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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C1936_Wilms_extraskeletal_Skeletal_uterus_cervix_lung_salivary
|full_id=C1936_Wilms_extraskeletal_Skeletal_uterus_cervix_lung_salivary
|id=C1936
|id=C1936

Revision as of 14:34, 12 September 2012


Full id: C1936_Wilms_extraskeletal_Skeletal_uterus_cervix_lung_salivary



Phase1 CAGE Peaks

Hg19::chr4:148402078..148402099,+p4@EDNRA
Hg19::chr4:148402109..148402132,+p2@EDNRA
Hg19::chr4:148402212..148402230,+p3@EDNRA
Hg19::chr4:148402237..148402276,+p1@EDNRA
Hg19::chr4:148402291..148402302,+p5@EDNRA


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
multi-tissue structure2.33e-27347
organism subdivision3.60e-25365
multi-cellular organism7.89e-18659
somite1.50e-1483
paraxial mesoderm1.50e-1483
presomitic mesoderm1.50e-1483
presumptive segmental plate1.50e-1483
trunk paraxial mesoderm1.50e-1483
presumptive paraxial mesoderm1.50e-1483
adult organism1.67e-14115
anatomical cluster4.47e-14286
cell layer4.63e-14312
embryo9.10e-14612
ectoderm1.35e-13173
presumptive ectoderm1.35e-13173
epithelium4.50e-13309
anatomical system5.45e-13625
anatomical group6.76e-13626
anterior region of body7.25e-13129
craniocervical region7.25e-13129
ectoderm-derived structure9.47e-13169
surface structure1.31e-1295
head1.79e-12123
dermomyotome2.92e-1270
embryonic structure3.80e-12605
developing anatomical structure3.80e-12605
germ layer9.52e-12604
embryonic tissue9.52e-12604
presumptive structure9.52e-12604
epiblast (generic)9.52e-12604
mesenchyme1.56e-11238
entire embryonic mesenchyme1.56e-11238
multilaminar epithelium6.53e-1182
muscle tissue9.37e-1163
musculature9.37e-1163
musculature of body9.37e-1163
trunk mesenchyme1.85e-10143
skeletal muscle tissue3.73e-1061
striated muscle tissue3.73e-1061
myotome3.73e-1061
organ3.02e-09511
neurectoderm6.08e-0990
anatomical conduit1.35e-08241
trunk1.41e-08216
organ part2.31e-08219
neural plate3.87e-0886
presumptive neural plate3.87e-0886
compound organ6.23e-0869
subdivision of head1.63e-0748
regional part of nervous system3.07e-0794
nervous system3.07e-0794
tissue6.27e-07787
central nervous system6.50e-0782
regional part of brain9.59e-0759


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
TCF7L2#6934510.77017656313736.89693748574565e-060.000200085903909386
ZNF263#1012758.221841637010682.6606316672286e-050.000572109760538786



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.