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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C2993_Wilms_rhabdomyosarcoma_neuroblastoma_retinoblastoma_brain_cerebellum_teratocarcinoma
|full_id=C2993_Wilms_rhabdomyosarcoma_neuroblastoma_retinoblastoma_brain_cerebellum_teratocarcinoma
|id=C2993
|id=C2993

Revision as of 15:49, 12 September 2012


Full id: C2993_Wilms_rhabdomyosarcoma_neuroblastoma_retinoblastoma_brain_cerebellum_teratocarcinoma



Phase1 CAGE Peaks

Hg19::chr10:135139745..135139753,-p4@CALY
Hg19::chr10:135139760..135139767,-p5@CALY
Hg19::chr10:135139771..135139785,-p2@CALY


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>disease_data<br>

Cell Type
Ontology termp-valuen
embryonic stem cell7.77e-075
Uber Anatomy
Ontology termp-valuen
regional part of nervous system4.45e-2694
nervous system4.45e-2694
neurectoderm1.54e-2390
central nervous system4.98e-2382
neural tube5.21e-2257
neural rod5.21e-2257
future spinal cord5.21e-2257
neural keel5.21e-2257
neural plate1.03e-2186
presumptive neural plate1.03e-2186
brain2.73e-1969
future brain2.73e-1969
regional part of brain3.65e-1859
pre-chordal neural plate5.84e-1661
ectoderm9.65e-16173
presumptive ectoderm9.65e-16173
ectoderm-derived structure2.30e-14169
regional part of forebrain3.26e-1441
forebrain3.26e-1441
future forebrain3.26e-1441
anterior neural tube1.15e-1342
head1.05e-12123
anterior region of body2.24e-11129
craniocervical region2.24e-11129
cerebral cortex4.30e-1125
pallium4.30e-1125
neocortex8.53e-1120
gray matter1.17e-1034
brain grey matter1.17e-1034
telencephalon1.19e-1034
cerebral hemisphere1.20e-1032
segmental subdivision of nervous system2.38e-1013
adult organism3.53e-10115
posterior neural tube4.04e-1015
chordal neural plate4.04e-1015
regional part of telencephalon5.76e-1033
regional part of cerebral cortex2.02e-0922
segmental subdivision of hindbrain2.20e-0912
hindbrain2.20e-0912
presumptive hindbrain2.20e-0912
tube1.64e-08194
epithelium3.70e-08309
cell layer7.35e-08312
multi-tissue structure1.73e-07347
regional part of metencephalon7.94e-079
metencephalon7.94e-079
future metencephalon7.94e-079
Disease
Ontology termp-valuen
germ cell and embryonal cancer2.69e-0822
germ cell cancer2.69e-0822


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
YY1#752834.911170749853860.008441455341808260.0327738719123834



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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