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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C4526_Lens_Smooth_mesenchymal_Ewing_Chondrocyte_Fibroblast_Mesenchymal
|full_id=C4526_Lens_Smooth_mesenchymal_Ewing_Chondrocyte_Fibroblast_Mesenchymal
|id=C4526
|id=C4526

Revision as of 17:37, 12 September 2012


Full id: C4526_Lens_Smooth_mesenchymal_Ewing_Chondrocyte_Fibroblast_Mesenchymal



Phase1 CAGE Peaks

Hg19::chr5:83680363..83680372,-p9@EDIL3
Hg19::chr5:83680417..83680428,-p7@EDIL3
Hg19::chr5:83680445..83680454,-p8@EDIL3


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>


Uber Anatomy
Ontology termp-valuen
central nervous system1.24e-1982
brain2.15e-1969
future brain2.15e-1969
organism subdivision1.72e-18365
regional part of brain2.47e-1859
regional part of nervous system2.84e-1894
nervous system2.84e-1894
multi-tissue structure2.33e-17347
neurectoderm3.19e-1790
neural plate3.24e-1786
presumptive neural plate3.24e-1786
neural tube2.05e-1657
neural rod2.05e-1657
future spinal cord2.05e-1657
neural keel2.05e-1657
anatomical cluster7.29e-16286
tube1.34e-15194
head1.83e-15123
anterior region of body5.85e-14129
craniocervical region5.85e-14129
adult organism1.46e-13115
ectoderm2.25e-13173
presumptive ectoderm2.25e-13173
ectoderm-derived structure3.63e-13169
anterior neural tube6.50e-1342
regional part of forebrain7.37e-1341
forebrain7.37e-1341
future forebrain7.37e-1341
telencephalon7.73e-1334
gray matter2.15e-1234
brain grey matter2.15e-1234
regional part of telencephalon2.94e-1233
cerebral hemisphere3.91e-1232
multi-cellular organism7.55e-12659
anatomical conduit7.67e-12241
pre-chordal neural plate1.75e-1161
cell layer5.01e-11312
epithelium1.63e-10309
regional part of cerebral cortex1.23e-0922
cerebral cortex3.27e-0925
pallium3.27e-0925
neocortex7.24e-0920
muscle tissue5.74e-0863
musculature5.74e-0863
musculature of body5.74e-0863
embryo6.63e-08612
anatomical system6.72e-08625
organ8.63e-08511
skeletal muscle tissue9.01e-0861
striated muscle tissue9.01e-0861
myotome9.01e-0861
anatomical group9.81e-08626
embryonic structure1.72e-07605
developing anatomical structure1.72e-07605
germ layer1.92e-07604
embryonic tissue1.92e-07604
presumptive structure1.92e-07604
epiblast (generic)1.92e-07604
organ part4.30e-07219
somite5.45e-0783
paraxial mesoderm5.45e-0783
presomitic mesoderm5.45e-0783
presumptive segmental plate5.45e-0783
trunk paraxial mesoderm5.45e-0783
presumptive paraxial mesoderm5.45e-0783


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.