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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C4102_cerebellum_caudate_putamen_argyrophil_insula_nucleus_temporal
|full_id=C4102_cerebellum_caudate_putamen_argyrophil_insula_nucleus_temporal
|id=C4102
|id=C4102

Revision as of 17:09, 12 September 2012


Full id: C4102_cerebellum_caudate_putamen_argyrophil_insula_nucleus_temporal



Phase1 CAGE Peaks

Hg19::chr22:39638219..39638270,+p@chr22:39638219..39638270
+
Hg19::chr5:137071512..137071564,-p2@KLHL3
Hg19::chr5:137071571..137071604,-p5@KLHL3


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
mature alpha-beta T cell1.94e-0918
alpha-beta T cell1.94e-0918
immature T cell1.94e-0918
mature T cell1.94e-0918
immature alpha-beta T cell1.94e-0918
T cell1.45e-0725
pro-T cell1.45e-0725
CD8-positive, alpha-beta T cell2.12e-0711
Uber Anatomy
Ontology termp-valuen
adult organism1.51e-42115
neural tube1.65e-2957
neural rod1.65e-2957
future spinal cord1.65e-2957
neural keel1.65e-2957
regional part of brain1.54e-2659
regional part of nervous system2.23e-2594
nervous system2.23e-2594
central nervous system2.63e-2582
neural plate3.46e-2586
presumptive neural plate3.46e-2586
neurectoderm1.54e-2490
regional part of forebrain1.99e-2441
forebrain1.99e-2441
future forebrain1.99e-2441
anterior neural tube2.50e-2442
brain4.73e-2369
future brain4.73e-2369
gray matter5.33e-2134
brain grey matter5.33e-2134
telencephalon6.41e-2134
cerebral hemisphere2.26e-2032
regional part of telencephalon3.12e-2033
pre-chordal neural plate4.84e-2061
regional part of cerebral cortex1.40e-1622
anterior region of body3.15e-16129
craniocervical region3.15e-16129
cerebral cortex1.23e-1525
pallium1.23e-1525
neocortex3.55e-1520
head1.01e-14123
ectoderm-derived structure1.14e-13169
ectoderm1.30e-13173
presumptive ectoderm1.30e-13173
anatomical conduit2.17e-09241
tube6.89e-09194
anatomical cluster3.82e-08286
basal ganglion3.62e-079
nuclear complex of neuraxis3.62e-079
aggregate regional part of brain3.62e-079
collection of basal ganglia3.62e-079
cerebral subcortex3.62e-079
nucleus of brain7.93e-079
neural nucleus7.93e-079


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

(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
EGR1#195834.988179094810140.008056488137383440.0321247542982662
SMC3#9126210.02995522995520.0126656379767470.0457632438904508



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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