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Coexpression cluster:C1781: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C1781_anaplastic_Hair_Pericytes_mesothelioma_Fibroblast_lens_transitionalcell
|full_id=C1781_anaplastic_Hair_Pericytes_mesothelioma_Fibroblast_lens_transitionalcell
|gostat_on_coexpression_clusters=GO:0007164!establishment of tissue polarity!0.0065936653714824!2535$GO:0004926!non-G-protein coupled 7TM receptor activity!0.00706464146944543!2535$GO:0030855!epithelial cell differentiation!0.0113034263511127!2535$GO:0002009!morphogenesis of an epithelium!0.0148357470858354!2535$GO:0016055!Wnt receptor signaling pathway!0.0273166136818556!2535
|gostat_on_coexpression_clusters=GO:0007164!establishment of tissue polarity!0.0065936653714824!2535$GO:0004926!non-G-protein coupled 7TM receptor activity!0.00706464146944543!2535$GO:0030855!epithelial cell differentiation!0.0113034263511127!2535$GO:0002009!morphogenesis of an epithelium!0.0148357470858354!2535$GO:0016055!Wnt receptor signaling pathway!0.0273166136818556!2535

Revision as of 14:23, 12 September 2012


Full id: C1781_anaplastic_Hair_Pericytes_mesothelioma_Fibroblast_lens_transitionalcell



Phase1 CAGE Peaks

Hg19::chr17:42634734..42634754,+p3@FZD2
Hg19::chr17:42634810..42634825,+p4@FZD2
Hg19::chr17:42634844..42634858,+p1@FZD2
Hg19::chr17:42635049..42635107,+p5@FZD2
Hg19::chr17:42635121..42635149,+p1@AB590852


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


GO IDGO nameFDR corrected p-value
GO:0007164establishment of tissue polarity0.0065936653714824
GO:0004926non-G-protein coupled 7TM receptor activity0.00706464146944543
GO:0030855epithelial cell differentiation0.0113034263511127
GO:0002009morphogenesis of an epithelium0.0148357470858354
GO:0016055Wnt receptor signaling pathway0.0273166136818556



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 cell1.03e-28180
fibroblast1.10e-1575
neurectodermal cell1.46e-0859
contractile cell5.63e-0859
electrically responsive cell7.84e-0860
electrically active cell7.84e-0860
skin fibroblast1.49e-0723
animal cell2.20e-07679
eukaryotic cell2.20e-07679
muscle precursor cell2.86e-0757
myoblast2.86e-0757
multi-potent skeletal muscle stem cell2.86e-0757
muscle cell6.90e-0754
Uber Anatomy
Ontology termp-valuen
somite1.32e-0983
paraxial mesoderm1.32e-0983
presomitic mesoderm1.32e-0983
presumptive segmental plate1.32e-0983
trunk paraxial mesoderm1.32e-0983
presumptive paraxial mesoderm1.32e-0983
organism subdivision2.61e-09365
multi-cellular organism8.94e-08659
dermomyotome1.03e-0770
trunk mesenchyme3.62e-07143
pigment epithelium of eye4.93e-0711
trunk5.91e-07216
vasculature of head8.18e-0711
vasculature of organ8.18e-0711


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
CTBP2#1488562.71700033932811.02712351233917e-099.518345386441e-08
EGR1#195854.988179094810140.0003237398000590710.00330735214500336
ELF1#199743.406478367046030.01235066105299550.0447350589482484
FOS#235335.398773185336640.01153895317278740.0421915320664058
GATA2#262437.64695904013240.004279061879252130.020329388327672
GATA3#2625316.34190981432360.0004678865195089230.00430154931434792
IRF3#3661328.18917132689379.33088977565955e-050.00135612134327875
MYC#460955.22228187160940.0002573944848850610.00276507124119635
NFYA#4800311.05534841989830.001470892907644430.0094123267190415
NFYB#4801310.05587595212190.001938165606725460.0113879087370352
RFX5#599337.228746496317060.00502918278958660.0234661493705774
SP2#6668315.69211829630680.0005272235913302770.0045638379324445
SRF#672238.278306957300690.003404846073776150.0173615232447567
TAF1#687253.343046285745290.002394600090870310.0135337214616811
TFAP2C#702236.485537165916130.006858951517940.0290593500297001
USF1#739156.361499277207969.59569864925045e-050.00136814357846972
YY1#752843.928936599883080.007193866269917620.0298427152591327



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.