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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C1379_pineal_cerebellum_small_occipital_parietal_temporal_hippocampus
|full_id=C1379_pineal_cerebellum_small_occipital_parietal_temporal_hippocampus
|gostat_on_coexpression_clusters=GO:0007158!neuron adhesion!0.0296662538128231!1501
|gostat_on_coexpression_clusters=GO:0007158!neuron adhesion!0.0296662538128231!1501

Revision as of 13:55, 12 September 2012


Full id: C1379_pineal_cerebellum_small_occipital_parietal_temporal_hippocampus



Phase1 CAGE Peaks

Hg19::chr13:25745685..25745777,-p1@FAM123A
Hg19::chr15:51973635..51973646,+p4@SCG3
Hg19::chr19:42470940..42470980,-p@chr19:42470940..42470980
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Hg19::chr5:11903337..11903377,-p18@CTNND2
Hg19::chr6:127837142..127837208,-p1@C6orf174
Hg19::chr6:25279289..25279415,+p3@LRRC16A


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

GO IDGO nameFDR corrected p-value
GO:0007158neuron adhesion0.0296662538128231



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 system8.71e-3794
nervous system8.71e-3794
central nervous system4.74e-3582
neural tube3.57e-3457
neural rod3.57e-3457
future spinal cord3.57e-3457
neural keel3.57e-3457
neurectoderm4.67e-3190
regional part of brain1.96e-2959
neural plate3.98e-2986
presumptive neural plate3.98e-2986
brain1.15e-2869
future brain1.15e-2869
adult organism5.93e-28115
anterior neural tube7.81e-2742
regional part of forebrain1.42e-2641
forebrain1.42e-2641
future forebrain1.42e-2641
gray matter2.03e-2234
brain grey matter2.03e-2234
telencephalon2.60e-2234
ectoderm6.10e-22173
presumptive ectoderm6.10e-22173
regional part of telencephalon1.09e-2133
cerebral hemisphere3.22e-2132
ectoderm-derived structure2.32e-20169
pre-chordal neural plate2.27e-1961
cerebral cortex4.60e-1725
pallium4.60e-1725
anterior region of body1.15e-16129
craniocervical region1.15e-16129
head4.11e-16123
regional part of cerebral cortex9.48e-1622
neocortex1.66e-1420
posterior neural tube1.86e-0815
chordal neural plate1.86e-0815
organism subdivision1.93e-08365
tube6.79e-08194
segmental subdivision of nervous system2.60e-0713
basal ganglion7.68e-079
nuclear complex of neuraxis7.68e-079
aggregate regional part of brain7.68e-079
collection of basal ganglia7.68e-079
cerebral subcortex7.68e-079
segmental subdivision of hindbrain8.32e-0712
hindbrain8.32e-0712
presumptive hindbrain8.32e-0712
nucleus of brain8.36e-079
neural nucleus8.36e-079


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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