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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C4859_rectum_amygdala_hippocampus_colon_smooth_brain_cerebral
|full_id=C4859_rectum_amygdala_hippocampus_colon_smooth_brain_cerebral
|id=C4859
|id=C4859

Revision as of 18:00, 12 September 2012


Full id: C4859_rectum_amygdala_hippocampus_colon_smooth_brain_cerebral



Phase1 CAGE Peaks

Hg19::chrX:152939231..152939251,-p6@PNCK
Hg19::chrX:152939252..152939291,-p1@PNCK
Hg19::chrX:152939378..152939398,-p3@PNCK


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 organism2.43e-57115
neural tube5.64e-4157
neural rod5.64e-4157
future spinal cord5.64e-4157
neural keel5.64e-4157
central nervous system5.87e-3782
neurectoderm3.84e-3690
regional part of forebrain4.82e-3541
forebrain4.82e-3541
future forebrain4.82e-3541
regional part of nervous system5.41e-3594
nervous system5.41e-3594
anterior neural tube7.33e-3442
neural plate1.46e-3386
presumptive neural plate1.46e-3386
regional part of brain1.61e-3359
brain2.73e-3369
future brain2.73e-3369
telencephalon5.22e-3334
gray matter5.63e-3334
brain grey matter5.63e-3334
cerebral hemisphere7.15e-3232
regional part of telencephalon7.25e-3233
pre-chordal neural plate3.95e-2761
regional part of cerebral cortex6.28e-2722
neocortex1.20e-2420
cerebral cortex2.55e-2425
pallium2.55e-2425
anterior region of body1.63e-19129
craniocervical region1.63e-19129
head2.25e-18123
ectoderm1.96e-17173
presumptive ectoderm1.96e-17173
ectoderm-derived structure1.04e-15169
organ part1.03e-13219
organ4.67e-12511
multi-cellular organism6.42e-12659
embryo1.46e-11612
temporal lobe1.47e-107
basal ganglion2.04e-109
nuclear complex of neuraxis2.04e-109
aggregate regional part of brain2.04e-109
collection of basal ganglia2.04e-109
cerebral subcortex2.04e-109
tube2.14e-10194
nucleus of brain4.92e-109
neural nucleus4.92e-109
male reproductive organ5.87e-0911
embryonic structure6.00e-09605
developing anatomical structure6.00e-09605
anatomical system7.91e-09625
anatomical group9.63e-09626
germ layer1.37e-08604
embryonic tissue1.37e-08604
presumptive structure1.37e-08604
epiblast (generic)1.37e-08604
gyrus1.93e-086
posterior neural tube1.98e-0815
chordal neural plate1.98e-0815
anatomical conduit2.82e-08241
telencephalic nucleus3.36e-087
multi-tissue structure7.23e-08347
limbic system3.07e-075
parietal lobe5.03e-075
occipital lobe9.98e-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

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.

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