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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C4050_MCF7_Burkitt_keratoacanthoma_colon_small_synovial_peripheral
|full_id=C4050_MCF7_Burkitt_keratoacanthoma_colon_small_synovial_peripheral
|id=C4050
|id=C4050

Revision as of 17:05, 12 September 2012


Full id: C4050_MCF7_Burkitt_keratoacanthoma_colon_small_synovial_peripheral



Phase1 CAGE Peaks

Hg19::chr20:55841403..55841458,-p2@BMP7
Hg19::chr20:55841618..55841629,-p6@BMP7
Hg19::chr20:55841662..55841736,-p1@BMP7


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 organism3.11e-37115
regional part of nervous system3.51e-3594
nervous system3.51e-3594
central nervous system1.48e-3482
neural tube1.38e-3057
neural rod1.38e-3057
future spinal cord1.38e-3057
neural keel1.38e-3057
neurectoderm4.66e-3090
neural plate7.09e-2986
presumptive neural plate7.09e-2986
brain6.88e-2869
future brain6.88e-2869
ectoderm1.73e-26173
presumptive ectoderm1.73e-26173
ectoderm-derived structure2.71e-25169
regional part of brain3.59e-2559
regional part of forebrain3.43e-2441
forebrain3.43e-2441
future forebrain3.43e-2441
anterior neural tube3.25e-2342
anterior region of body3.55e-23129
craniocervical region3.55e-23129
head3.31e-22123
pre-chordal neural plate4.16e-2161
gray matter5.71e-2134
brain grey matter5.71e-2134
telencephalon6.67e-2134
regional part of telencephalon2.47e-2033
cerebral hemisphere2.39e-1932
organ part2.63e-16219
cerebral cortex4.33e-1525
pallium4.33e-1525
regional part of cerebral cortex8.20e-1422
organ1.38e-13511
neocortex2.16e-1220
multi-cellular organism3.19e-12659
embryo5.81e-12612
organism subdivision5.81e-12365
multi-tissue structure1.11e-11347
embryonic structure2.05e-09605
developing anatomical structure2.05e-09605
germ layer4.51e-09604
embryonic tissue4.51e-09604
presumptive structure4.51e-09604
epiblast (generic)4.51e-09604
anatomical group7.75e-09626
anatomical system1.40e-08625
posterior neural tube1.79e-0815
chordal neural plate1.79e-0815
gastrointestinal system3.03e-0835
anatomical conduit2.04e-07241
nucleus of brain2.19e-079
neural nucleus2.19e-079
segmental subdivision of nervous system3.22e-0713
basal ganglion4.86e-079
nuclear complex of neuraxis4.86e-079
aggregate regional part of brain4.86e-079
collection of basal ganglia4.86e-079
cerebral subcortex4.86e-079
cavitated compound organ5.62e-0732
intestine5.79e-0727


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
ZNF263#1012738.221841637010680.001799043925565870.0109589004690682



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.