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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C3393_hereditary_caudate_parietal_breast_locus_putamen_pons
|full_id=C3393_hereditary_caudate_parietal_breast_locus_putamen_pons
|id=C3393
|id=C3393

Revision as of 16:18, 12 September 2012


Full id: C3393_hereditary_caudate_parietal_breast_locus_putamen_pons



Phase1 CAGE Peaks

Hg19::chr14:100485771..100485833,+p4@EVL
Hg19::chr14:100485908..100485924,+p25@EVL
Hg19::chr14:100485927..100485938,+p29@EVL


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 organism2.60e-44115
neural tube1.37e-4157
neural rod1.37e-4157
future spinal cord1.37e-4157
neural keel1.37e-4157
neural plate6.06e-4186
presumptive neural plate6.06e-4186
neurectoderm2.45e-3990
regional part of nervous system7.41e-3894
nervous system7.41e-3894
central nervous system1.10e-3782
regional part of brain1.25e-3759
brain2.23e-3569
future brain2.23e-3569
pre-chordal neural plate6.87e-3461
anterior neural tube1.52e-3342
regional part of forebrain7.40e-3341
forebrain7.40e-3341
future forebrain7.40e-3341
gray matter7.39e-2734
brain grey matter7.39e-2734
telencephalon1.22e-2634
regional part of telencephalon9.69e-2633
cerebral hemisphere5.87e-2532
anterior region of body1.07e-23129
craniocervical region1.07e-23129
head1.75e-23123
ectoderm-derived structure5.37e-23169
ectoderm1.38e-22173
presumptive ectoderm1.38e-22173
regional part of cerebral cortex4.71e-2222
neocortex1.27e-2020
organ part1.68e-18219
cerebral cortex2.56e-1825
pallium2.56e-1825
epithelium1.27e-16309
cell layer4.43e-16312
tube2.09e-15194
multi-tissue structure3.33e-15347
organism subdivision2.33e-12365
organ2.66e-11511
anatomical conduit8.56e-11241
nucleus of brain3.69e-109
neural nucleus3.69e-109
anatomical cluster3.93e-10286
embryo4.45e-10612
basal ganglion1.42e-099
nuclear complex of neuraxis1.42e-099
aggregate regional part of brain1.42e-099
collection of basal ganglia1.42e-099
cerebral subcortex1.42e-099
posterior neural tube3.43e-0915
chordal neural plate3.43e-0915
multi-cellular organism4.24e-09659
brainstem7.85e-098
embryonic structure7.91e-09605
developing anatomical structure7.91e-09605
temporal lobe1.21e-087
germ layer1.44e-08604
embryonic tissue1.44e-08604
presumptive structure1.44e-08604
epiblast (generic)1.44e-08604
telencephalic nucleus3.57e-087
diencephalon1.27e-077
future diencephalon1.27e-077
segmental subdivision of nervous system1.58e-0713
gyrus2.86e-076
organ segment5.25e-0797


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
FOXA2#3170216.42030916844350.004810682352105480.0225818173478154
TRIM28#10155318.59052504526250.0001555969297255280.00196688304812447
USF1#739136.361499277207960.00388404057290560.0189846638926236



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.

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