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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C4774_neuroectodermal_neuroblastoma_alveolar_parietal_temporal_occipital_duodenum
|full_id=C4774_neuroectodermal_neuroblastoma_alveolar_parietal_temporal_occipital_duodenum
|id=C4774
|id=C4774

Revision as of 17:54, 12 September 2012


Full id: C4774_neuroectodermal_neuroblastoma_alveolar_parietal_temporal_occipital_duodenum



Phase1 CAGE Peaks

Hg19::chr8:81553800..81553804,-p@chr8:81553800..81553804
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Hg19::chr8:81786618..81786644,-p@chr8:81786618..81786644
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Hg19::chr8:81786662..81786712,-p@chr8:81786662..81786712
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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
adult organism4.60e-33115
neural tube1.63e-2357
neural rod1.63e-2357
future spinal cord1.63e-2357
neural keel1.63e-2357
regional part of nervous system8.08e-2394
nervous system8.08e-2394
central nervous system2.78e-2282
regional part of brain4.67e-1959
brain6.83e-1869
future brain6.83e-1869
anterior neural tube1.01e-1742
neurectoderm2.11e-1790
regional part of forebrain3.91e-1741
forebrain3.91e-1741
future forebrain3.91e-1741
neural plate2.58e-1586
presumptive neural plate2.58e-1586
gray matter2.89e-1534
brain grey matter2.89e-1534
telencephalon4.20e-1534
regional part of telencephalon7.86e-1533
cerebral hemisphere4.35e-1432
ectoderm4.92e-13173
presumptive ectoderm4.92e-13173
ectoderm-derived structure1.70e-11169
cerebral cortex2.67e-1125
pallium2.67e-1125
regional part of cerebral cortex4.19e-1122
pre-chordal neural plate7.01e-1161
neocortex2.02e-1020
anterior region of body1.24e-09129
craniocervical region1.24e-09129
anatomical conduit3.56e-09241
head7.32e-09123
tube1.06e-08194
anatomical cluster4.55e-08286
multi-cellular organism2.87e-07659
posterior neural tube5.26e-0715
chordal neural plate5.26e-0715


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
GATA3#2625218.15767757147070.003944546819279620.0189600757206712
NANOG#79923219.49651898734180.003427255648501020.0174630020331657
TRIM28#10155212.39368336350830.008368344129438470.032944381338702



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.