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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C2543_pineal_parietal_occipital_temporal_hippocampus_duodenum_brain
|full_id=C2543_pineal_parietal_occipital_temporal_hippocampus_duodenum_brain
|id=C2543
|id=C2543

Revision as of 15:17, 12 September 2012


Full id: C2543_pineal_parietal_occipital_temporal_hippocampus_duodenum_brain



Phase1 CAGE Peaks

Hg19::chr1:181286826..181286889,+p@chr1:181286826..181286889
+
Hg19::chr3:77088989..77088997,+p10@ROBO2
Hg19::chr3:77185657..77185661,+p@chr3:77185657..77185661
+
Hg19::chr3:77596949..77596954,+p@chr3:77596949..77596954
+


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>disease_data<br>

Cell Type
Ontology termp-valuen
neuronal stem cell6.06e-078
Uber Anatomy
Ontology termp-valuen
central nervous system2.69e-4882
regional part of nervous system2.77e-4794
nervous system2.77e-4794
neural tube1.38e-4557
neural rod1.38e-4557
future spinal cord1.38e-4557
neural keel1.38e-4557
regional part of forebrain2.73e-3841
forebrain2.73e-3841
future forebrain2.73e-3841
brain1.56e-3769
future brain1.56e-3769
anterior neural tube5.05e-3742
regional part of brain5.85e-3759
neurectoderm4.12e-3390
cerebral hemisphere2.85e-3232
telencephalon7.64e-3234
gray matter8.06e-3234
brain grey matter8.06e-3234
adult organism3.35e-31115
regional part of telencephalon8.53e-3133
ectoderm2.48e-30173
presumptive ectoderm2.48e-30173
neural plate6.99e-3086
presumptive neural plate6.99e-3086
ectoderm-derived structure1.31e-27169
cerebral cortex2.24e-2525
pallium2.24e-2525
regional part of cerebral cortex1.09e-2322
pre-chordal neural plate1.10e-2361
anterior region of body1.27e-23129
craniocervical region1.27e-23129
head4.68e-23123
neocortex2.48e-2120
temporal lobe2.83e-107
posterior neural tube1.04e-0915
chordal neural plate1.04e-0915
organ part1.70e-08219
basal ganglion2.57e-089
nuclear complex of neuraxis2.57e-089
aggregate regional part of brain2.57e-089
collection of basal ganglia2.57e-089
cerebral subcortex2.57e-089
tube3.28e-08194
nucleus of brain6.47e-089
neural nucleus6.47e-089
diencephalon8.99e-087
future diencephalon8.99e-087
gyrus1.56e-076
segmental subdivision of nervous system1.78e-0713
limbic system1.93e-075
parietal lobe6.80e-075
Disease
Ontology termp-valuen
neuroectodermal tumor3.53e-0710


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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