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Coexpression cluster:C2514: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000475!3.20e-19!365;UBERON:0000481!2.00e-17!347;UBERON:0003075!2.25e-12!86;UBERON:0007284!2.25e-12!86;UBERON:0002346!5.54e-11!90;UBERON:0000119!6.73e-11!312;UBERON:0000064!7.51e-11!219;UBERON:0004121!8.12e-11!169;UBERON:0000033!2.64e-10!123;UBERON:0000483!2.86e-10!309;UBERON:0000153!3.51e-10!129;UBERON:0007811!3.51e-10!129;UBERON:0000924!5.81e-10!173;UBERON:0006601!5.81e-10!173;UBERON:0007023!6.17e-10!115;UBERON:0005256!3.24e-09!143;UBERON:0000062!1.26e-08!511;UBERON:0003056!2.54e-08!61;UBERON:0002100!1.38e-07!216;UBERON:0000914!2.38e-07!83;UBERON:0002329!2.38e-07!83;UBERON:0003077!2.38e-07!83;UBERON:0003059!2.38e-07!83;UBERON:0007282!2.38e-07!83;UBERON:0009618!2.38e-07!83;UBERON:0007285!2.38e-07!83;UBERON:0000468!3.72e-07!659;UBERON:0007625!3.91e-07!11;UBERON:0001032!3.97e-07!24;UBERON:0004456!3.97e-07!24;UBERON:0002104!4.30e-07!21;UBERON:0001444!5.09e-07!48;UBERON:0000020!5.81e-07!23;UBERON:0000970!6.19e-07!20;UBERON:0001456!8.31e-07!21;UBERON:0002200!8.44e-07!11;UBERON:0006876!8.44e-07!11;UBERON:0002616!9.83e-07!59
|ontology_enrichment_uberon=UBERON:0000475!3.20e-19!365;UBERON:0000481!2.00e-17!347;UBERON:0003075!2.25e-12!86;UBERON:0007284!2.25e-12!86;UBERON:0002346!5.54e-11!90;UBERON:0000119!6.73e-11!312;UBERON:0000064!7.51e-11!219;UBERON:0004121!8.12e-11!169;UBERON:0000033!2.64e-10!123;UBERON:0000483!2.86e-10!309;UBERON:0000153!3.51e-10!129;UBERON:0007811!3.51e-10!129;UBERON:0000924!5.81e-10!173;UBERON:0006601!5.81e-10!173;UBERON:0007023!6.17e-10!115;UBERON:0005256!3.24e-09!143;UBERON:0000062!1.26e-08!511;UBERON:0003056!2.54e-08!61;UBERON:0002100!1.38e-07!216;UBERON:0000914!2.38e-07!83;UBERON:0002329!2.38e-07!83;UBERON:0003077!2.38e-07!83;UBERON:0003059!2.38e-07!83;UBERON:0007282!2.38e-07!83;UBERON:0009618!2.38e-07!83;UBERON:0007285!2.38e-07!83;UBERON:0000468!3.72e-07!659;UBERON:0007625!3.91e-07!11;UBERON:0001032!3.97e-07!24;UBERON:0004456!3.97e-07!24;UBERON:0002104!4.30e-07!21;UBERON:0001444!5.09e-07!48;UBERON:0000020!5.81e-07!23;UBERON:0000970!6.19e-07!20;UBERON:0001456!8.31e-07!21;UBERON:0002200!8.44e-07!11;UBERON:0006876!8.44e-07!11;UBERON:0002616!9.83e-07!59
|tf_chipseq_enrich=CTBP2#1488;3:47.0377502544961:1.60047699357395e-05:0.000370297334363912!FOSL1#8061;3:29.7851847872798:6.26173959487248e-05:0.00102503106825844!JUND#3727;3:5.24599795640327:0.0104343275174842:0.0386944122287588!SMARCB1#6598;3:13.6895368358681:0.000630578340937934:0.00518191607122644!SUZ12#23512;3:37.5868356832972:3.12785741999833e-05:0.000631735256405347!TFAP2A#7020;3:12.3889757797837:0.00084694130358843:0.00638055996577018!TFAP2C#7022;3:8.10692145739517:0.00294701173986644:0.0157176467725417!ZEB1#6935;3:12.6663240131579:0.00079333607591285:0.00613242738748147!ZNF143#7702;3:10.1256574141709:0.00153486161068818:0.00976720763823198!ZNF263#10127;3:6.16638122775801:0.00653981434797598:0.0279762296505392
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}}
}}

Revision as of 11:56, 5 September 2012


Full id: C2514_Mesothelial_mesothelioma_Retinal_retina_Meningeal_Smooth_renal



Phase1 CAGE Peaks

Hg19::chr1:113051552..113051561,+p4@WNT2B
Hg19::chr1:113051579..113051596,+p1@WNT2B
Hg19::chr1:113051605..113051641,+p2@WNT2B
Hg19::chr1:113063958..113063969,+p@chr1:113063958..113063969
+


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 cell3.65e-10180
fibroblast9.52e-0975
Uber Anatomy
Ontology termp-valuen
organism subdivision3.20e-19365
multi-tissue structure2.00e-17347
neural plate2.25e-1286
presumptive neural plate2.25e-1286
neurectoderm5.54e-1190
cell layer6.73e-11312
organ part7.51e-11219
ectoderm-derived structure8.12e-11169
head2.64e-10123
epithelium2.86e-10309
anterior region of body3.51e-10129
craniocervical region3.51e-10129
ectoderm5.81e-10173
presumptive ectoderm5.81e-10173
adult organism6.17e-10115
trunk mesenchyme3.24e-09143
organ1.26e-08511
pre-chordal neural plate2.54e-0861
trunk1.38e-07216
somite2.38e-0783
paraxial mesoderm2.38e-0783
presomitic mesoderm2.38e-0783
presumptive segmental plate2.38e-0783
trunk paraxial mesoderm2.38e-0783
presumptive paraxial mesoderm2.38e-0783
multi-cellular organism3.72e-07659
pigment epithelium of eye3.91e-0711
sensory system3.97e-0724
entire sense organ system3.97e-0724
visual system4.30e-0721
subdivision of head5.09e-0748
sense organ5.81e-0723
eye6.19e-0720
face8.31e-0721
vasculature of head8.44e-0711
vasculature of organ8.44e-0711
regional part of brain9.83e-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
CTBP2#1488347.03775025449611.60047699357395e-050.000370297334363912
FOSL1#8061329.78518478727986.26173959487248e-050.00102503106825844
JUND#372735.245997956403270.01043432751748420.0386944122287588
SMARCB1#6598313.68953683586810.0006305783409379340.00518191607122644
SUZ12#23512337.58683568329723.12785741999833e-050.000631735256405347
TFAP2A#7020312.38897577978370.000846941303588430.00638055996577018
TFAP2C#702238.106921457395170.002947011739866440.0157176467725417
ZEB1#6935312.66632401315790.000793336075912850.00613242738748147
ZNF143#7702310.12565741417090.001534861610688180.00976720763823198
ZNF263#1012736.166381227758010.006539814347975980.0279762296505392



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.

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=Coexpression_cluster:C2514&oldid=2130723"