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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C4345_caudate_melanoma_merkel_smallcell_occipital_pons_amygdala
|full_id=C4345_caudate_melanoma_merkel_smallcell_occipital_pons_amygdala
|id=C4345
|id=C4345

Revision as of 17:24, 12 September 2012


Full id: C4345_caudate_melanoma_merkel_smallcell_occipital_pons_amygdala



Phase1 CAGE Peaks

Hg19::chr3:76359866..76359898,+p5@ROBO2
Hg19::chr3:76360015..76360051,+p3@ROBO2
Hg19::chr3:76360054..76360097,+p4@ROBO2


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
neural tube1.72e-3857
neural rod1.72e-3857
future spinal cord1.72e-3857
neural keel1.72e-3857
adult organism1.40e-36115
regional part of brain2.15e-3459
regional part of forebrain6.16e-3441
forebrain6.16e-3441
future forebrain6.16e-3441
anterior neural tube9.20e-3342
central nervous system3.76e-3282
brain5.11e-3269
future brain5.11e-3269
neurectoderm6.94e-3190
neural plate6.15e-3086
presumptive neural plate6.15e-3086
gray matter1.78e-2934
brain grey matter1.78e-2934
telencephalon2.15e-2934
regional part of telencephalon2.36e-2833
cerebral hemisphere5.86e-2832
regional part of nervous system3.13e-2794
nervous system3.13e-2794
pre-chordal neural plate4.10e-2561
regional part of cerebral cortex8.20e-2322
head1.38e-21123
anterior region of body4.17e-21129
craniocervical region4.17e-21129
neocortex6.02e-2120
ectoderm7.69e-21173
presumptive ectoderm7.69e-21173
cerebral cortex1.27e-2025
pallium1.27e-2025
ectoderm-derived structure6.88e-20169
organism subdivision7.00e-14365
basal ganglion1.02e-109
nuclear complex of neuraxis1.02e-109
aggregate regional part of brain1.02e-109
collection of basal ganglia1.02e-109
cerebral subcortex1.02e-109
nucleus of brain2.29e-109
neural nucleus2.29e-109
telencephalic nucleus1.60e-087
gyrus6.34e-086
epithelium9.56e-08309
organ part9.59e-08219
cell layer1.03e-07312
temporal lobe1.93e-077
tube2.40e-07194
posterior neural tube2.70e-0715
chordal neural plate2.70e-0715
parietal lobe6.91e-075
anatomical cluster8.29e-07286
brainstem8.86e-078


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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