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Coexpression cluster:C3925: Difference between revisions

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|full_id=C3925_Mast_testicular_breast_choriocarcinoma_Mesenchymal_gastrointestinal_smallcell
|full_id=C3925_Mast_testicular_breast_choriocarcinoma_Mesenchymal_gastrointestinal_smallcell
|id=C3925
|id=C3925
|ontology_enrichment_celltype=CL:0000066!6.98e-25!254;CL:0002139!2.44e-08!24;CL:0000076!9.41e-08!62;CL:0000115!1.05e-07!35;CL:0000223!2.14e-07!59;CL:0000071!2.19e-07!18;CL:0002546!2.19e-07!18;CL:0000148!5.96e-07!10;CL:0000541!5.96e-07!10
|ontology_enrichment_celltype=CL:0000066!1.05e-23!253;CL:0002139!8.47e-09!24;CL:0000115!4.96e-08!36;CL:0000223!8.55e-08!58;CL:0000071!1.37e-07!18;CL:0002546!1.37e-07!18;CL:0000076!1.95e-07!63;CL:0000148!6.90e-07!10;CL:0000541!6.90e-07!10
|ontology_enrichment_disease=DOID:305!6.34e-16!106;DOID:0050687!3.58e-10!143
|ontology_enrichment_disease=DOID:305!2.14e-15!106;DOID:0050687!9.93e-10!143
|ontology_enrichment_uberon=UBERON:0007023!2.99e-19!115;UBERON:0000468!3.14e-19!659;UBERON:0004111!5.01e-18!241;UBERON:0000467!2.05e-15!625;UBERON:0000480!4.40e-15!626;UBERON:0000025!3.44e-14!194;UBERON:0000477!3.93e-14!286;UBERON:0000922!4.58e-13!612;UBERON:0000483!5.26e-13!309;UBERON:0000064!5.63e-13!219;UBERON:0004921!1.86e-12!129;UBERON:0004185!1.86e-12!129;UBERON:0000119!1.99e-12!312;UBERON:0000062!2.91e-12!511;UBERON:0004119!4.76e-12!169;UBERON:0000925!4.76e-12!169;UBERON:0006595!4.76e-12!169;UBERON:0001007!3.06e-11!155;UBERON:0001555!3.06e-11!155;UBERON:0007026!3.06e-11!155;UBERON:0002050!4.83e-11!605;UBERON:0005423!4.83e-11!605;UBERON:0000466!5.01e-11!126;UBERON:0000475!5.59e-11!365;UBERON:0000923!9.80e-11!604;UBERON:0005291!9.80e-11!604;UBERON:0006598!9.80e-11!604;UBERON:0002532!9.80e-11!604;UBERON:0000077!1.04e-10!130;UBERON:0000481!1.22e-09!347;UBERON:0001041!1.73e-09!98;UBERON:0001049!1.98e-09!57;UBERON:0005068!1.98e-09!57;UBERON:0006241!1.98e-09!57;UBERON:0007135!1.98e-09!57;UBERON:0005177!7.86e-09!107;UBERON:0005743!1.72e-08!86;UBERON:0001017!2.33e-08!82;UBERON:0000464!4.34e-08!104;UBERON:0009569!6.42e-08!113;UBERON:0001048!1.43e-07!168;UBERON:0001986!2.19e-07!18;UBERON:0004638!2.19e-07!18;UBERON:0004852!2.19e-07!18;UBERON:0000955!4.19e-07!69;UBERON:0006238!4.19e-07!69;UBERON:0004121!4.50e-07!169;UBERON:0003075!5.91e-07!86;UBERON:0007284!5.91e-07!86;UBERON:0002616!6.96e-07!59;UBERON:0000073!7.40e-07!94;UBERON:0001016!7.40e-07!94
|ontology_enrichment_uberon=UBERON:0007023!2.03e-18!114;UBERON:0000468!1.03e-15!656;UBERON:0004111!1.46e-15!240;UBERON:0000477!4.20e-15!373;UBERON:0011216!6.83e-13!223;UBERON:0000025!1.93e-12!192;UBERON:0000064!2.22e-12!218;UBERON:0000466!9.09e-12!117;UBERON:0000467!1.43e-11!624;UBERON:0000480!2.71e-11!625;UBERON:0000483!3.34e-11!306;UBERON:0000119!9.77e-11!309;UBERON:0004921!3.02e-10!118;UBERON:0000922!6.06e-10!592;UBERON:0004119!9.80e-10!160;UBERON:0000925!9.80e-10!160;UBERON:0006595!9.80e-10!160;UBERON:0001007!3.55e-09!145;UBERON:0001555!3.55e-09!145;UBERON:0007026!3.55e-09!145;UBERON:0000464!3.92e-09!95;UBERON:0000062!5.06e-09!503;UBERON:0005177!5.61e-09!101;UBERON:0000481!1.49e-08!342;UBERON:0001049!2.69e-08!56;UBERON:0005068!2.69e-08!56;UBERON:0006241!2.69e-08!56;UBERON:0007135!2.69e-08!56;UBERON:0009569!3.91e-08!112;UBERON:0000923!9.09e-08!560;UBERON:0010316!9.09e-08!560;UBERON:0005291!9.09e-08!560;UBERON:0006598!9.09e-08!560;UBERON:0010317!9.09e-08!560;UBERON:0002532!9.09e-08!560;UBERON:0002050!9.40e-08!564;UBERON:0001041!1.06e-07!87;UBERON:0005423!1.08e-07!581;UBERON:0004638!1.37e-07!18;UBERON:0001986!1.37e-07!18;UBERON:0004852!1.37e-07!18;UBERON:0000073!2.16e-07!53;UBERON:0002616!2.16e-07!53;UBERON:0001017!2.50e-07!81
|tf_chipseq_enrich=CTCF#10664;3:5.36025637307503:0.006492509252767:0.0279593919614767!NR2C2#7182;2:21.7430739368272:0.00276220797549601:0.0151386565256522!SMC3#9126;2:10.0299552299552:0.012665637976747:0.0457537464858871!ZNF263#10127;3:8.22184163701068:0.00179904392556587:0.0109486829754778
|tf_chipseq_enrich=CTCF#10664;3:5.36025637307503:0.006492509252767:0.0279593919614767!NR2C2#7182;2:21.7430739368272:0.00276220797549601:0.0151386565256522!SMC3#9126;2:10.0299552299552:0.012665637976747:0.0457537464858871!ZNF263#10127;3:8.22184163701068:0.00179904392556587:0.0109486829754778
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59274,0.316866,0.171683,0.158847,0.271275,0.071111,0.270604,0.101021,0.222548,0.175934,0.157274,0.215705,0.252796,0.205954,0.361435
}}
}}

