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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C2014_medulloblastoma_gastrointestinal_neuroblastoma_somatostatinoma_nonsmall_smallcell_small
|full_id=C2014_medulloblastoma_gastrointestinal_neuroblastoma_somatostatinoma_nonsmall_smallcell_small
|id=C2014
|id=C2014

Revision as of 14:40, 12 September 2012


Full id: C2014_medulloblastoma_gastrointestinal_neuroblastoma_somatostatinoma_nonsmall_smallcell_small



Phase1 CAGE Peaks

Hg19::chr8:73449214..73449261,+p1@KCNB2
Hg19::chr8:73449625..73449668,+p2@KCNB2
Hg19::chr8:73450059..73450081,+p7@KCNB2
Hg19::chr8:73480095..73480099,+p12@KCNB2
Hg19::chr8:73610219..73610231,+p@chr8:73610219..73610231
+


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
neuron5.63e-076
neuroblast5.63e-076
electrically signaling cell5.63e-076
Uber Anatomy
Ontology termp-valuen
central nervous system2.66e-4182
neural tube2.73e-4157
neural rod2.73e-4157
future spinal cord2.73e-4157
neural keel2.73e-4157
regional part of nervous system5.74e-3994
nervous system5.74e-3994
neural plate3.19e-3886
presumptive neural plate3.19e-3886
regional part of forebrain1.79e-3741
forebrain1.79e-3741
future forebrain1.79e-3741
neurectoderm7.67e-3790
anterior neural tube2.95e-3642
brain1.32e-3469
future brain1.32e-3469
adult organism1.80e-34115
regional part of brain5.61e-3459
pre-chordal neural plate1.38e-3361
gray matter9.30e-3134
brain grey matter9.30e-3134
telencephalon1.18e-3034
regional part of telencephalon1.68e-2933
cerebral hemisphere2.41e-2932
regional part of cerebral cortex2.66e-2422
anterior region of body9.92e-24129
craniocervical region9.92e-24129
ectoderm-derived structure1.44e-23169
ectoderm3.23e-23173
presumptive ectoderm3.23e-23173
cerebral cortex2.52e-2225
pallium2.52e-2225
neocortex4.26e-2220
head7.01e-22123
organ part8.10e-12219
temporal lobe2.50e-107
tube4.25e-10194
nucleus of brain7.53e-109
neural nucleus7.53e-109
basal ganglion8.73e-109
nuclear complex of neuraxis8.73e-109
aggregate regional part of brain8.73e-109
collection of basal ganglia8.73e-109
cerebral subcortex8.73e-109
embryo2.34e-09612
gyrus3.60e-086
diencephalon3.60e-087
future diencephalon3.60e-087
telencephalic nucleus7.42e-087
multi-cellular organism2.03e-07659
organ2.08e-07511
germ layer2.15e-07604
embryonic tissue2.15e-07604
presumptive structure2.15e-07604
epiblast (generic)2.15e-07604
anatomical conduit2.16e-07241
organism subdivision2.26e-07365
embryonic structure2.54e-07605
developing anatomical structure2.54e-07605
epithelium5.05e-07309
parietal lobe5.42e-075
posterior neural tube6.06e-0715
chordal neural plate6.06e-0715
anatomical cluster6.15e-07286
limbic system7.39e-075
cell layer9.10e-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.