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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C859_Fibroblast_Synoviocyte_Preadipocyte_mesothelioma_tenocyte_Mesothelial_Smooth
|full_id=C859_Fibroblast_Synoviocyte_Preadipocyte_mesothelioma_tenocyte_Mesothelial_Smooth
|id=C859
|id=C859

Revision as of 18:37, 12 September 2012


Full id: C859_Fibroblast_Synoviocyte_Preadipocyte_mesothelioma_tenocyte_Mesothelial_Smooth



Phase1 CAGE Peaks

Hg19::chr5:168310297..168310307,-p@chr5:168310297..168310307
-
Hg19::chr5:168727744..168727755,-p10@SLIT3
Hg19::chr5:168727761..168727778,-p6@SLIT3
Hg19::chr5:168727788..168727838,-p2@SLIT3
Hg19::chr5:168727902..168727913,-p9@SLIT3
Hg19::chr5:168727914..168727925,-p7@SLIT3
Hg19::chr5:168727941..168727995,-p3@SLIT3
Hg19::chr5:168728001..168728012,-p8@SLIT3
Hg19::chr5:168728014..168728036,-p4@SLIT3
Hg19::chr5:168728103..168728177,-p1@SLIT3


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>


Cell Type
Ontology termp-valuen
non-terminally differentiated cell4.72e-17180
fibroblast5.37e-1675
fat cell4.27e-0915
skin fibroblast3.59e-0723
Uber Anatomy
Ontology termp-valuen
organism subdivision1.15e-23365
adult organism7.08e-16115
multi-cellular organism1.83e-14659
multi-tissue structure8.28e-14347
epithelium2.60e-12309
cell layer7.00e-12312
anatomical system2.36e-11625
anatomical group3.98e-11626
ectoderm-derived structure7.74e-11169
anterior region of body1.00e-10129
craniocervical region1.00e-10129
head2.27e-10123
surface structure2.28e-1095
neural plate4.79e-1086
presumptive neural plate4.79e-1086
ectoderm1.31e-09173
presumptive ectoderm1.31e-09173
anatomical cluster2.33e-09286
anatomical conduit5.22e-09241
tube5.78e-09194
splanchnic layer of lateral plate mesoderm6.40e-0984
neurectoderm2.11e-0890
organ2.56e-08511
embryo2.75e-08612
integument4.59e-0845
integumental system4.59e-0845
organ part7.56e-08219
primary circulatory organ7.95e-0827
embryonic structure1.00e-07605
developing anatomical structure1.00e-07605
heart1.21e-0724
primitive heart tube1.21e-0724
primary heart field1.21e-0724
anterior lateral plate mesoderm1.21e-0724
heart tube1.21e-0724
heart primordium1.21e-0724
cardiac mesoderm1.21e-0724
cardiogenic plate1.21e-0724
heart rudiment1.21e-0724
somite1.25e-0783
paraxial mesoderm1.25e-0783
presomitic mesoderm1.25e-0783
presumptive segmental plate1.25e-0783
trunk paraxial mesoderm1.25e-0783
presumptive paraxial mesoderm1.25e-0783
multilaminar epithelium1.56e-0782
germ layer1.81e-07604
embryonic tissue1.81e-07604
presumptive structure1.81e-07604
epiblast (generic)1.81e-07604
artery3.82e-0742
arterial blood vessel3.82e-0742
arterial system3.82e-0742
neural tube5.01e-0757
neural rod5.01e-0757
future spinal cord5.01e-0757
neural keel5.01e-0757


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#1066494.824230735767522.27590399695328e-068.12904027147073e-05
ESR1#2099927.6917429665393.90514076512165e-135.7605790447534e-11
GATA2#262456.3724658667770.0005348865075213680.00462327335587388
POLR2A#543091.932707858902260.005980089183606110.0268164248281081
RAD21#588599.31953050591076.65848137862758e-095.22861005039463e-07
ZNF263#1012775.755289145907473.37110736015453e-050.000669344261572583



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.