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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C2492_medial_brain_temporal_postcentral_cerebellum_pons_eye
|full_id=C2492_medial_brain_temporal_postcentral_cerebellum_pons_eye
|id=C2492
|id=C2492

Revision as of 15:14, 12 September 2012


Full id: C2492_medial_brain_temporal_postcentral_cerebellum_pons_eye



Phase1 CAGE Peaks

Hg19::chr19:42473625..42473655,-p@chr19:42473625..42473655
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Hg19::chr19:42479863..42479884,-p@chr19:42479863..42479884
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Hg19::chr19:42479906..42479929,-p@chr19:42479906..42479929
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Hg19::chr19:42492239..42492251,-p5@ATP1A3


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><br>

Cell Type
Ontology termp-valuen
neuron7.39e-076
neuroblast7.39e-076
electrically signaling cell7.39e-076
Uber Anatomy
Ontology termp-valuen
central nervous system1.12e-4882
regional part of nervous system2.41e-4794
nervous system2.41e-4794
neural tube8.23e-4757
neural rod8.23e-4757
future spinal cord8.23e-4757
neural keel8.23e-4757
brain2.55e-4069
future brain2.55e-4069
regional part of brain9.75e-3959
neurectoderm1.45e-3790
regional part of forebrain1.42e-3641
forebrain1.42e-3641
future forebrain1.42e-3641
neural plate7.03e-3686
presumptive neural plate7.03e-3686
anterior neural tube2.25e-3542
adult organism1.69e-34115
cerebral hemisphere1.05e-2932
gray matter2.04e-2934
brain grey matter2.04e-2934
telencephalon2.06e-2934
regional part of telencephalon3.60e-2833
regional part of cerebral cortex3.17e-2622
pre-chordal neural plate1.53e-2461
neocortex6.48e-2420
ectoderm5.01e-23173
presumptive ectoderm5.01e-23173
cerebral cortex3.49e-2225
pallium3.49e-2225
ectoderm-derived structure1.35e-21169
anterior region of body1.53e-20129
craniocervical region1.53e-20129
head4.00e-19123
posterior neural tube3.15e-1215
chordal neural plate3.15e-1215
segmental subdivision of hindbrain1.30e-0912
hindbrain1.30e-0912
presumptive hindbrain1.30e-0912
gyrus4.33e-096
basal ganglion1.15e-089
nuclear complex of neuraxis1.15e-089
aggregate regional part of brain1.15e-089
collection of basal ganglia1.15e-089
cerebral subcortex1.15e-089
segmental subdivision of nervous system1.19e-0813
nucleus of brain1.24e-089
neural nucleus1.24e-089
diencephalon1.46e-087
future diencephalon1.46e-087
temporal lobe1.71e-087
tube4.29e-08194
parietal lobe1.21e-075
occipital lobe2.04e-075
limbic system3.11e-075


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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