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Coexpression cluster:C945: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000475!2.19e-19!365;UBERON:0005256!9.08e-12!143;UBERON:0002100!1.18e-11!216;UBERON:0000914!5.05e-11!83;UBERON:0002329!5.05e-11!83;UBERON:0003077!5.05e-11!83;UBERON:0003059!5.05e-11!83;UBERON:0007282!5.05e-11!83;UBERON:0009618!5.05e-11!83;UBERON:0007285!5.05e-11!83;UBERON:0000119!1.00e-10!312;UBERON:0000483!3.29e-10!309;UBERON:0004290!9.03e-10!70;UBERON:0001134!3.92e-08!61;UBERON:0002036!3.92e-08!61;UBERON:0003082!3.92e-08!61;UBERON:0002385!6.38e-08!63;UBERON:0001015!6.38e-08!63;UBERON:0000383!6.38e-08!63;UBERON:0000486!2.04e-07!82;UBERON:0004923!2.48e-07!57;UBERON:0002199!6.22e-07!45;UBERON:0002416!6.22e-07!45
|ontology_enrichment_uberon=UBERON:0000475!2.19e-19!365;UBERON:0005256!9.08e-12!143;UBERON:0002100!1.18e-11!216;UBERON:0000914!5.05e-11!83;UBERON:0002329!5.05e-11!83;UBERON:0003077!5.05e-11!83;UBERON:0003059!5.05e-11!83;UBERON:0007282!5.05e-11!83;UBERON:0009618!5.05e-11!83;UBERON:0007285!5.05e-11!83;UBERON:0000119!1.00e-10!312;UBERON:0000483!3.29e-10!309;UBERON:0004290!9.03e-10!70;UBERON:0001134!3.92e-08!61;UBERON:0002036!3.92e-08!61;UBERON:0003082!3.92e-08!61;UBERON:0002385!6.38e-08!63;UBERON:0001015!6.38e-08!63;UBERON:0000383!6.38e-08!63;UBERON:0000486!2.04e-07!82;UBERON:0004923!2.48e-07!57;UBERON:0002199!6.22e-07!45;UBERON:0002416!6.22e-07!45
|tf_chipseq_enrich=CCNT2#905;7:4.92815678208205:6.52167806614696e-05:0.0010589513923357!CTCF#10664;8:4.76467233162225:1.10088565904027e-05:0.000285086529492949!CTCFL#140690;7:15.3583689458689:2.80301943713286e-08:1.91837842067313e-06!MYC#4609;7:4.06177478902954:0.000235555679657337:0.00256877932836302!NRF1#4899;7:9.49688401488626:7.65865712776971e-07:3.36642462864958e-05!PAX5#5079;7:5.18743985758276:4.62776729125731e-05:0.000812847945058228!POLR2A#5430;8:1.90884726805162:0.011661228959883:0.0425879319978046!RAD21#5885;8:9.20447457373896:6.21516790927479e-08:3.8408634395074e-06!SMC3#9126;7:11.7016144349478:1.82762584901624e-07:9.9882478307382e-06!SUZ12#23512;8:44.5473608098337:2.2052477624887e-13:3.31864367531063e-11!YY1#7528;7:3.81979947210855:0.000352967281214194:0.00353708979876504!ZNF143#7702;7:10.5006817628439:3.84602726591188e-07:1.87698711039519e-05
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}}
}}

Revision as of 14:07, 5 September 2012


Full id: C945_Olfactory_mesothelioma_Fibroblast_basal_Adipocyte_Mesenchymal_neurofibroma



Phase1 CAGE Peaks

Hg19::chr3:8809723..8809735,-p9@OXTR
Hg19::chr3:8811050..8811055,-p6@OXTR
Hg19::chr3:8811079..8811088,-p5@OXTR
Hg19::chr3:8811090..8811097,-p7@OXTR
Hg19::chr3:8811108..8811149,-p2@OXTR
Hg19::chr3:8811162..8811175,-p3@OXTR
Hg19::chr3:8811276..8811287,-p4@OXTR
Hg19::chr3:8811288..8811305,-p1@OXTR
Hg19::chr9:81628797..81628811,+p@chr9:81628797..81628811
+


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
organism subdivision2.19e-19365
trunk mesenchyme9.08e-12143
trunk1.18e-11216
somite5.05e-1183
paraxial mesoderm5.05e-1183
presomitic mesoderm5.05e-1183
presumptive segmental plate5.05e-1183
trunk paraxial mesoderm5.05e-1183
presumptive paraxial mesoderm5.05e-1183
cell layer1.00e-10312
epithelium3.29e-10309
dermomyotome9.03e-1070
skeletal muscle tissue3.92e-0861
striated muscle tissue3.92e-0861
myotome3.92e-0861
muscle tissue6.38e-0863
musculature6.38e-0863
musculature of body6.38e-0863
multilaminar epithelium2.04e-0782
organ component layer2.48e-0757
integument6.22e-0745
integumental system6.22e-0745


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
CCNT2#90574.928156782082056.52167806614696e-050.0010589513923357
CTCF#1066484.764672331622251.10088565904027e-050.000285086529492949
CTCFL#140690715.35836894586892.80301943713286e-081.91837842067313e-06
MYC#460974.061774789029540.0002355556796573370.00256877932836302
NRF1#489979.496884014886267.65865712776971e-073.36642462864958e-05
PAX5#507975.187439857582764.62776729125731e-050.000812847945058228
POLR2A#543081.908847268051620.0116612289598830.0425879319978046
RAD21#588589.204474573738966.21516790927479e-083.8408634395074e-06
SMC3#9126711.70161443494781.82762584901624e-079.9882478307382e-06
SUZ12#23512844.54736080983372.2052477624887e-133.31864367531063e-11
YY1#752873.819799472108550.0003529672812141940.00353708979876504
ZNF143#7702710.50068176284393.84602726591188e-071.87698711039519e-05



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.