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Coexpression cluster:C4572: Difference between revisions

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|full_id=C4572_breast_lung_choriocarcinoma_thyroid_immature_throat_amniotic
|full_id=C4572_breast_lung_choriocarcinoma_thyroid_immature_throat_amniotic
|id=C4572
|id=C4572
|ontology_enrichment_celltype=CL:0002076!1.15e-16!43;CL:0000223!1.66e-11!59;CL:0000066!1.81e-08!254;CL:0002251!3.49e-07!21;CL:0002368!3.57e-07!13
|ontology_enrichment_celltype=CL:0002076!5.61e-16!42;CL:0000223!6.46e-12!58;CL:0002251!4.31e-09!20
|ontology_enrichment_disease=DOID:305!1.12e-08!106;DOID:1749!1.81e-07!14;DOID:299!3.63e-07!25
|ontology_enrichment_disease=DOID:305!5.31e-10!106;DOID:299!3.99e-09!25;DOID:0050687!9.48e-07!143
|ontology_enrichment_uberon=UBERON:0004119!1.42e-18!169;UBERON:0000925!1.42e-18!169;UBERON:0006595!1.42e-18!169;UBERON:0001007!1.72e-15!155;UBERON:0001555!1.72e-15!155;UBERON:0007026!1.72e-15!155;UBERON:0007023!3.49e-15!115;UBERON:0004921!1.16e-13!129;UBERON:0004185!1.16e-13!129;UBERON:0001004!8.95e-13!72;UBERON:0000077!1.14e-12!130;UBERON:0000062!1.01e-11!511;UBERON:0005153!1.22e-10!37;UBERON:0005631!1.15e-09!14;UBERON:0000158!1.15e-09!14;UBERON:0000161!1.70e-09!35;UBERON:0000468!2.31e-09!659;UBERON:0000064!2.56e-09!219;UBERON:0000464!4.57e-09!104;UBERON:0000065!9.24e-09!53;UBERON:0000922!4.06e-08!612;UBERON:0000166!7.26e-08!21;UBERON:0005911!9.08e-08!82;UBERON:0005178!2.32e-07!34;UBERON:0002224!2.32e-07!34;UBERON:0000466!2.67e-07!126;UBERON:0001041!2.78e-07!98;UBERON:0002048!3.16e-07!22;UBERON:0000117!3.16e-07!22;UBERON:0000171!3.16e-07!22;UBERON:0000170!3.16e-07!22;UBERON:0005597!3.16e-07!22;UBERON:0000118!3.16e-07!22;UBERON:0003124!3.24e-07!7;UBERON:0005156!3.73e-07!59;UBERON:0000990!3.73e-07!59;UBERON:0000480!4.89e-07!626;UBERON:0005181!5.39e-07!35;UBERON:0000344!5.57e-07!12;UBERON:0000467!8.26e-07!625;UBERON:0000153!9.16e-07!129;UBERON:0007811!9.16e-07!129;UBERON:0004121!9.56e-07!169
|ontology_enrichment_uberon=UBERON:0004119!5.04e-14!160;UBERON:0000925!5.04e-14!160;UBERON:0006595!5.04e-14!160;UBERON:0001007!1.03e-13!145;UBERON:0001555!1.03e-13!145;UBERON:0007026!1.03e-13!145;UBERON:0001004!5.90e-12!74;UBERON:0004921!4.86e-11!118;UBERON:0007023!1.32e-09!114;UBERON:0005153!4.76e-09!37;UBERON:0000065!8.60e-09!54;UBERON:0000464!1.81e-08!95;UBERON:0000161!2.16e-08!36;UBERON:0005911!2.32e-08!82;UBERON:0011216!7.49e-08!223;UBERON:0000062!8.96e-08!503;UBERON:0001041!1.57e-07!87;UBERON:0000166!3.47e-07!22;UBERON:0000466!5.53e-07!117;UBERON:0005178!5.58e-07!34;UBERON:0002224!5.58e-07!34;UBERON:0005157!5.72e-07!47;UBERON:0005156!6.10e-07!59;UBERON:0000990!6.10e-07!59;UBERON:0003101!7.21e-07!22;UBERON:0000079!7.21e-07!22
|tf_chipseq_enrich=BCL11A#53335;3:28.3694551036071:4.37778126761649e-05:0.000779691503766368!EP300#2033;3:6.7739417262232:0.00321688050010379:0.0168269950190494!FOXA1#3169;3:11.0814197493855:0.00073475527569867:0.00583729699062021!GATA3#2625;3:27.236516357206:4.94721007899563e-05:0.00085444298567922!JUND#3727;3:6.99466394187103:0.00292184504273499:0.0157556058662846!MYC#4609;3:5.2222818716094:0.00702084375574015:0.0295832284759843!NANOG#79923;3:29.2447784810127:3.99627955670032e-05:0.000740538397129569!NR3C1#2908;3:14.973023331173:0.000297833119467548:0.00309999931872347!SP1#6667;3:5.6983813781409:0.00540396270171217:0.0247689133943701!SPI1#6688;3:8.20432350852273:0.00181059318941052:0.0109367577853583!TAF7#6879;3:11.4330694049239:0.000669018198194583:0.00545232864621491!TCF12#6938;3:10.6344649021864:0.000831352399020207:0.00631688710085641!YY1#7528;3:4.91117074985386:0.00844145534180826:0.0330999494816262
|tf_chipseq_enrich=BCL11A#53335;3:28.3694551036071:4.37778126761649e-05:0.000779691503766368!EP300#2033;3:6.7739417262232:0.00321688050010379:0.0168269950190494!FOXA1#3169;3:11.0814197493855:0.00073475527569867:0.00583729699062021!GATA3#2625;3:27.236516357206:4.94721007899563e-05:0.00085444298567922!JUND#3727;3:6.99466394187103:0.00292184504273499:0.0157556058662846!MYC#4609;3:5.2222818716094:0.00702084375574015:0.0295832284759843!NANOG#79923;3:29.2447784810127:3.99627955670032e-05:0.000740538397129569!NR3C1#2908;3:14.973023331173:0.000297833119467548:0.00309999931872347!SP1#6667;3:5.6983813781409:0.00540396270171217:0.0247689133943701!SPI1#6688;3:8.20432350852273:0.00181059318941052:0.0109367577853583!TAF7#6879;3:11.4330694049239:0.000669018198194583:0.00545232864621491!TCF12#6938;3:10.6344649021864:0.000831352399020207:0.00631688710085641!YY1#7528;3:4.91117074985386:0.00844145534180826:0.0330999494816262
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435
}}
}}

