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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C3082_parietal_pineal_temporal_occipital_hippocampus_middle_amygdala
|full_id=C3082_parietal_pineal_temporal_occipital_hippocampus_middle_amygdala
|id=C3082
|id=C3082

Revision as of 15:56, 12 September 2012


Full id: C3082_parietal_pineal_temporal_occipital_hippocampus_middle_amygdala



Phase1 CAGE Peaks

Hg19::chr11:113146130..113146180,+p@chr11:113146130..113146180
+
Hg19::chr5:166996114..166996115,+p@chr5:166996114..166996115
+
Hg19::chr6:161186211..161186236,-p@chr6:161186211..161186236
-


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 tube7.08e-4257
neural rod7.08e-4257
future spinal cord7.08e-4257
neural keel7.08e-4257
regional part of nervous system3.89e-4094
nervous system3.89e-4094
central nervous system1.75e-3982
regional part of brain9.28e-3559
regional part of forebrain1.91e-3441
forebrain1.91e-3441
future forebrain1.91e-3441
brain2.41e-3469
future brain2.41e-3469
neurectoderm1.95e-3390
anterior neural tube3.96e-3342
neural plate5.75e-3386
presumptive neural plate5.75e-3386
adult organism1.79e-29115
gray matter5.55e-2934
brain grey matter5.55e-2934
telencephalon1.13e-2834
regional part of telencephalon6.45e-2833
cerebral hemisphere2.63e-2732
ectoderm1.51e-23173
presumptive ectoderm1.51e-23173
pre-chordal neural plate2.06e-2361
ectoderm-derived structure7.62e-23169
cerebral cortex1.27e-2125
pallium1.27e-2125
regional part of cerebral cortex1.90e-2022
neocortex1.12e-1820
anterior region of body1.40e-17129
craniocervical region1.40e-17129
head1.83e-17123
posterior neural tube8.74e-1015
chordal neural plate8.74e-1015
basal ganglion6.83e-099
nuclear complex of neuraxis6.83e-099
aggregate regional part of brain6.83e-099
collection of basal ganglia6.83e-099
cerebral subcortex6.83e-099
nucleus of brain9.14e-099
neural nucleus9.14e-099
tube1.87e-08194
temporal lobe3.35e-087
segmental subdivision of nervous system4.70e-0813
segmental subdivision of hindbrain1.92e-0712
hindbrain1.92e-0712
presumptive hindbrain1.92e-0712
telencephalic nucleus3.89e-077
diencephalon3.96e-077
future diencephalon3.96e-077


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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