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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C3391_amygdala_brain_parietal_occipital_insula_putamen_middle
|full_id=C3391_amygdala_brain_parietal_occipital_insula_putamen_middle
|id=C3391
|id=C3391

Revision as of 16:18, 12 September 2012


Full id: C3391_amygdala_brain_parietal_occipital_insula_putamen_middle



Phase1 CAGE Peaks

Hg19::chr13:99668217..99668224,-p23@DOCK9
Hg19::chr14:51562005..51562012,-p5@TRIM9
Hg19::chr7:140984977..140984981,+p@chr7:140984977..140984981
+


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 tube2.50e-5157
neural rod2.50e-5157
future spinal cord2.50e-5157
neural keel2.50e-5157
regional part of forebrain1.76e-4841
forebrain1.76e-4841
future forebrain1.76e-4841
central nervous system3.80e-4882
anterior neural tube5.09e-4742
regional part of nervous system3.57e-4594
nervous system3.57e-4594
regional part of brain2.80e-4459
brain1.23e-4269
future brain1.23e-4269
gray matter9.82e-3934
brain grey matter9.82e-3934
telencephalon1.17e-3834
neurectoderm3.17e-3790
regional part of telencephalon4.12e-3733
cerebral hemisphere1.73e-3632
neural plate1.21e-3486
presumptive neural plate1.21e-3486
adult organism1.54e-34115
pre-chordal neural plate5.57e-3061
cerebral cortex5.74e-2925
pallium5.74e-2925
neocortex4.77e-2620
regional part of cerebral cortex4.95e-2622
ectoderm3.22e-25173
presumptive ectoderm3.22e-25173
ectoderm-derived structure3.45e-23169
head4.76e-22123
anterior region of body2.99e-20129
craniocervical region2.99e-20129
tube2.93e-12194
basal ganglion2.81e-119
nuclear complex of neuraxis2.81e-119
aggregate regional part of brain2.81e-119
collection of basal ganglia2.81e-119
cerebral subcortex2.81e-119
diencephalon3.67e-117
future diencephalon3.67e-117
nucleus of brain4.38e-119
neural nucleus4.38e-119
gyrus1.97e-106
temporal lobe2.74e-107
anatomical conduit4.63e-09241
parietal lobe8.57e-095
brainstem1.20e-088
telencephalic nucleus2.76e-087
corpus striatum9.06e-084
striatum9.06e-084
ventral part of telencephalon9.06e-084
future corpus striatum9.06e-084
anatomical cluster1.37e-07286
gland of diencephalon2.15e-074
neuroendocrine gland2.15e-074
epithelium2.70e-07309
cell layer4.62e-07312
posterior neural tube4.80e-0715
chordal neural plate4.80e-0715
organism subdivision9.16e-07365


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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