Revision as of 16:03, 19 October 2012


Full id: C4572_breast_lung_choriocarcinoma_thyroid_immature_throat_amniotic



Phase1 CAGE Peaks

Hg19::chr6:144651917..144651928,+p@chr6:144651917..144651928
+
Hg19::chr6:144651933..144651949,+p@chr6:144651933..144651949
+
Hg19::chr6:144651950..144651997,+p@chr6:144651950..144651997
+


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
endo-epithelial cell5.61e-1642
endodermal cell6.46e-1258
epithelial cell of alimentary canal4.31e-0920
Uber Anatomy
Ontology termp-valuen
endoderm-derived structure5.04e-14160
endoderm5.04e-14160
presumptive endoderm5.04e-14160
digestive system1.03e-13145
digestive tract1.03e-13145
primitive gut1.03e-13145
respiratory system5.90e-1274
subdivision of digestive tract4.86e-11118
adult organism1.32e-09114
epithelial bud4.76e-0937
respiratory tract8.60e-0954
anatomical space1.81e-0895
orifice2.16e-0836
endo-epithelium2.32e-0882
organ system subdivision7.49e-08223
organ8.96e-08503
foregut1.57e-0787
oral opening3.47e-0722
immaterial anatomical entity5.53e-07117
thoracic cavity element5.58e-0734
thoracic cavity5.58e-0734
epithelial fold5.72e-0747
reproductive structure6.10e-0759
reproductive system6.10e-0759
male organism7.21e-0722
male reproductive system7.21e-0722
Disease
Ontology termp-valuen
carcinoma5.31e-10106
adenocarcinoma3.99e-0925
cell type cancer9.48e-07143


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
BCL11A#53335328.36945510360714.37778126761649e-050.000779691503766368
EP300#203336.77394172622320.003216880500103790.0168269950190494
FOXA1#3169311.08141974938550.000734755275698670.00583729699062021
GATA3#2625327.2365163572064.94721007899563e-050.00085444298567922
JUND#372736.994663941871030.002921845042734990.0157556058662846
MYC#460935.22228187160940.007020843755740150.0295832284759843
NANOG#79923329.24477848101273.99627955670032e-050.000740538397129569
NR3C1#2908314.9730233311730.0002978331194675480.00309999931872347
SP1#666735.69838137814090.005403962701712170.0247689133943701
SPI1#668838.204323508522730.001810593189410520.0109367577853583
TAF7#6879311.43306940492390.0006690181981945830.00545232864621491
TCF12#6938310.63446490218640.0008313523990202070.00631688710085641
YY1#752834.911170749853860.008441455341808260.0330999494816262



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.