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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C2077_optic_hippocampus_occipital_middle_amygdala_locus_medial
|full_id=C2077_optic_hippocampus_occipital_middle_amygdala_locus_medial
|id=C2077
|id=C2077

Revision as of 14:45, 12 September 2012


Full id: C2077_optic_hippocampus_occipital_middle_amygdala_locus_medial



Phase1 CAGE Peaks

Hg19::chr10:83823278..83823283,+p@chr10:83823278..83823283
+
Hg19::chr11:83167654..83167665,-p43@DLG2
Hg19::chr13:84385839..84385842,-p@chr13:84385839..84385842
-
Hg19::chr5:132028817..132028824,-p@chr5:132028817..132028824
-


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 tube1.08e-4557
neural rod1.08e-4557
future spinal cord1.08e-4557
neural keel1.08e-4557
brain7.77e-4169
future brain7.77e-4169
central nervous system2.43e-4082
regional part of brain6.25e-3959
regional part of forebrain1.54e-3541
forebrain1.54e-3541
future forebrain1.54e-3541
neurectoderm2.20e-3590
regional part of nervous system2.84e-3594
nervous system2.84e-3594
neural plate1.62e-3486
presumptive neural plate1.62e-3486
anterior neural tube2.11e-3442
gray matter1.34e-3234
brain grey matter1.34e-3234
telencephalon1.20e-3134
regional part of telencephalon1.82e-3033
cerebral hemisphere9.23e-3032
ectoderm3.32e-25173
presumptive ectoderm3.32e-25173
adult organism8.27e-25115
ectoderm-derived structure3.16e-24169
pre-chordal neural plate7.59e-2461
head2.12e-23123
anterior region of body1.97e-22129
craniocervical region1.97e-22129
cerebral cortex6.49e-2125
pallium6.49e-2125
regional part of cerebral cortex1.22e-2022
neocortex6.15e-1820
nucleus of brain1.27e-139
neural nucleus1.27e-139
posterior neural tube4.25e-1215
chordal neural plate4.25e-1215
telencephalic nucleus7.48e-117
basal ganglion1.14e-109
nuclear complex of neuraxis1.14e-109
aggregate regional part of brain1.14e-109
collection of basal ganglia1.14e-109
cerebral subcortex1.14e-109
segmental subdivision of nervous system4.92e-1013
tube1.05e-09194
gyrus2.43e-096
brainstem6.18e-098
segmental subdivision of hindbrain9.73e-0912
hindbrain9.73e-0912
presumptive hindbrain9.73e-0912
parietal lobe1.00e-075
anatomical conduit1.31e-07241
anatomical cluster3.53e-07286
organ part6.51e-07219
temporal lobe6.80e-077
corpus striatum8.82e-074
striatum8.82e-074
ventral part of telencephalon8.82e-074
future corpus striatum8.82e-074


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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