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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C3108_occipital_retina_eye_pineal_parietal_medial_paracentral
|full_id=C3108_occipital_retina_eye_pineal_parietal_medial_paracentral
|id=C3108
|id=C3108

Revision as of 15:58, 12 September 2012


Full id: C3108_occipital_retina_eye_pineal_parietal_medial_paracentral



Phase1 CAGE Peaks

Hg19::chr11:123396370..123396395,+p3@GRAMD1B
Hg19::chr15:33486388..33486392,-p@chr15:33486388..33486392
-
Hg19::chr15:33486907..33486928,-p1@FMN1


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
central nervous system1.05e-3582
neural tube4.05e-3557
neural rod4.05e-3557
future spinal cord4.05e-3557
neural keel4.05e-3557
regional part of nervous system2.43e-3494
nervous system2.43e-3494
brain7.25e-3069
future brain7.25e-3069
adult organism2.53e-29115
neural plate4.28e-2986
presumptive neural plate4.28e-2986
neurectoderm5.75e-2990
regional part of brain5.77e-2959
regional part of forebrain1.19e-2841
forebrain1.19e-2841
future forebrain1.19e-2841
anterior neural tube1.54e-2742
pre-chordal neural plate3.03e-2361
telencephalon4.74e-2334
gray matter4.81e-2334
brain grey matter4.81e-2334
regional part of telencephalon3.87e-2233
cerebral hemisphere1.63e-2132
regional part of cerebral cortex2.31e-1822
ectoderm3.30e-18173
presumptive ectoderm3.30e-18173
ectoderm-derived structure6.26e-18169
neocortex8.46e-1720
anterior region of body1.92e-16129
craniocervical region1.92e-16129
head2.05e-16123
cerebral cortex4.34e-1625
pallium4.34e-1625
organ4.84e-10511
posterior neural tube1.11e-0815
chordal neural plate1.11e-0815
basal ganglion1.59e-089
nuclear complex of neuraxis1.59e-089
aggregate regional part of brain1.59e-089
collection of basal ganglia1.59e-089
cerebral subcortex1.59e-089
nucleus of brain1.62e-089
neural nucleus1.62e-089
embryo9.32e-08612
diencephalon4.67e-077
future diencephalon4.67e-077
gyrus5.05e-076
telencephalic nucleus6.71e-077


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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