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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C988_pineal_small_colon_eye_renal_cerebellum_neuroblastoma
|full_id=C988_pineal_small_colon_eye_renal_cerebellum_neuroblastoma
|id=C988
|id=C988

Revision as of 18:47, 12 September 2012


Full id: C988_pineal_small_colon_eye_renal_cerebellum_neuroblastoma



Phase1 CAGE Peaks

Hg19::chr11:115067312..115067316,-p@chr11:115067312..115067316
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Hg19::chr11:115078302..115078307,-p@chr11:115078302..115078307
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Hg19::chr11:115211232..115211238,-p@chr11:115211232..115211238
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Hg19::chr11:115239731..115239744,-p@chr11:115239731..115239744
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Hg19::chr11:115256343..115256351,-p@chr11:115256343..115256351
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Hg19::chr11:115261379..115261392,-p@chr11:115261379..115261392
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Hg19::chr11:115278588..115278591,-p@chr11:115278588..115278591
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Hg19::chr11:115375126..115375140,-p1@CADM1


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
regional part of nervous system1.03e-3194
nervous system1.03e-3194
central nervous system1.09e-3182
neural tube8.07e-3157
neural rod8.07e-3157
future spinal cord8.07e-3157
neural keel8.07e-3157
brain3.78e-2869
future brain3.78e-2869
adult organism4.24e-28115
neural plate1.35e-2786
presumptive neural plate1.35e-2786
neurectoderm5.16e-2790
regional part of brain9.82e-2759
ectoderm-derived structure2.50e-26169
ectoderm3.18e-26173
presumptive ectoderm3.18e-26173
regional part of forebrain6.65e-2441
forebrain6.65e-2441
future forebrain6.65e-2441
anterior neural tube9.24e-2442
anterior region of body1.37e-22129
craniocervical region1.37e-22129
pre-chordal neural plate1.79e-2261
head2.83e-22123
gray matter3.23e-2034
brain grey matter3.23e-2034
telencephalon7.64e-2034
regional part of telencephalon2.03e-1933
cerebral hemisphere9.18e-1932
cerebral cortex4.57e-1525
pallium4.57e-1525
organ4.06e-14511
regional part of cerebral cortex1.68e-1322
neocortex2.88e-1220
organ part6.43e-11219
posterior neural tube3.52e-0815
chordal neural plate3.52e-0815
multi-cellular organism5.03e-08659
anatomical system2.63e-07625
anatomical group3.59e-07626
segmental subdivision of nervous system3.70e-0713
embryo4.60e-07612
organism subdivision5.68e-07365
tube5.92e-07194
epithelium6.68e-07309


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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