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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C4045_neuroblastoma_cord_dura_salivary_seminal_medulloblastoma_small
|full_id=C4045_neuroblastoma_cord_dura_salivary_seminal_medulloblastoma_small
|id=C4045
|id=C4045

Revision as of 17:05, 12 September 2012


Full id: C4045_neuroblastoma_cord_dura_salivary_seminal_medulloblastoma_small



Phase1 CAGE Peaks

Hg19::chr20:45523452..45523459,+p5@EYA2
Hg19::chr20:45523463..45523535,+p1@EYA2
Hg19::chr20:45523539..45523563,+p3@EYA2


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
fat cell4.37e-0715
Uber Anatomy
Ontology termp-valuen
adult organism7.13e-34115
anterior region of body2.35e-21129
craniocervical region2.35e-21129
head2.96e-20123
neural plate2.64e-1986
presumptive neural plate2.64e-1986
neurectoderm4.28e-1790
neural tube7.44e-1757
neural rod7.44e-1757
future spinal cord7.44e-1757
neural keel7.44e-1757
organism subdivision6.12e-16365
pre-chordal neural plate6.47e-1561
central nervous system9.31e-1582
brain1.56e-1469
future brain1.56e-1469
regional part of brain2.81e-1459
regional part of nervous system5.72e-1494
nervous system5.72e-1494
anterior neural tube7.78e-1342
ectoderm-derived structure1.12e-12169
regional part of forebrain2.34e-1241
forebrain2.34e-1241
future forebrain2.34e-1241
ectoderm1.49e-11173
presumptive ectoderm1.49e-11173
gray matter1.26e-1034
brain grey matter1.26e-1034
telencephalon1.82e-1034
regional part of telencephalon3.91e-1033
cerebral hemisphere1.10e-0932
regional part of cerebral cortex1.48e-0822
multi-tissue structure5.32e-08347
neocortex7.67e-0820
subdivision of head2.18e-0748
multi-cellular organism3.21e-07659
cerebral cortex4.98e-0725
pallium4.98e-0725
organ part8.98e-07219


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#1066435.360256373075030.0064925092527670.0279859331317732
PAX5#507936.669565531177830.003370290999677260.0173129615717522



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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