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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C2113_brain_medial_hippocampus_diencephalon_amygdala_substantia_olfactory
|full_id=C2113_brain_medial_hippocampus_diencephalon_amygdala_substantia_olfactory
|gostat_on_coexpression_clusters=GO:0005918!septate junction!0.00423878488166725!7082$GO:0015018!galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase activity!0.00953487963183759!27087$GO:0008499!UDP-galactose:beta-N-acetylglucosamine beta-1,3-galactosyltransferase activity!0.00953487963183759!27087$GO:0048531!beta-1,3-galactosyltransferase activity!0.00953487963183759!27087$GO:0005913!cell-cell adherens junction!0.00953487963183759!7082$GO:0007043!intercellular junction assembly!0.00953487963183759!7082$GO:0035250!UDP-galactosyltransferase activity!0.00953487963183759!27087$GO:0045216!intercellular junction assembly and maintenance!0.00953487963183759!7082$GO:0007028!cytoplasm organization and biogenesis!0.0112995998696127!7082$GO:0015020!glucuronosyltransferase activity!0.014404868632055!27087$GO:0008378!galactosyltransferase activity!0.015404915412871!27087$GO:0005912!adherens junction!0.0190596523614523!7082$GO:0016323!basolateral plasma membrane!0.026911659244122!7082$GO:0005923!tight junction!0.026911659244122!7082$GO:0043296!apical junction complex!0.027774445781206!7082$GO:0016327!apicolateral plasma membrane!0.027774445781206!7082$GO:0008194!UDP-glycosyltransferase activity!0.0343395765145704!27087$GO:0030145!manganese ion binding!0.0345423555680781!27087$GO:0005911!intercellular junction!0.0349728933440095!7082$GO:0006486!protein amino acid glycosylation!0.0349728933440095!27087$GO:0043413!biopolymer glycosylation!0.0349728933440095!27087$GO:0009101!glycoprotein biosynthetic process!0.0349728933440095!27087$GO:0009100!glycoprotein metabolic process!0.0382165680597289!27087$GO:0016758!transferase activity, transferring hexosyl groups!0.0494245767274581!27087
|gostat_on_coexpression_clusters=GO:0005918!septate junction!0.00423878488166725!7082$GO:0015018!galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase activity!0.00953487963183759!27087$GO:0008499!UDP-galactose:beta-N-acetylglucosamine beta-1,3-galactosyltransferase activity!0.00953487963183759!27087$GO:0048531!beta-1,3-galactosyltransferase activity!0.00953487963183759!27087$GO:0005913!cell-cell adherens junction!0.00953487963183759!7082$GO:0007043!intercellular junction assembly!0.00953487963183759!7082$GO:0035250!UDP-galactosyltransferase activity!0.00953487963183759!27087$GO:0045216!intercellular junction assembly and maintenance!0.00953487963183759!7082$GO:0007028!cytoplasm organization and biogenesis!0.0112995998696127!7082$GO:0015020!glucuronosyltransferase activity!0.014404868632055!27087$GO:0008378!galactosyltransferase activity!0.015404915412871!27087$GO:0005912!adherens junction!0.0190596523614523!7082$GO:0016323!basolateral plasma membrane!0.026911659244122!7082$GO:0005923!tight junction!0.026911659244122!7082$GO:0043296!apical junction complex!0.027774445781206!7082$GO:0016327!apicolateral plasma membrane!0.027774445781206!7082$GO:0008194!UDP-glycosyltransferase activity!0.0343395765145704!27087$GO:0030145!manganese ion binding!0.0345423555680781!27087$GO:0005911!intercellular junction!0.0349728933440095!7082$GO:0006486!protein amino acid glycosylation!0.0349728933440095!27087$GO:0043413!biopolymer glycosylation!0.0349728933440095!27087$GO:0009101!glycoprotein biosynthetic process!0.0349728933440095!27087$GO:0009100!glycoprotein metabolic process!0.0382165680597289!27087$GO:0016758!transferase activity, transferring hexosyl groups!0.0494245767274581!27087

Revision as of 14:47, 12 September 2012


Full id: C2113_brain_medial_hippocampus_diencephalon_amygdala_substantia_olfactory



