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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C3818_pineal_cerebellum_thalamus_optic_occipital_globus_pituitary
|full_id=C3818_pineal_cerebellum_thalamus_optic_occipital_globus_pituitary
|id=C3818
|id=C3818

Revision as of 16:47, 12 September 2012


Full id: C3818_pineal_cerebellum_thalamus_optic_occipital_globus_pituitary



Phase1 CAGE Peaks

Hg19::chr19:52097613..52097642,-p1@FLJ30403
Hg19::chr19:52097643..52097664,-p2@FLJ30403
Hg19::chr19:57183322..57183358,+p1@FJ997633


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


No GOStat results

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
adult organism9.07e-41115
neural tube1.03e-3257
neural rod1.03e-3257
future spinal cord1.03e-3257
neural keel1.03e-3257
regional part of brain9.39e-2859
brain3.14e-2769
future brain3.14e-2769
central nervous system3.27e-2782
regional part of nervous system1.30e-2594
nervous system1.30e-2594
anterior neural tube9.09e-2542
regional part of forebrain3.23e-2441
forebrain3.23e-2441
future forebrain3.23e-2441
neural plate3.62e-2486
presumptive neural plate3.62e-2486
neurectoderm3.27e-2390
anterior region of body6.55e-20129
craniocervical region6.55e-20129
gray matter1.12e-1934
brain grey matter1.12e-1934
telencephalon1.21e-1934
head2.33e-19123
pre-chordal neural plate3.54e-1961
regional part of telencephalon4.91e-1933
cerebral hemisphere2.65e-1832
ectoderm-derived structure1.39e-17169
ectoderm2.94e-17173
presumptive ectoderm2.94e-17173
regional part of cerebral cortex1.01e-1422
cerebral cortex2.71e-1425
pallium2.71e-1425
neocortex1.17e-1320
posterior neural tube5.23e-0915
chordal neural plate5.23e-0915
organ part1.84e-08219
segmental subdivision of nervous system6.45e-0813
segmental subdivision of hindbrain3.04e-0712
hindbrain3.04e-0712
presumptive hindbrain3.04e-0712
nucleus of brain6.97e-079
neural nucleus6.97e-079
basal ganglion8.49e-079
nuclear complex of neuraxis8.49e-079
aggregate regional part of brain8.49e-079
collection of basal ganglia8.49e-079
cerebral subcortex8.49e-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


(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
ATF3#467214.97544968400580.005768294540793880.0259569526281172
BCLAF1#9774214.43509840674790.006201147435546130.0273855823510931
ESR1#2099220.51240219743630.003099741577095180.0163090131269644
SETDB1#9869226.8800174520070.001814468907964410.0108933845871979
SIX5#147912211.3911435703060.009873820081429030.0370739491455821
ZBTB33#10009221.10981668665410.002928597060603240.0156378009311489
ZNF143#7702313.50087655222790.0004062804962997170.00389030244366426



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.