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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C2350_medial_brain_amygdala_hippocampus_neuroectodermal_occipital_small
|full_id=C2350_medial_brain_amygdala_hippocampus_neuroectodermal_occipital_small
|gostat_on_coexpression_clusters=GO:0035235!ionotropic glutamate receptor signaling pathway!0.0147744428218659!478$GO:0006928!cell motility!0.0147744428218659!8936;478$GO:0051674!localization of cell!0.0147744428218659!8936;478$GO:0008542!visual learning!0.0147744428218659!478$GO:0005890!sodium:potassium-exchanging ATPase complex!0.0147744428218659!478$GO:0007632!visual behavior!0.0147744428218659!478$GO:0007613!memory!0.0147744428218659!478$GO:0030641!cellular hydrogen ion homeostasis!0.0147744428218659!478$GO:0008344!adult locomotory behavior!0.0147744428218659!478$GO:0030004!cellular monovalent inorganic cation homeostasis!0.0147744428218659!478$GO:0055067!monovalent inorganic cation homeostasis!0.0147744428218659!478$GO:0005391!sodium:potassium-exchanging ATPase activity!0.0147744428218659!478$GO:0007612!learning!0.0147744428218659!478$GO:0030317!sperm motility!0.0158154819779361!478$GO:0007215!glutamate signaling pathway!0.0158154819779361!478$GO:0030534!adult behavior!0.0190599366900479!478$GO:0030041!actin filament polymerization!0.0205939328850991!8936$GO:0007611!learning and/or memory!0.0275956377504917!478$GO:0008154!actin polymerization and/or depolymerization!0.0355408482650936!8936$GO:0042493!response to drug!0.0355408482650936!478$GO:0009416!response to light stimulus!0.0434963365107109!478$GO:0031402!sodium ion binding!0.0474286948824892!478$GO:0051258!protein polymerization!0.0474286948824892!8936$GO:0009314!response to radiation!0.0474286948824892!478
|gostat_on_coexpression_clusters=GO:0035235!ionotropic glutamate receptor signaling pathway!0.0147744428218659!478$GO:0006928!cell motility!0.0147744428218659!8936;478$GO:0051674!localization of cell!0.0147744428218659!8936;478$GO:0008542!visual learning!0.0147744428218659!478$GO:0005890!sodium:potassium-exchanging ATPase complex!0.0147744428218659!478$GO:0007632!visual behavior!0.0147744428218659!478$GO:0007613!memory!0.0147744428218659!478$GO:0030641!cellular hydrogen ion homeostasis!0.0147744428218659!478$GO:0008344!adult locomotory behavior!0.0147744428218659!478$GO:0030004!cellular monovalent inorganic cation homeostasis!0.0147744428218659!478$GO:0055067!monovalent inorganic cation homeostasis!0.0147744428218659!478$GO:0005391!sodium:potassium-exchanging ATPase activity!0.0147744428218659!478$GO:0007612!learning!0.0147744428218659!478$GO:0030317!sperm motility!0.0158154819779361!478$GO:0007215!glutamate signaling pathway!0.0158154819779361!478$GO:0030534!adult behavior!0.0190599366900479!478$GO:0030041!actin filament polymerization!0.0205939328850991!8936$GO:0007611!learning and/or memory!0.0275956377504917!478$GO:0008154!actin polymerization and/or depolymerization!0.0355408482650936!8936$GO:0042493!response to drug!0.0355408482650936!478$GO:0009416!response to light stimulus!0.0434963365107109!478$GO:0031402!sodium ion binding!0.0474286948824892!478$GO:0051258!protein polymerization!0.0474286948824892!8936$GO:0009314!response to radiation!0.0474286948824892!478

Revision as of 15:03, 12 September 2012


Full id: C2350_medial_brain_amygdala_hippocampus_neuroectodermal_occipital_small



Phase1 CAGE Peaks

Hg19::chr15:77907614..77907624,-p17@LINGO1
Hg19::chr15:77907723..77907735,-p13@LINGO1
Hg19::chr19:42486186..42486199,-p6@ATP1A3
Hg19::chr6:110448757..110448782,-p9@WASF1


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:0035235ionotropic glutamate receptor signaling pathway0.0147744428218659
GO:0006928cell motility0.0147744428218659
GO:0051674localization of cell0.0147744428218659
GO:0008542visual learning0.0147744428218659
GO:0005890sodium:potassium-exchanging ATPase complex0.0147744428218659
GO:0007632visual behavior0.0147744428218659
GO:0007613memory0.0147744428218659
GO:0030641cellular hydrogen ion homeostasis0.0147744428218659
GO:0008344adult locomotory behavior0.0147744428218659
GO:0030004cellular monovalent inorganic cation homeostasis0.0147744428218659
GO:0055067monovalent inorganic cation homeostasis0.0147744428218659
GO:0005391sodium:potassium-exchanging ATPase activity0.0147744428218659
GO:0007612learning0.0147744428218659
GO:0030317sperm motility0.0158154819779361
GO:0007215glutamate signaling pathway0.0158154819779361
GO:0030534adult behavior0.0190599366900479
GO:0030041actin filament polymerization0.0205939328850991
GO:0007611learning and/or memory0.0275956377504917
GO:0008154actin polymerization and/or depolymerization0.0355408482650936
GO:0042493response to drug0.0355408482650936
GO:0009416response to light stimulus0.0434963365107109
GO:0031402sodium ion binding0.0474286948824892
GO:0051258protein polymerization0.0474286948824892
GO:0009314response to radiation0.0474286948824892



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>disease_data<br>


Cell Type
Ontology termp-valuen
neurectodermal cell2.27e-0759
Uber Anatomy
Ontology termp-valuen
regional part of nervous system2.48e-3194
nervous system2.48e-3194
central nervous system4.98e-3082
neural tube4.39e-2657
neural rod4.39e-2657
future spinal cord4.39e-2657
neural keel4.39e-2657
neurectoderm8.14e-2590
brain3.37e-2469
future brain3.37e-2469
gray matter1.02e-2234
brain grey matter1.02e-2234
telencephalon1.18e-2234
regional part of forebrain1.56e-2241
forebrain1.56e-2241
future forebrain1.56e-2241
neural plate5.21e-2286
presumptive neural plate5.21e-2286
regional part of telencephalon8.72e-2233
regional part of brain1.04e-2159
anterior neural tube1.27e-2142
cerebral hemisphere1.60e-2132
ectoderm4.13e-21173
presumptive ectoderm4.13e-21173
regional part of cerebral cortex4.56e-1922
ectoderm-derived structure7.05e-19169
cerebral cortex3.56e-1825
pallium3.56e-1825
neocortex2.49e-1720
pre-chordal neural plate4.60e-1761
head1.21e-15123
anterior region of body4.76e-15129
craniocervical region4.76e-15129
adult organism5.68e-14115
gyrus7.21e-076
Disease
Ontology termp-valuen
neuroectodermal tumor6.80e-0710


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.