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Coexpression cluster:C3080: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0001049!8.76e-109!56;UBERON:0005068!8.76e-109!56;UBERON:0006241!8.76e-109!56;UBERON:0007135!8.76e-109!56;UBERON:0000073!3.73e-97!53;UBERON:0002616!3.73e-97!53;UBERON:0001017!1.14e-84!81;UBERON:0000955!3.70e-82!68;UBERON:0006238!3.70e-82!68;UBERON:0003075!5.08e-76!82;UBERON:0007284!5.08e-76!82;UBERON:0001016!1.46e-75!89;UBERON:0002346!3.84e-72!86;UBERON:0002780!1.24e-68!41;UBERON:0001890!1.24e-68!41;UBERON:0003080!1.24e-68!41;UBERON:0006240!1.24e-68!41;UBERON:0003528!1.42e-65!34;UBERON:0002020!1.42e-65!34;UBERON:0001893!5.53e-65!34;UBERON:0007023!4.05e-59!114;UBERON:0010371!2.43e-58!104;UBERON:0001869!4.99e-58!32;UBERON:0002791!6.10e-58!32;UBERON:0003056!6.96e-48!61;UBERON:0010314!9.20e-47!132;UBERON:0003076!1.06e-40!15;UBERON:0003057!1.06e-40!15;UBERON:0000125!1.09e-39!9;UBERON:0002308!1.09e-39!9;UBERON:0002420!4.13e-39!9;UBERON:0007245!4.13e-39!9;UBERON:0010009!4.13e-39!9;UBERON:0010011!4.13e-39!9;UBERON:0000454!4.13e-39!9;UBERON:0004121!6.60e-38!171;UBERON:0000924!6.60e-38!171;UBERON:0006601!6.60e-38!171;UBERON:0002619!1.21e-37!22;UBERON:0001950!3.06e-36!20;UBERON:0000956!6.64e-33!25;UBERON:0000203!6.64e-33!25;UBERON:0009663!3.26e-31!7;UBERON:0004733!5.64e-29!12;UBERON:0002028!5.64e-29!12;UBERON:0007277!5.64e-29!12;UBERON:0011216!1.36e-28!223;UBERON:0002298!5.41e-27!6;UBERON:0004732!1.28e-26!13;UBERON:0000025!2.95e-26!192;UBERON:0004111!2.40e-19!240;UBERON:0000369!3.64e-19!4;UBERON:0002435!3.64e-19!4;UBERON:0000204!3.64e-19!4;UBERON:0010082!3.64e-19!4;UBERON:0002680!1.70e-17!9;UBERON:0001895!1.70e-17!9;UBERON:0010092!1.70e-17!9;UBERON:0005383!7.19e-15!3;UBERON:0005382!7.19e-15!3;UBERON:0000477!1.27e-14!373;UBERON:0000988!2.21e-14!3;UBERON:0001896!2.21e-14!3;UBERON:0005290!2.21e-14!3;UBERON:0010096!2.21e-14!3;UBERON:0000483!2.38e-14!306;UBERON:0000064!3.78e-14!218;UBERON:0000119!3.97e-14!309;UBERON:0002240!4.91e-14!3;UBERON:0005174!4.91e-14!3;UBERON:0001137!4.91e-14!3;UBERON:0000349!5.01e-14!5;UBERON:0002021!1.38e-13!5;UBERON:0000200!9.60e-12!6;UBERON:0000481!7.17e-11!342;UBERON:0001873!1.76e-10!2;UBERON:0010122!1.76e-10!2;UBERON:0002148!3.32e-10!2;UBERON:0006331!3.32e-10!2;UBERON:0009662!3.32e-10!2;UBERON:0001875!4.96e-10!2;UBERON:0006514!4.96e-10!2;UBERON:0001897!5.42e-10!2;UBERON:0010225!5.42e-10!2;UBERON:0001871!5.65e-10!6;UBERON:0001876!1.25e-09!2;UBERON:0000062!1.59e-08!503;UBERON:0001872!3.82e-08!5;UBERON:0002037!3.50e-07!6;UBERON:0006215!3.50e-07!6
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}}
}}

Revision as of 15:55, 26 November 2012


Full id: C3080_locus_putamen_caudate_globus_medulla_nucleus_diencephalon



Phase1 CAGE Peaks

Hg19::chr11:107462738..107462754,-p@chr11:107462738..107462754
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Hg19::chr11:47616752..47616783,-p@chr11:47616752..47616783
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Hg19::chr5:75379158..75379169,+p4@SV2C


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
neural tube8.76e-10956
neural rod8.76e-10956
future spinal cord8.76e-10956
neural keel8.76e-10956
regional part of nervous system3.73e-9753
regional part of brain3.73e-9753
central nervous system1.14e-8481
brain3.70e-8268
future brain3.70e-8268
neural plate5.08e-7682
presumptive neural plate5.08e-7682
nervous system1.46e-7589
neurectoderm3.84e-7286
regional part of forebrain1.24e-6841
forebrain1.24e-6841
anterior neural tube1.24e-6841
future forebrain1.24e-6841
brain grey matter1.42e-6534
gray matter1.42e-6534
telencephalon5.53e-6534
adult organism4.05e-59114
ecto-epithelium2.43e-58104
cerebral hemisphere4.99e-5832
regional part of telencephalon6.10e-5832
pre-chordal neural plate6.96e-4861
structure with developmental contribution from neural crest9.20e-47132
posterior neural tube1.06e-4015
chordal neural plate1.06e-4015
neural nucleus1.09e-399
nucleus of brain1.09e-399
basal ganglion4.13e-399
nuclear complex of neuraxis4.13e-399
aggregate regional part of brain4.13e-399
collection of basal ganglia4.13e-399
cerebral subcortex4.13e-399
ectoderm-derived structure6.60e-38171
ectoderm6.60e-38171
presumptive ectoderm6.60e-38171
regional part of cerebral cortex1.21e-3722
neocortex3.06e-3620
cerebral cortex6.64e-3325
pallium6.64e-3325
telencephalic nucleus3.26e-317
segmental subdivision of hindbrain5.64e-2912
hindbrain5.64e-2912
presumptive hindbrain5.64e-2912
organ system subdivision1.36e-28223
brainstem5.41e-276
segmental subdivision of nervous system1.28e-2613
tube2.95e-26192
anatomical conduit2.40e-19240
corpus striatum3.64e-194
striatum3.64e-194
ventral part of telencephalon3.64e-194
future corpus striatum3.64e-194
regional part of metencephalon1.70e-179
metencephalon1.70e-179
future metencephalon1.70e-179
caudate-putamen7.19e-153
dorsal striatum7.19e-153
anatomical cluster1.27e-14373
pons2.21e-143
medulla oblongata2.21e-143
myelencephalon2.21e-143
future myelencephalon2.21e-143
epithelium2.38e-14306
organ part3.78e-14218
cell layer3.97e-14309
spinal cord4.91e-143
dorsal region element4.91e-143
dorsum4.91e-143
limbic system5.01e-145
occipital lobe1.38e-135
gyrus9.60e-126
multi-tissue structure7.17e-11342
caudate nucleus1.76e-102
future caudate nucleus1.76e-102
locus ceruleus3.32e-102
brainstem nucleus3.32e-102
hindbrain nucleus3.32e-102
globus pallidus4.96e-102
pallidum4.96e-102
dorsal plus ventral thalamus5.42e-102
thalamic complex5.42e-102
temporal lobe5.65e-106
amygdala1.25e-092
organ1.59e-08503
parietal lobe3.82e-085
cerebellum3.50e-076
rhombic lip3.50e-076


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.