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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C4542_Astrocyte_eye_caudate_Neural_amygdala_brain_hippocampus
|full_id=C4542_Astrocyte_eye_caudate_Neural_amygdala_brain_hippocampus
|id=C4542
|id=C4542

Revision as of 17:38, 12 September 2012


Full id: C4542_Astrocyte_eye_caudate_Neural_amygdala_brain_hippocampus



Phase1 CAGE Peaks

Hg19::chr6:108487220..108487236,+p2@NR2E1
Hg19::chr6:108487245..108487256,+p3@NR2E1
Hg19::chr6:108487289..108487302,+p1@NR2E1


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><br>

Cell Type
Ontology termp-valuen
astrocyte of the cerebral cortex1.09e-083
neuronal stem cell1.62e-078
neural cell5.97e-0725
Uber Anatomy
Ontology termp-valuen
telencephalon1.24e-7134
regional part of telencephalon1.77e-6933
regional part of forebrain2.58e-6941
forebrain2.58e-6941
future forebrain2.58e-6941
cerebral hemisphere1.02e-6732
anterior neural tube2.00e-6742
gray matter8.51e-6734
brain grey matter8.51e-6734
central nervous system1.83e-6582
regional part of nervous system1.08e-6194
nervous system1.08e-6194
brain3.07e-5869
future brain3.07e-5869
neural tube7.24e-5857
neural rod7.24e-5857
future spinal cord7.24e-5857
neural keel7.24e-5857
pre-chordal neural plate6.61e-5761
regional part of brain1.64e-5559
cerebral cortex1.08e-5225
pallium1.08e-5225
neural plate2.82e-4986
presumptive neural plate2.82e-4986
neurectoderm1.38e-4890
regional part of cerebral cortex1.40e-4522
neocortex2.49e-4120
head8.97e-37123
anterior region of body6.87e-36129
craniocervical region6.87e-36129
ectoderm2.21e-33173
presumptive ectoderm2.21e-33173
ectoderm-derived structure3.40e-33169
adult organism8.61e-24115
basal ganglion3.93e-209
nuclear complex of neuraxis3.93e-209
aggregate regional part of brain3.93e-209
collection of basal ganglia3.93e-209
cerebral subcortex3.93e-209
telencephalic nucleus6.19e-167
nucleus of brain2.55e-159
neural nucleus2.55e-159
gyrus2.96e-146
temporal lobe3.70e-147
parietal lobe2.16e-125
limbic system3.93e-125
occipital lobe9.50e-125
tube4.13e-11194
organ part4.80e-11219
corpus striatum2.29e-104
striatum2.29e-104
ventral part of telencephalon2.29e-104
future corpus striatum2.29e-104
organism subdivision4.72e-09365
epithelium1.78e-08309
caudate-putamen2.70e-083
dorsal striatum2.70e-083
cell layer2.87e-08312
middle temporal gyrus5.33e-083
anatomical conduit2.17e-07241
multi-tissue structure6.46e-07347
anatomical cluster7.51e-07286


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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