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Coexpression cluster:C3422: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007100!3.44e-18!27;UBERON:0000948!1.59e-13!24;UBERON:0005498!1.59e-13!24;UBERON:0004140!1.59e-13!24;UBERON:0009881!1.59e-13!24;UBERON:0004141!1.59e-13!24;UBERON:0003084!1.59e-13!24;UBERON:0007005!1.59e-13!24;UBERON:0004139!1.59e-13!24;UBERON:0004291!1.59e-13!24;UBERON:0001009!1.24e-11!113;UBERON:0003103!6.89e-11!69;UBERON:0004872!1.08e-10!84;UBERON:0000025!8.79e-10!194;UBERON:0004535!2.49e-09!110;UBERON:0004111!4.13e-09!241;UBERON:0003914!5.76e-09!118;UBERON:0003978!1.50e-07!3;UBERON:0009751!1.50e-07!3;UBERON:0000946!1.50e-07!3;UBERON:0002523!1.50e-07!3;UBERON:0005983!1.50e-07!3;UBERON:0002165!1.50e-07!3;UBERON:0002062!1.50e-07!3;UBERON:0007280!1.50e-07!3;UBERON:0004151!1.59e-07!3;UBERON:0000477!4.88e-07!286;UBERON:0004573!5.32e-07!33;UBERON:0004571!5.32e-07!33;UBERON:0000483!6.55e-07!309
|ontology_enrichment_uberon=UBERON:0007100!3.44e-18!27;UBERON:0000948!1.59e-13!24;UBERON:0005498!1.59e-13!24;UBERON:0004140!1.59e-13!24;UBERON:0009881!1.59e-13!24;UBERON:0004141!1.59e-13!24;UBERON:0003084!1.59e-13!24;UBERON:0007005!1.59e-13!24;UBERON:0004139!1.59e-13!24;UBERON:0004291!1.59e-13!24;UBERON:0001009!1.24e-11!113;UBERON:0003103!6.89e-11!69;UBERON:0004872!1.08e-10!84;UBERON:0000025!8.79e-10!194;UBERON:0004535!2.49e-09!110;UBERON:0004111!4.13e-09!241;UBERON:0003914!5.76e-09!118;UBERON:0003978!1.50e-07!3;UBERON:0009751!1.50e-07!3;UBERON:0000946!1.50e-07!3;UBERON:0002523!1.50e-07!3;UBERON:0005983!1.50e-07!3;UBERON:0002165!1.50e-07!3;UBERON:0002062!1.50e-07!3;UBERON:0007280!1.50e-07!3;UBERON:0004151!1.59e-07!3;UBERON:0000477!4.88e-07!286;UBERON:0004573!5.32e-07!33;UBERON:0004571!5.32e-07!33;UBERON:0000483!6.55e-07!309
|tf_chipseq_enrich=EP300#2033;3:6.7739417262232:0.00321688050010379:0.0167173101731771!FOS#2353;3:8.9979553088944:0.00137249927241713:0.00896002322240108!GATA2#2624;3:12.744931733554:0.000482952770428379:0.00436475462017735!JUND#3727;3:6.99466394187103:0.00292184504273499:0.0156417332727561!PRDM1#639;3:131.830955777461:4.35536935195671e-07:2.07893244857864e-05!RAD21#5885;3:10.3550338954563:0.000900491207356542:0.00662812045987102!STAT3#6774;3:10.5194649971542:0.000858918453041531:0.00641939203643942!TRIM28#10155;3:18.5905250452625:0.000155596929725528:0.00196735929099326!YY1#7528;3:4.91117074985386:0.00844145534180826:0.0328581549119717
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}}
}}

Revision as of 13:17, 5 September 2012


Full id: C3422_melanoma_astrocytoma_heart_left_hepatoma_bronchioalveolar_Melanocyte



Phase1 CAGE Peaks

Hg19::chr14:32887555..32887564,+p@chr14:32887555..32887564
+
Hg19::chr14:32887572..32887584,+p@chr14:32887572..32887584
+
Hg19::chr14:32887588..32887603,+p@chr14:32887588..32887603
+


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
pigment cell2.33e-0814
cardiac fibroblast6.61e-086
melanocyte2.24e-0710
melanoblast2.24e-0710
Uber Anatomy
Ontology termp-valuen
primary circulatory organ3.44e-1827
heart1.59e-1324
primitive heart tube1.59e-1324
primary heart field1.59e-1324
anterior lateral plate mesoderm1.59e-1324
heart tube1.59e-1324
heart primordium1.59e-1324
cardiac mesoderm1.59e-1324
cardiogenic plate1.59e-1324
heart rudiment1.59e-1324
circulatory system1.24e-11113
compound organ6.89e-1169
splanchnic layer of lateral plate mesoderm1.08e-1084
tube8.79e-10194
cardiovascular system2.49e-09110
anatomical conduit4.13e-09241
epithelial tube5.76e-09118
valve1.50e-073
cardiac mesenchyme1.50e-073
cardial valve1.50e-073
tunica intima1.50e-073
heart layer1.50e-073
endocardium1.50e-073
endocardial cushion1.50e-073
presumptive endocardium1.50e-073
cardiac chamber1.59e-073
anatomical cluster4.88e-07286
systemic artery5.32e-0733
systemic arterial system5.32e-0733
epithelium6.55e-07309


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
EP300#203336.77394172622320.003216880500103790.0167173101731771
FOS#235338.99795530889440.001372499272417130.00896002322240108
GATA2#2624312.7449317335540.0004829527704283790.00436475462017735
JUND#372736.994663941871030.002921845042734990.0156417332727561
PRDM1#6393131.8309557774614.35536935195671e-072.07893244857864e-05
RAD21#5885310.35503389545630.0009004912073565420.00662812045987102
STAT3#6774310.51946499715420.0008589184530415310.00641939203643942
TRIM28#10155318.59052504526250.0001555969297255280.00196735929099326
YY1#752834.911170749853860.008441455341808260.0328581549119717



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.

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