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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C4770_Fibroblast_dura_glioblastoma_glioma_neuroblastoma_small_osteosarcoma
|full_id=C4770_Fibroblast_dura_glioblastoma_glioma_neuroblastoma_small_osteosarcoma
|id=C4770
|id=C4770

Revision as of 17:54, 12 September 2012


Full id: C4770_Fibroblast_dura_glioblastoma_glioma_neuroblastoma_small_osteosarcoma



Phase1 CAGE Peaks

Hg19::chr8:72274290..72274320,-p2@EYA1
Hg19::chr8:72274327..72274338,-p6@EYA1
Hg19::chr8:72274355..72274372,-p4@EYA1


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
anterior region of body6.37e-20129
craniocervical region6.37e-20129
central nervous system3.47e-1982
head5.40e-19123
ectoderm1.38e-18173
presumptive ectoderm1.38e-18173
regional part of nervous system3.88e-1894
nervous system3.88e-1894
ectoderm-derived structure1.55e-17169
brain1.56e-1669
future brain1.56e-1669
regional part of brain3.17e-1659
neural tube3.26e-1557
neural rod3.26e-1557
future spinal cord3.26e-1557
neural keel3.26e-1557
organism subdivision8.71e-14365
regional part of forebrain1.74e-1341
forebrain1.74e-1341
future forebrain1.74e-1341
anterior neural tube7.40e-1342
neurectoderm7.71e-1390
neural plate7.81e-1286
presumptive neural plate7.81e-1286
multi-tissue structure9.43e-12347
pre-chordal neural plate2.71e-1061
telencephalon2.73e-1034
gray matter3.37e-1034
brain grey matter3.37e-1034
regional part of telencephalon5.74e-1033
cerebral hemisphere1.26e-0932
adult organism1.15e-08115
embryo1.99e-08612
regional part of cerebral cortex7.83e-0822
anatomical cluster8.49e-08286
neocortex4.38e-0720
embryonic structure9.07e-07605
developing anatomical structure9.07e-07605
cerebral cortex9.77e-0725
pallium9.77e-0725


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
E2F1#186934.907389214879320.008460985347239390.0328009223712077
GABPB1#255337.067683836182170.002832212825417420.0154914358056861
GATA2#2624312.7449317335540.0004829527704283790.00439250234178956
REST#597839.650028716128020.001112636247114590.00771853982148128
ZNF263#1012738.221841637010680.001799043925565870.0110193154971658



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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