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Coexpression cluster:C3270: Difference between revisions

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|full_id=C3270_giant_testicular_gastric_ductal_Fibroblast_anaplastic_basal
|full_id=C3270_giant_testicular_gastric_ductal_Fibroblast_anaplastic_basal
|id=C3270
|id=C3270
|ontology_enrichment_celltype=CL:0000055!3.71e-22!180;CL:0000057!9.42e-14!75
|ontology_enrichment_celltype=CL:0000057!2.65e-13!76;CL:0000055!3.60e-09!106
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000475!2.33e-19!365;UBERON:0000468!6.19e-19!659;UBERON:0000480!2.44e-16!626;UBERON:0000467!3.17e-16!625;UBERON:0000477!3.71e-16!286;UBERON:0000481!3.90e-16!347;UBERON:0004111!1.80e-12!241;UBERON:0000483!2.17e-12!309;UBERON:0000119!2.38e-12!312;UBERON:0000922!2.49e-11!612;UBERON:0002050!1.60e-10!605;UBERON:0005423!1.60e-10!605;UBERON:0000062!1.94e-10!511;UBERON:0000025!2.14e-10!194;UBERON:0004121!2.73e-10!169;UBERON:0000923!3.59e-10!604;UBERON:0005291!3.59e-10!604;UBERON:0006598!3.59e-10!604;UBERON:0002532!3.59e-10!604;UBERON:0000914!8.54e-10!83;UBERON:0002329!8.54e-10!83;UBERON:0003077!8.54e-10!83;UBERON:0003059!8.54e-10!83;UBERON:0007282!8.54e-10!83;UBERON:0009618!8.54e-10!83;UBERON:0007285!8.54e-10!83;UBERON:0000033!1.04e-09!123;UBERON:0000924!2.58e-09!173;UBERON:0006601!2.58e-09!173;UBERON:0003075!3.12e-09!86;UBERON:0007284!3.12e-09!86;UBERON:0004872!8.82e-09!84;UBERON:0002049!1.15e-08!79;UBERON:0007798!1.15e-08!79;UBERON:0005743!1.65e-08!86;UBERON:0000153!1.81e-08!129;UBERON:0007811!1.81e-08!129;UBERON:0000073!3.04e-08!94;UBERON:0001016!3.04e-08!94;UBERON:0004458!3.62e-08!49;UBERON:0002100!4.11e-08!216;UBERON:0004290!4.81e-08!70;UBERON:0002346!6.16e-08!90;UBERON:0001017!7.10e-08!82;UBERON:0000064!1.29e-07!219;UBERON:0002323!1.59e-07!46;UBERON:0001048!2.55e-07!168;UBERON:0007023!3.92e-07!115;UBERON:0000055!5.59e-07!69;UBERON:0000948!5.88e-07!24;UBERON:0005498!5.88e-07!24;UBERON:0004140!5.88e-07!24;UBERON:0009881!5.88e-07!24;UBERON:0004141!5.88e-07!24;UBERON:0003084!5.88e-07!24;UBERON:0007005!5.88e-07!24;UBERON:0004139!5.88e-07!24;UBERON:0004291!5.88e-07!24;UBERON:0007100!6.07e-07!27;UBERON:0004573!6.24e-07!33;UBERON:0004571!6.24e-07!33;UBERON:0000955!6.35e-07!69;UBERON:0006238!6.35e-07!69;UBERON:0000486!7.20e-07!82
|ontology_enrichment_uberon=UBERON:0010314!8.12e-14!132;UBERON:0000468!9.26e-14!656;UBERON:0000480!2.67e-12!625;UBERON:0000467!3.72e-12!624;UBERON:0000477!5.04e-12!373;UBERON:0000481!3.10e-10!342;UBERON:0002049!9.10e-09!78;UBERON:0007798!9.10e-09!78;UBERON:0004121!9.14e-09!171;UBERON:0000924!9.14e-09!171;UBERON:0006601!9.14e-09!171;UBERON:0000483!1.04e-08!306;UBERON:0007524!1.28e-08!73;UBERON:0004872!1.56e-08!83;UBERON:0000119!1.60e-08!309;UBERON:0002329!3.22e-08!71;UBERON:0003059!3.22e-08!71;UBERON:0007282!3.22e-08!71;UBERON:0004290!3.22e-08!71;UBERON:0009618!3.22e-08!71;UBERON:0003077!3.49e-08!72;UBERON:0007285!3.49e-08!72;UBERON:0004111!5.62e-08!240;UBERON:0003075!7.32e-08!82;UBERON:0007284!7.32e-08!82;UBERON:0004573!2.46e-07!33;UBERON:0004571!2.46e-07!33;UBERON:0004458!2.52e-07!49;UBERON:0002323!3.52e-07!46;UBERON:0000055!5.96e-07!68;UBERON:0002346!7.64e-07!86;UBERON:0001009!8.30e-07!112;UBERON:0000948!9.09e-07!24;UBERON:0005498!9.09e-07!24;UBERON:0004140!9.09e-07!24;UBERON:0009881!9.09e-07!24;UBERON:0004141!9.09e-07!24;UBERON:0003084!9.09e-07!24;UBERON:0007005!9.09e-07!24;UBERON:0004139!9.09e-07!24;UBERON:0004291!9.09e-07!24;UBERON:0001637!9.26e-07!42;UBERON:0003509!9.26e-07!42;UBERON:0004572!9.26e-07!42;UBERON:0004535!9.28e-07!109
|tf_chipseq_enrich=CCNT2#905;3:6.33620157696263:0.00393075003576489:0.0189408324714058!CTCF#10664;3:5.36025637307503:0.006492509252767:0.0278605955234503!E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0324016151613499!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0320858477655601!EGR1#1958;3:4.98817909481014:0.00805648813738344:0.0319430380236206!MAX#4149;3:6.45255550900712:0.00372191383426551:0.0185969265590305
|tf_chipseq_enrich=CCNT2#905;3:6.33620157696263:0.00393075003576489:0.0189408324714058!CTCF#10664;3:5.36025637307503:0.006492509252767:0.0278605955234503!E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0324016151613499!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0320858477655601!EGR1#1958;3:4.98817909481014:0.00805648813738344:0.0319430380236206!MAX#4149;3:6.45255550900712:0.00372191383426551:0.0185969265590305
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}}
}}