Phase1 CAGE Peaks

Hg19::chr11:134281749..134281759,-p5@B3GAT1
Hg19::chr15:30248510..30248535,-p32@TJP1
Hg19::chr20:58349377..58349415,+p@chr20:58349377..58349415
+
Hg19::chr3:58551422..58551434,-p@chr3:58551422..58551434
-


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:0005918septate junction0.00423878488166725
GO:0015018galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase activity0.00953487963183759
GO:0008499UDP-galactose:beta-N-acetylglucosamine beta-1,3-galactosyltransferase activity0.00953487963183759
GO:0048531beta-1,3-galactosyltransferase activity0.00953487963183759
GO:0005913cell-cell adherens junction0.00953487963183759
GO:0007043intercellular junction assembly0.00953487963183759
GO:0035250UDP-galactosyltransferase activity0.00953487963183759
GO:0045216intercellular junction assembly and maintenance0.00953487963183759
GO:0007028cytoplasm organization and biogenesis0.0112995998696127
GO:0015020glucuronosyltransferase activity0.014404868632055
GO:0008378galactosyltransferase activity0.015404915412871
GO:0005912adherens junction0.0190596523614523
GO:0016323basolateral plasma membrane0.026911659244122
GO:0005923tight junction0.026911659244122
GO:0043296apical junction complex0.027774445781206
GO:0016327apicolateral plasma membrane0.027774445781206
GO:0008194UDP-glycosyltransferase activity0.0343395765145704
GO:0030145manganese ion binding0.0345423555680781
GO:0005911intercellular junction0.0349728933440095
GO:0006486protein amino acid glycosylation0.0349728933440095
GO:0043413biopolymer glycosylation0.0349728933440095
GO:0009101glycoprotein biosynthetic process0.0349728933440095
GO:0009100glycoprotein metabolic process0.0382165680597289
GO:0016758transferase activity, transferring hexosyl groups0.0494245767274581



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
neurectodermal cell5.35e-0859
neuronal stem cell1.28e-078
neural cell4.31e-0725
Uber Anatomy
Ontology termp-valuen
central nervous system2.38e-5882
regional part of nervous system1.03e-5694
nervous system1.03e-5694
neural tube4.15e-5357
neural rod4.15e-5357
future spinal cord4.15e-5357
neural keel4.15e-5357
brain2.18e-4569
future brain2.18e-4569
regional part of brain2.66e-4359
gray matter4.71e-3834
brain grey matter4.71e-3834
telencephalon5.90e-3834
regional part of forebrain3.47e-3741
forebrain3.47e-3741
future forebrain3.47e-3741
regional part of telencephalon1.30e-3633
anterior neural tube5.05e-3642
adult organism6.66e-36115
cerebral hemisphere5.45e-3532
neural plate5.83e-3486
presumptive neural plate5.83e-3486
neurectoderm3.25e-3390
ectoderm-derived structure6.16e-29169
ectoderm7.89e-29173
presumptive ectoderm7.89e-29173
cerebral cortex2.52e-2525
pallium2.52e-2525
regional part of cerebral cortex1.13e-2422
pre-chordal neural plate1.30e-2261
head3.82e-22123
neocortex7.82e-2220
anterior region of body3.41e-21129
craniocervical region3.41e-21129
posterior neural tube6.54e-1815
chordal neural plate6.54e-1815
segmental subdivision of nervous system4.73e-1513
nucleus of brain2.05e-149
neural nucleus2.05e-149
basal ganglion2.86e-149
nuclear complex of neuraxis2.86e-149
aggregate regional part of brain2.86e-149
collection of basal ganglia2.86e-149
cerebral subcortex2.86e-149
segmental subdivision of hindbrain1.03e-1312
hindbrain1.03e-1312
presumptive hindbrain1.03e-1312
telencephalic nucleus1.42e-117
tube1.97e-11194
gyrus3.71e-106
regional part of metencephalon6.24e-109
metencephalon6.24e-109
future metencephalon6.24e-109
temporal lobe6.40e-107
brainstem1.65e-098
limbic system1.28e-085
anatomical conduit6.92e-08241
corpus striatum2.53e-074
striatum2.53e-074
ventral part of telencephalon2.53e-074
future corpus striatum2.53e-074
organ part8.32e-07219


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.