.66e-2341
neural tube1.89e-2257
neural rod1.89e-2257
future spinal cord1.89e-2257
neural keel1.89e-2257
cerebral hemisphere1.13e-2132
regional part of brain1.37e-2159
telencephalon8.15e-2134
gray matter1.19e-2034
brain grey matter1.19e-2034
regional part of telencephalon3.44e-2033
neurectoderm4.59e-1990
pre-chordal neural plate7.27e-1961
neural plate1.34e-1886
presumptive neural plate1.34e-1886
cerebral cortex5.35e-1725
pallium5.35e-1725
regional part of cerebral cortex1.01e-1522
neocortex2.13e-1420
adult organism2.39e-14115
ectoderm4.37e-12173
presumptive ectoderm4.37e-12173
head4.84e-12123
anterior region of body5.98e-12129
craniocervical region5.98e-12129
ectoderm-derived structure1.37e-11169


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
CTCF#1066435.360256373075030.0064925092527670.0278903905005649
E2F1#186934.907389214879320.008460985347239390.0324396787327582
E2F6#187635.017155731697390.00791769806886330.0321294816262196
EBF1#187938.9064668465690.00141523283560980.00913733321700373
NFYB#4801316.75979325353650.0002123649923296180.00245317856806913
PBX3#5090321.91451268674419.49854535978121e-050.00136397439685163
ZBTB7A#5134137.35190930787590.002516255860282270.0139851655469118



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.