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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C2183_pineal_parietal_temporal_cerebellum_hippocampus_middle_Cardiac
|full_id=C2183_pineal_parietal_temporal_cerebellum_hippocampus_middle_Cardiac
|id=C2183
|id=C2183

Revision as of 14:52, 12 September 2012


Full id: C2183_pineal_parietal_temporal_cerebellum_hippocampus_middle_Cardiac



Phase1 CAGE Peaks

Hg19::chr12:109293077..109293088,-p@chr12:109293077..109293088
-
Hg19::chr16:67210038..67210055,-p@chr16:67210038..67210055
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Hg19::chr16:67210067..67210086,-p@chr16:67210067..67210086
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Hg19::chr1:57889939..57889948,-p13@DAB1


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>disease_data<br>


Uber Anatomy
Ontology termp-valuen
regional part of nervous system1.66e-3094
nervous system1.66e-3094
central nervous system1.90e-2982
neural tube1.99e-2757
neural rod1.99e-2757
future spinal cord1.99e-2757
neural keel1.99e-2757
brain6.54e-2569
future brain6.54e-2569
regional part of forebrain9.26e-2441
forebrain9.26e-2441
future forebrain9.26e-2441
regional part of brain7.83e-2359
anterior neural tube1.96e-2242
neural plate3.61e-2086
presumptive neural plate3.61e-2086
neurectoderm8.67e-2090
gray matter1.11e-1934
brain grey matter1.11e-1934
telencephalon1.72e-1934
regional part of telencephalon5.81e-1933
cerebral hemisphere1.78e-1832
pre-chordal neural plate2.19e-1661
ectoderm-derived structure5.25e-15169
ectoderm5.34e-15173
presumptive ectoderm5.34e-15173
regional part of cerebral cortex6.92e-1522
cerebral cortex1.54e-1425
pallium1.54e-1425
neocortex1.56e-1320
head2.66e-13123
anterior region of body8.08e-13129
craniocervical region8.08e-13129
adult organism7.59e-10115
basal ganglion9.18e-079
nuclear complex of neuraxis9.18e-079
aggregate regional part of brain9.18e-079
collection of basal ganglia9.18e-079
cerebral subcortex9.18e-079
Disease
Ontology termp-valuen
disease of cellular proliferation2.80e-07239
cancer6.58e-07235


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.