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|ontology_enrichment_disease=
|ontology_enrichment_disease=
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}}
}}

Revision as of 18:10, 8 August 2012


Full id: C2297_cerebellum_pituitary_insula_putamen_nucleus_parietal_caudate



Phase1 CAGE Peaks

Hg19::chr14:50159813..50159853,+p1@KLHDC1
Hg19::chr14:50159858..50159893,+p2@KLHDC1
Hg19::chr1:8585945..8586056,-p3@RERE
Hg19::chr6:163148780..163148813,-p1@PARK2


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:0008267poly-glutamine tract binding0.00529848110208407
GO:0006607NLS-bearing substrate import into nucleus0.0344340443057272



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
mature alpha-beta T cell5.63e-0718
alpha-beta T cell5.63e-0718
immature T cell5.63e-0718
mature T cell5.63e-0718
immature alpha-beta T cell5.63e-0718
Uber Anatomy
Ontology termp-valuen
adult organism1.96e-50115
neural tube1.96e-2957
neural rod1.96e-2957
future spinal cord1.96e-2957
neural keel1.96e-2957
regional part of brain1.59e-2759
brain5.11e-2569
future brain5.11e-2569
central nervous system1.10e-2382
anterior neural tube8.98e-2342
regional part of forebrain1.31e-2241
forebrain1.31e-2241
future forebrain1.31e-2241
regional part of nervous system3.24e-2294
nervous system3.24e-2294
neural plate1.23e-2086
presumptive neural plate1.23e-2086
neurectoderm5.15e-2090
telencephalon1.39e-1834
gray matter2.46e-1834
brain grey matter2.46e-1834
regional part of telencephalon6.41e-1833
anterior region of body1.09e-17129
craniocervical region1.09e-17129
cerebral hemisphere2.30e-1732
head1.01e-16123
pre-chordal neural plate8.12e-1561
regional part of cerebral cortex1.30e-1422
neocortex1.31e-1320
ectoderm-derived structure2.64e-13169
ectoderm3.56e-13173
presumptive ectoderm3.56e-13173
cerebral cortex6.51e-1325
pallium6.51e-1325
posterior neural tube8.23e-0815
chordal neural plate8.23e-0815
basal ganglion3.95e-079
nuclear complex of neuraxis3.95e-079
aggregate regional part of brain3.95e-079
collection of basal ganglia3.95e-079
cerebral subcortex3.95e-079
nucleus of brain5.51e-079
neural nucleus5.51e-079
segmental subdivision of nervous system7.67e-0713


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.