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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C4014_neuroectodermal_neuroblastoma_smallcell_gastrointestinal_peripheral_thyroid_pineal
|full_id=C4014_neuroectodermal_neuroblastoma_smallcell_gastrointestinal_peripheral_thyroid_pineal
|id=C4014
|id=C4014

Revision as of 17:03, 12 September 2012


Full id: C4014_neuroectodermal_neuroblastoma_smallcell_gastrointestinal_peripheral_thyroid_pineal



Phase1 CAGE Peaks

Hg19::chr20:17207665..17207699,+p1@PCSK2
Hg19::chr20:17349884..17349887,+p@chr20:17349884..17349887
+
Hg19::chr20:17402931..17402956,+p@chr20:17402931..17402956
+


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
adult organism1.75e-62115
central nervous system1.06e-4582
regional part of nervous system4.48e-4594
nervous system4.48e-4594
neural tube1.34e-4457
neural rod1.34e-4457
future spinal cord1.34e-4457
neural keel1.34e-4457
neurectoderm6.81e-3790
regional part of brain1.13e-3659
brain1.60e-3669
future brain1.60e-3669
regional part of forebrain3.47e-3641
forebrain3.47e-3641
future forebrain3.47e-3641
anterior neural tube6.39e-3542
neural plate3.63e-3386
presumptive neural plate3.63e-3386
ectoderm1.50e-31173
presumptive ectoderm1.50e-31173
gray matter3.81e-3034
brain grey matter3.81e-3034
telencephalon4.58e-3034
regional part of telencephalon4.26e-2933
cerebral hemisphere6.61e-2932
ectoderm-derived structure1.61e-28169
pre-chordal neural plate5.07e-2461
regional part of cerebral cortex1.70e-2322
cerebral cortex1.95e-2225
pallium1.95e-2225
anterior region of body3.68e-22129
craniocervical region3.68e-22129
head6.00e-22123
neocortex1.25e-2120
posterior neural tube1.26e-1015
chordal neural plate1.26e-1015
organism subdivision1.92e-09365
tube2.25e-09194
basal ganglion2.35e-099
nuclear complex of neuraxis2.35e-099
aggregate regional part of brain2.35e-099
collection of basal ganglia2.35e-099
cerebral subcortex2.35e-099
multi-cellular organism2.42e-09659
temporal lobe2.58e-097
nucleus of brain4.17e-099
neural nucleus4.17e-099
segmental subdivision of nervous system6.62e-0913
anatomical conduit1.80e-08241
organ part2.01e-08219
segmental subdivision of hindbrain2.60e-0812
hindbrain2.60e-0812
presumptive hindbrain2.60e-0812
embryo1.54e-07612
diencephalon1.83e-077
future diencephalon1.83e-077
gyrus1.94e-076
telencephalic nucleus2.00e-077
organ2.26e-07511
Disease
Ontology termp-valuen
neuroectodermal tumor3.07e-0710


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.

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