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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C2027_cerebellum_middle_pineal_occipital_medial_parietal_medulla
|full_id=C2027_cerebellum_middle_pineal_occipital_medial_parietal_medulla
|id=C2027
|id=C2027

Revision as of 14:41, 12 September 2012


Full id: C2027_cerebellum_middle_pineal_occipital_medial_parietal_medulla



Phase1 CAGE Peaks

Hg19::chrX:1480354..1480394,-p@chrX:1480354..1480394
-
Hg19::chrX:1534966..1534978,+p@chrX:1534966..1534978
+
Hg19::chrX:1535807..1535821,+p@chrX:1535807..1535821
+
Hg19::chrX:1535840..1535859,+p@chrX:1535840..1535859
+
Hg19::chrX:1535864..1535880,+p@chrX:1535864..1535880
+


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 tube3.43e-2057
neural rod3.43e-2057
future spinal cord3.43e-2057
neural keel3.43e-2057
regional part of forebrain6.54e-1641
forebrain6.54e-1641
future forebrain6.54e-1641
central nervous system2.14e-1582
anterior neural tube2.57e-1542
regional part of brain4.31e-1559
gray matter7.01e-1434
brain grey matter7.01e-1434
brain7.38e-1469
future brain7.38e-1469
neurectoderm7.25e-1390
neural plate1.51e-1286
presumptive neural plate1.51e-1286
regional part of nervous system3.22e-1294
nervous system3.22e-1294
regional part of telencephalon1.74e-1133
telencephalon5.84e-1134
cerebral hemisphere1.36e-1032
basal ganglion1.51e-099
nuclear complex of neuraxis1.51e-099
aggregate regional part of brain1.51e-099
collection of basal ganglia1.51e-099
cerebral subcortex1.51e-099
nucleus of brain1.88e-099
neural nucleus1.88e-099
regional part of cerebral cortex7.00e-0922
pre-chordal neural plate8.16e-0961
adult organism8.62e-09115
female organism5.57e-0841
cerebral cortex2.40e-0725
pallium2.40e-0725
diencephalon2.72e-077
future diencephalon2.72e-077
telencephalic nucleus3.26e-077
ectoderm3.29e-07173
presumptive ectoderm3.29e-07173
organ3.73e-07511
neocortex4.35e-0720
ectoderm-derived structure6.74e-07169
female reproductive organ8.37e-0737
female reproductive system8.37e-0737


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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