Revision as of 15:30, 19 October 2012


Full id: C3925_Mast_testicular_breast_choriocarcinoma_Mesenchymal_gastrointestinal_smallcell



Phase1 CAGE Peaks

Hg19::chr1:204042233..204042249,+p1@SOX13
Hg19::chr1:204042275..204042286,+p4@SOX13
Hg19::chr1:204042723..204042784,+p3@SOX13


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>

Uber Anatomy
Ontology termp-valuen
adult organism2.03e-18114
multi-cellular organism1.03e-15656
anatomical conduit1.46e-15240
anatomical cluster4.20e-15373
organ system subdivision6.83e-13223
tube1.93e-12192
organ part2.22e-12218
immaterial anatomical entity9.09e-12117
anatomical system1.43e-11624
anatomical group2.71e-11625
epithelium3.34e-11306
cell layer9.77e-11309
subdivision of digestive tract3.02e-10118
embryo6.06e-10592
endoderm-derived structure9.80e-10160
endoderm9.80e-10160
presumptive endoderm9.80e-10160
digestive system3.55e-09145
digestive tract3.55e-09145
primitive gut3.55e-09145
anatomical space3.92e-0995
organ5.06e-09503
trunk region element5.61e-09101
multi-tissue structure1.49e-08342
neural tube2.69e-0856
neural rod2.69e-0856
future spinal cord2.69e-0856
neural keel2.69e-0856
subdivision of trunk3.91e-08112
germ layer9.09e-08560
germ layer / neural crest9.09e-08560
embryonic tissue9.09e-08560
presumptive structure9.09e-08560
germ layer / neural crest derived structure9.09e-08560
epiblast (generic)9.09e-08560
embryonic structure9.40e-08564
foregut1.06e-0787
developing anatomical structure1.08e-07581
blood vessel endothelium1.37e-0718
endothelium1.37e-0718
cardiovascular system endothelium1.37e-0718
regional part of nervous system2.16e-0753
regional part of brain2.16e-0753
central nervous system2.50e-0781
Disease
Ontology termp-valuen
carcinoma2.14e-15106
cell type cancer9.93e-10143


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#1066435.360256373075030.0064925092527670.0279593919614767
NR2C2#7182221.74307393682720.002762207975496010.0151386565256522
SMC3#9126210.02995522995520.0126656379767470.0457537464858871
ZNF263#1012738.221841637010680.001799043925565870.0109486829754778



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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