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|ontology_enrichment_disease=
|ontology_enrichment_disease=
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}}
}}

Revision as of 20:49, 8 August 2012


Full id: C787_cerebellum_pons_locus_brain_medulla_paracentral_temporal



Phase1 CAGE Peaks

Hg19::chr10:73848474..73848491,-p10@SPOCK2
Hg19::chr11:105480740..105480750,+p9@GRIA4
Hg19::chr15:79724672..79724683,+p1@KIAA1024
Hg19::chr17:26902537..26902548,-p3@ALDOC
Hg19::chr17:26903863..26903893,-p2@ALDOC
Hg19::chr1:111148241..111148250,-p25@KCNA2
Hg19::chr1:111148637..111148657,-p7@KCNA2
Hg19::chr22:47016277..47016290,+p4@GRAMD4
Hg19::chr3:9745510..9745528,+p1@CPNE9
Hg19::chr5:175308178..175308191,+p18@CPLX2


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:0043303mast cell degranulation0.0362732334316763
GO:0002448mast cell mediated immunity0.0362732334316763
GO:0045576mast cell activation0.0362732334316763
GO:0043299leukocyte degranulation0.0362732334316763
GO:0004332fructose-bisphosphate aldolase activity0.0362732334316763
GO:0002444myeloid leukocyte mediated immunity0.0362732334316763
GO:0005251delayed rectifier potassium channel activity0.0376409746877379
GO:0016832aldehyde-lyase activity0.0376409746877379
GO:0022836gated channel activity0.0376409746877379
GO:0019905syntaxin binding0.0376409746877379
GO:0000149SNARE binding0.0376409746877379
GO:0007215glutamate signaling pathway0.0376409746877379
GO:0006000fructose metabolic process0.0376409746877379
GO:0007416synaptogenesis0.0376409746877379
GO:0002274myeloid leukocyte activation0.0376409746877379
GO:0005216ion channel activity0.0376409746877379
GO:0022838substrate specific channel activity0.0376409746877379
GO:0022803passive transmembrane transporter activity0.0376409746877379
GO:0015267channel activity0.0376409746877379
GO:0006904vesicle docking during exocytosis0.0376409746877379
GO:0004970ionotropic glutamate receptor activity0.0376409746877379
GO:0048278vesicle docking0.0376409746877379
GO:0022406membrane docking0.0376409746877379
GO:0050808synapse organization and biogenesis0.0376409746877379
GO:0005234extracellular-glutamate-gated ion channel activity0.0376409746877379
GO:0030198extracellular matrix organization and biogenesis0.0426674863585992
GO:0045055regulated secretory pathway0.0473152348550167



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 tube1.94e-2857
neural rod1.94e-2857
future spinal cord1.94e-2857
neural keel1.94e-2857
regional part of nervous system1.57e-2494
nervous system1.57e-2494
central nervous system2.10e-2482
regional part of brain2.83e-2359
regional part of forebrain1.62e-2241
forebrain1.62e-2241
future forebrain1.62e-2241
anterior neural tube3.73e-2242
adult organism1.42e-21115
neural plate4.21e-2186
presumptive neural plate4.21e-2186
brain6.86e-2169
future brain6.86e-2169
neurectoderm3.45e-2090
gray matter1.48e-1834
brain grey matter1.48e-1834
telencephalon1.61e-1834
regional part of telencephalon7.39e-1833
cerebral hemisphere2.27e-1732
pre-chordal neural plate2.95e-1661
regional part of cerebral cortex2.82e-1522
neocortex4.25e-1420
cerebral cortex3.45e-1325
pallium3.45e-1325
tube4.39e-11194
anterior region of body2.30e-10129
craniocervical region2.30e-10129
head1.04e-09123
ectoderm-derived structure1.37e-09169
ectoderm2.25e-09173
presumptive ectoderm2.25e-09173
posterior neural tube1.84e-0715
chordal neural plate1.84e-0715
anatomical cluster2.04e-07286
anatomical conduit2.27e-07241
nucleus of brain6.56e-079
neural nucleus6.56e-079
basal ganglion7.99e-079
nuclear complex of neuraxis7.99e-079
aggregate regional part of brain7.99e-079
collection of basal ganglia7.99e-079
cerebral subcortex7.99e-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)

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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.