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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C2761_Wilms_duodenum_amygdala_cerebellum_hippocampus_neuroblastoma_temporal
|full_id=C2761_Wilms_duodenum_amygdala_cerebellum_hippocampus_neuroblastoma_temporal
|id=C2761
|id=C2761

Revision as of 15:32, 12 September 2012


Full id: C2761_Wilms_duodenum_amygdala_cerebellum_hippocampus_neuroblastoma_temporal



Phase1 CAGE Peaks

Hg19::chr3:96532496..96532521,+p@chr3:96532496..96532521
+
Hg19::chr3:96533374..96533391,+p4@EPHA6
Hg19::chr3:96533397..96533411,+p2@EPHA6
Hg19::chr3:96533413..96533443,+p1@EPHA6


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 organism1.09e-50115
neural tube7.07e-4057
neural rod7.07e-4057
future spinal cord7.07e-4057
neural keel7.07e-4057
regional part of nervous system3.04e-3794
nervous system3.04e-3794
central nervous system1.62e-3682
neural plate3.69e-3586
presumptive neural plate3.69e-3586
neurectoderm9.94e-3490
regional part of brain1.41e-3259
regional part of forebrain1.50e-3141
forebrain1.50e-3141
future forebrain1.50e-3141
brain1.74e-3069
future brain1.74e-3069
anterior neural tube1.95e-3042
telencephalon2.19e-3034
gray matter2.39e-3034
brain grey matter2.39e-3034
cerebral hemisphere2.23e-2932
regional part of telencephalon2.38e-2933
regional part of cerebral cortex1.08e-2422
pre-chordal neural plate7.28e-2461
neocortex1.72e-2220
cerebral cortex2.97e-2225
pallium2.97e-2225
ectoderm-derived structure2.14e-21169
ectoderm5.55e-21173
presumptive ectoderm5.55e-21173
anterior region of body3.22e-20129
craniocervical region3.22e-20129
head6.09e-19123
organ part2.25e-12219
organ1.56e-10511
posterior neural tube2.18e-1015
chordal neural plate2.18e-1015
multi-tissue structure3.79e-10347
basal ganglion5.83e-109
nuclear complex of neuraxis5.83e-109
aggregate regional part of brain5.83e-109
collection of basal ganglia5.83e-109
cerebral subcortex5.83e-109
tube1.37e-09194
nucleus of brain1.68e-099
neural nucleus1.68e-099
temporal lobe1.85e-097
embryo3.91e-09612
anatomical conduit4.65e-09241
organism subdivision2.14e-08365
multi-cellular organism2.97e-08659
segmental subdivision of hindbrain4.15e-0812
hindbrain4.15e-0812
presumptive hindbrain4.15e-0812
anatomical cluster5.31e-08286
telencephalic nucleus9.01e-087
gyrus1.39e-076
segmental subdivision of nervous system3.04e-0713
limbic system4.67e-075
embryonic structure4.75e-07605
developing anatomical structure4.75e-07605
epithelium7.12e-07309
germ layer8.07e-07604
embryonic tissue8.07e-07604
presumptive structure8.07e-07604
epiblast (generic)8.07e-07604


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
CTCF#1066445.360256373075030.001211145381643620.00818922779447613
MYC#460945.22228187160940.001344309395272740.00888878309166758
ZNF263#1012736.166381227758010.006539814347975980.0279853999298641



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.