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Coexpression cluster:C1193: Difference between revisions

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|tf_chipseq_enrich=CTCF#10664;6:4.59450546263574:0.000247839207568764:0.00267480407143476!EP300#2033;6:5.80623576533417:6.3256174139893e-05:0.0010320905438207!MYC#4609;6:4.47624160423663:0.000288361195091082:0.00306401005739317!RAD21#5885;6:8.87574333896257:5.20411262905738e-06:0.00015948131422128!TFAP2C#7022;6:9.2650530941659:4.03752634749879e-06:0.000130267288911469
|tf_chipseq_enrich=CTCF#10664;6:4.59450546263574:0.000247839207568764:0.00267480407143476!EP300#2033;6:5.80623576533417:6.3256174139893e-05:0.0010320905438207!MYC#4609;6:4.47624160423663:0.000288361195091082:0.00306401005739317!RAD21#5885;6:8.87574333896257:5.20411262905738e-06:0.00015948131422128!TFAP2C#7022;6:9.2650530941659:4.03752634749879e-06:0.000130267288911469
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|tfbs_overrepresentation_for_novel_motifs=0.392069,1.1011,0.384703,0.529489,0.343148,0.52784,0.604235,0.226729,0.224331,1.18097,0.497563,0.647852,0.541517,0.592674,0.341795,1.70388,0.827563,0.28906,2.41114,0.32524,0.384762,2.98987,0.520063,0.338096,0.430372,0.670692,0.49486,0.517892,0.346214,0.898182,0.475674,0.864517,0.714156,4.82749,0.309012,0.442372,0.305874,0.529001,0.282922,1.7673,0.307642,0.459366,1.38248,0.340293,2.56059,0.415364,0.60533,0.486696,0.0670664,0.346342,0.684981,0.617179,1.23204,0.941629,1.09491,0.595623,1.65331,1.38261,5.23536,0.561701,0.905643,1.47735,0.638689,0.799729,0.625758,0.76514,1.18348,1.55228,0.854088,1.38987,0.4462,0.232216,0.115253,1.0929,0.179863,0.971313,0.156354,0.782748,0.850825,0.424224,0.200147,0.798651,0.625403,0.229431,1.04131,0.0324537,0.097572,0.146388,0.711163,1.65172,1.27705,1.01423,0.881388,0.26423,0.343884,0.759662,0.194299,0.924148,0.715799,0.132387,0.28424,0.875714,0.918549,0.831244,0.753567,0.493026,0.815341,0.589207,0.43012,0.327379,0.395884,0.915771,0.988112,0.507004,1.22894,0.304323,0.039977,1.19482,0.762789,0.26701,1.0846,0.708722,0.525076,0.636741,1.33983,0.783512,0.597853,0.886402,1.12733,1.39367,1.01492,1.20354,1.14174,0.633392,1.28996,0.140417,0.469685,0.518459,1.24743,2.10682,1.70417,1.21002,1.4603,0.920609,0.755332,0.554217,0.738579,1.94751,0.456039,0.26104,1.16062,0.0685123,1.0153,5.20109,0.607223,1.42052,0.694887,0.329354,0.430431,0.401655,1.2088,0.996724,0.850033,0.404861,0.7715,0.624608,2.78458,0.602897,6.89655
}}
}}

Revision as of 14:44, 26 November 2012


Full id: C1193_mesothelioma_Mesothelial_Retinal_clear_amniotic_serous_Urothelial



Phase1 CAGE Peaks

Hg19::chr14:100003871..100003888,-p@chr14:100003871..100003888
-
Hg19::chr7:76139713..76139729,+p3@UPK3B
Hg19::chr7:76139741..76139750,+p6@UPK3B
Hg19::chr7:76139833..76139844,+p5@UPK3B
Hg19::chr7:76139845..76139887,+p1@UPK3B
Hg19::chr7:76139896..76139907,+p4@UPK3B
Hg19::chr7:76139925..76139937,+p2@UPK3B


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>disease_data<br>


Cell Type
Ontology termp-valuen
epithelial cell7.11e-21253
endo-epithelial cell3.66e-1342
mesothelial cell1.23e-1019
endodermal cell2.72e-0958
squamous epithelial cell1.76e-0863
Uber Anatomy
Ontology termp-valuen
endoderm-derived structure3.28e-11160
endoderm3.28e-11160
presumptive endoderm3.28e-11160
digestive system5.03e-08145
digestive tract5.03e-08145
primitive gut5.03e-08145
endo-epithelium6.61e-0882
anatomical space1.47e-0795
subdivision of digestive tract2.24e-07118
trunk region element2.41e-07101
respiratory tract4.29e-0754
thoracic segment organ7.43e-0735
Disease
Ontology termp-valuen
carcinoma7.20e-14106
adenocarcinoma4.13e-1225
cell type cancer4.53e-11143
cancer2.59e-07235
disease of cellular proliferation7.65e-07239


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#1066464.594505462635740.0002478392075687640.00267480407143476
EP300#203365.806235765334176.3256174139893e-050.0010320905438207
MYC#460964.476241604236630.0002883611950910820.00306401005739317
RAD21#588568.875743338962575.20411262905738e-060.00015948131422128
TFAP2C#702269.26505309416594.03752634749879e-060.000130267288911469



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.