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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C4597_putamen_caudate_nucleus_left_insula_heart_temporal
|full_id=C4597_putamen_caudate_nucleus_left_insula_heart_temporal
|id=C4597
|id=C4597

Revision as of 17:42, 12 September 2012


Full id: C4597_putamen_caudate_nucleus_left_insula_heart_temporal



Phase1 CAGE Peaks

Hg19::chr6:36807213..36807231,-p3@CPNE5
Hg19::chr6:36807240..36807269,-p4@CPNE5
Hg19::chr6:36807270..36807282,-p7@CPNE5


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>cell_data<br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
adult organism9.20e-61115
neural tube1.54e-3857
neural rod1.54e-3857
future spinal cord1.54e-3857
neural keel1.54e-3857
central nervous system1.30e-3482
anterior neural tube1.73e-3242
brain6.70e-3269
future brain6.70e-3269
regional part of forebrain8.05e-3241
forebrain8.05e-3241
future forebrain8.05e-3241
regional part of brain1.64e-3159
neural plate2.51e-3086
presumptive neural plate2.51e-3086
regional part of nervous system1.88e-2994
nervous system1.88e-2994
neurectoderm4.87e-2890
telencephalon1.40e-2634
gray matter2.85e-2634
brain grey matter2.85e-2634
regional part of telencephalon1.94e-2533
cerebral hemisphere4.69e-2532
tube8.14e-23194
pre-chordal neural plate2.11e-2261
anatomical conduit7.14e-22241
neocortex2.97e-2120
regional part of cerebral cortex7.17e-2122
anatomical cluster7.84e-19286
cerebral cortex1.71e-1725
pallium1.71e-1725
anterior region of body2.22e-17129
craniocervical region2.22e-17129
endothelium1.45e-1618
blood vessel endothelium1.45e-1618
cardiovascular system endothelium1.45e-1618
head3.32e-16123
ectoderm-derived structure5.53e-15169
ectoderm3.88e-14173
presumptive ectoderm3.88e-14173
epithelium1.42e-13309
cell layer3.77e-13312
simple squamous epithelium1.99e-1222
squamous epithelium1.97e-1125
basal ganglion8.74e-119
nuclear complex of neuraxis8.74e-119
aggregate regional part of brain8.74e-119
collection of basal ganglia8.74e-119
cerebral subcortex8.74e-119
multi-cellular organism1.05e-10659
nucleus of brain1.67e-109
neural nucleus1.67e-109
endothelial tube3.58e-099
arterial system endothelium3.58e-099
endothelium of artery3.58e-099
telencephalic nucleus7.35e-097
anatomical system7.43e-09625
anatomical group9.06e-09626
gyrus4.67e-086
posterior neural tube1.55e-0715
chordal neural plate1.55e-0715
temporal lobe1.59e-077
brainstem1.98e-078
organ part3.91e-07219
embryo4.71e-07612
parietal lobe5.16e-075
organism subdivision6.14e-07365
occipital lobe8.76e-075


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
EGR1#195834.988179094810140.008056488137383440.0322244098111979



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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