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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C3628_caudate_putamen_Pericytes_diencephalon_cerebral_thalamus_ductus
|full_id=C3628_caudate_putamen_Pericytes_diencephalon_cerebral_thalamus_ductus
|id=C3628
|id=C3628

Revision as of 16:35, 12 September 2012


Full id: C3628_caudate_putamen_Pericytes_diencephalon_cerebral_thalamus_ductus



Phase1 CAGE Peaks

Hg19::chr17:37783139..37783148,+p6@PPP1R1B
Hg19::chr17:37783170..37783182,+p2@PPP1R1B
Hg19::chr17:37783186..37783195,+p5@PPP1R1B


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
adult organism1.26e-57115
central nervous system7.70e-5382
neural tube7.54e-5157
neural rod7.54e-5157
future spinal cord7.54e-5157
neural keel7.54e-5157
regional part of nervous system1.08e-4994
nervous system1.08e-4994
brain1.33e-4869
future brain1.33e-4869
regional part of brain2.29e-4859
neurectoderm1.66e-4490
neural plate5.98e-4486
presumptive neural plate5.98e-4486
anterior neural tube9.97e-3842
regional part of forebrain3.55e-3741
forebrain3.55e-3741
future forebrain3.55e-3741
anterior region of body9.48e-36129
craniocervical region9.48e-36129
head7.09e-35123
pre-chordal neural plate1.76e-3361
ectoderm7.43e-33173
presumptive ectoderm7.43e-33173
ectoderm-derived structure6.07e-32169
telencephalon3.01e-3134
gray matter4.15e-3134
brain grey matter4.15e-3134
regional part of telencephalon2.70e-3033
cerebral hemisphere2.07e-2932
regional part of cerebral cortex9.70e-2322
cerebral cortex6.15e-2225
pallium6.15e-2225
neocortex8.10e-2120
posterior neural tube8.41e-1415
chordal neural plate8.41e-1415
segmental subdivision of nervous system6.02e-1213
embryo1.27e-11612
segmental subdivision of hindbrain3.48e-1112
hindbrain3.48e-1112
presumptive hindbrain3.48e-1112
basal ganglion7.63e-119
nuclear complex of neuraxis7.63e-119
aggregate regional part of brain7.63e-119
collection of basal ganglia7.63e-119
cerebral subcortex7.63e-119
nucleus of brain1.19e-109
neural nucleus1.19e-109
organ2.97e-10511
organism subdivision1.44e-09365
organ part2.80e-09219
embryonic structure3.47e-09605
developing anatomical structure3.47e-09605
multi-tissue structure3.88e-09347
temporal lobe5.36e-097
telencephalic nucleus5.79e-097
germ layer7.97e-09604
embryonic tissue7.97e-09604
presumptive structure7.97e-09604
epiblast (generic)7.97e-09604
anatomical cluster1.07e-08286
multi-cellular organism1.46e-08659
brainstem1.97e-088
regional part of metencephalon3.06e-089
metencephalon3.06e-089
future metencephalon3.06e-089
anatomical conduit1.34e-07241
gyrus2.02e-076
tube2.23e-07194
diencephalon2.90e-077
future diencephalon2.90e-077
cell layer6.01e-07312


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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