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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C3600_neuroectodermal_occipital_middle_parietal_medial_pituitary_olfactory
|full_id=C3600_neuroectodermal_occipital_middle_parietal_medial_pituitary_olfactory
|id=C3600
|id=C3600

Revision as of 16:33, 12 September 2012


Full id: C3600_neuroectodermal_occipital_middle_parietal_medial_pituitary_olfactory



Phase1 CAGE Peaks

Hg19::chr16:88584331..88584360,-p@chr16:88584331..88584360
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Hg19::chr21:42035250..42035310,-p@chr21:42035250..42035310
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Hg19::chr5:132802985..132802999,-p@chr5:132802985..132802999
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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 tube1.77e-3857
neural rod1.77e-3857
future spinal cord1.77e-3857
neural keel1.77e-3857
central nervous system2.35e-3682
regional part of forebrain6.09e-3541
forebrain6.09e-3541
future forebrain6.09e-3541
regional part of nervous system2.13e-3494
nervous system2.13e-3494
anterior neural tube9.70e-3442
regional part of brain7.36e-3159
gray matter4.26e-3034
brain grey matter4.26e-3034
telencephalon5.87e-3034
brain5.54e-2969
future brain5.54e-2969
regional part of telencephalon5.63e-2933
neurectoderm1.78e-2890
cerebral hemisphere5.98e-2832
neural plate1.28e-2586
presumptive neural plate1.28e-2586
adult organism2.01e-25115
regional part of cerebral cortex6.48e-2322
pre-chordal neural plate3.80e-2261
cerebral cortex6.38e-2125
pallium6.38e-2125
ectoderm6.43e-21173
presumptive ectoderm6.43e-21173
neocortex8.03e-2120
ectoderm-derived structure9.33e-19169
anterior region of body2.18e-15129
craniocervical region2.18e-15129
head4.78e-15123
nucleus of brain1.05e-109
neural nucleus1.05e-109
basal ganglion1.26e-109
nuclear complex of neuraxis1.26e-109
aggregate regional part of brain1.26e-109
collection of basal ganglia1.26e-109
cerebral subcortex1.26e-109
telencephalic nucleus1.17e-087
gyrus5.85e-086
temporal lobe1.46e-077
parietal lobe8.64e-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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