Revision as of 14:56, 19 October 2012


Full id: C3270_giant_testicular_gastric_ductal_Fibroblast_anaplastic_basal



Phase1 CAGE Peaks

Hg19::chr12:26111591..26111662,+p1@RASSF8
Hg19::chr12:26111665..26111684,+p5@RASSF8
Hg19::chr12:26111706..26111717,+p4@RASSF8


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
fibroblast2.65e-1376
non-terminally differentiated cell3.60e-09106
Uber Anatomy
Ontology termp-valuen
structure with developmental contribution from neural crest8.12e-14132
multi-cellular organism9.26e-14656
anatomical group2.67e-12625
anatomical system3.72e-12624
anatomical cluster5.04e-12373
multi-tissue structure3.10e-10342
vasculature9.10e-0978
vascular system9.10e-0978
ectoderm-derived structure9.14e-09171
ectoderm9.14e-09171
presumptive ectoderm9.14e-09171
epithelium1.04e-08306
dense mesenchyme tissue1.28e-0873
splanchnic layer of lateral plate mesoderm1.56e-0883
cell layer1.60e-08309
somite3.22e-0871
presomitic mesoderm3.22e-0871
presumptive segmental plate3.22e-0871
dermomyotome3.22e-0871
trunk paraxial mesoderm3.22e-0871
paraxial mesoderm3.49e-0872
presumptive paraxial mesoderm3.49e-0872
anatomical conduit5.62e-08240
neural plate7.32e-0882
presumptive neural plate7.32e-0882
systemic artery2.46e-0733
systemic arterial system2.46e-0733
body cavity or lining2.52e-0749
body cavity3.52e-0746
vessel5.96e-0768
neurectoderm7.64e-0786
circulatory system8.30e-07112
heart9.09e-0724
primitive heart tube9.09e-0724
primary heart field9.09e-0724
anterior lateral plate mesoderm9.09e-0724
heart tube9.09e-0724
heart primordium9.09e-0724
cardiac mesoderm9.09e-0724
cardiogenic plate9.09e-0724
heart rudiment9.09e-0724
artery9.26e-0742
arterial blood vessel9.26e-0742
arterial system9.26e-0742
cardiovascular system9.28e-07109


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#90536.336201576962630.003930750035764890.0189408324714058
CTCF#1066435.360256373075030.0064925092527670.0278605955234503
E2F1#186934.907389214879320.008460985347239390.0324016151613499
E2F6#187635.017155731697390.00791769806886330.0320858477655601
EGR1#195834.988179094810140.008056488137383440.0319430380236206
MAX#414936.452555509007120.003721913834265510.0185969265590305



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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