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Coexpression cluster:C4726: Difference between revisions

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|full_id=C4726_clear_oral_giant_anaplastic_ductal_squamous_serous
|full_id=C4726_clear_oral_giant_anaplastic_ductal_squamous_serous
|id=C4726
|id=C4726
|ontology_enrichment_celltype=CL:0000066!1.72e-49!254;CL:0000220!1.92e-29!246;CL:0002321!1.05e-28!248;CL:0002076!5.48e-21!43;CL:0000548!3.66e-17!679;CL:0000004!3.66e-17!679;CL:0000255!3.66e-17!679;CL:0000222!1.02e-16!119;CL:0000012!1.35e-16!682;CL:0000223!2.17e-15!59;CL:0000076!3.90e-14!62;CL:0000680!4.53e-11!57;CL:0000056!4.53e-11!57;CL:0000355!4.53e-11!57;CL:0000183!1.59e-10!59;CL:0000187!3.14e-10!54;CL:0000003!5.24e-10!722;CL:0000192!1.91e-09!42;CL:0000514!1.91e-09!42;CL:0002251!5.44e-09!21;CL:0000393!7.75e-09!60;CL:0000211!7.75e-09!60;CL:0000115!1.46e-08!35;CL:0002139!2.27e-08!24;CL:0000359!2.82e-08!32;CL:0002368!4.11e-08!13;CL:1000497!8.80e-08!18;CL:0002518!8.80e-08!18;CL:1000449!1.18e-07!16;CL:0002078!3.57e-07!44;CL:0000071!9.84e-07!18;CL:0002546!9.84e-07!18
|ontology_enrichment_celltype=CL:0000066!4.93e-39!253;CL:0002076!1.95e-26!42;CL:0000223!5.38e-20!58;CL:0002321!2.30e-19!250;CL:0002368!4.34e-11!13;CL:0000076!4.41e-11!63;CL:0000548!9.43e-10!679;CL:0000255!9.43e-10!679;CL:0002251!4.91e-09!20;CL:0002149!6.27e-08!6;CL:0002255!6.27e-08!6;CL:0002202!8.88e-08!9;CL:0002632!8.88e-08!9
|ontology_enrichment_disease=DOID:305!2.68e-18!106;DOID:0050687!4.94e-11!143;DOID:1749!2.10e-10!14;DOID:299!5.57e-10!25
|ontology_enrichment_disease=DOID:305!3.91e-23!106;DOID:0050687!5.27e-15!143;DOID:1749!3.07e-14!14;DOID:299!4.31e-12!25;DOID:3001!6.27e-08!6
|ontology_enrichment_uberon=UBERON:0003104!6.06e-20!238;UBERON:0009142!6.06e-20!238;UBERON:0000481!1.12e-15!347;UBERON:0000490!1.56e-14!138;UBERON:0002049!1.66e-14!79;UBERON:0007798!1.66e-14!79;UBERON:0000119!2.21e-14!312;UBERON:0000483!1.09e-13!309;UBERON:0004119!1.68e-13!169;UBERON:0000925!1.68e-13!169;UBERON:0006595!1.68e-13!169;UBERON:0002100!2.30e-13!216;UBERON:0003914!4.44e-13!118;UBERON:0000055!8.68e-13!69;UBERON:0001004!2.30e-12!72;UBERON:0001637!2.63e-12!42;UBERON:0003509!2.63e-12!42;UBERON:0004572!2.63e-12!42;UBERON:0000464!3.39e-12!104;UBERON:0001981!6.19e-12!60;UBERON:0007500!6.19e-12!60;UBERON:0004537!6.19e-12!60;UBERON:0006965!6.19e-12!60;UBERON:0000065!1.96e-11!53;UBERON:0000072!5.42e-11!46;UBERON:0008947!7.09e-11!38;UBERON:0003258!7.09e-11!38;UBERON:0000477!7.40e-11!286;UBERON:0000467!1.23e-10!625;UBERON:0000486!1.43e-10!82;UBERON:0000480!1.75e-10!626;UBERON:0005256!2.89e-10!143;UBERON:0000468!3.15e-10!659;UBERON:0000077!4.17e-10!130;UBERON:0004111!4.60e-10!241;UBERON:0004573!4.99e-10!33;UBERON:0004571!4.99e-10!33;UBERON:0000923!5.70e-10!604;UBERON:0005291!5.70e-10!604;UBERON:0006598!5.70e-10!604;UBERON:0002532!5.70e-10!604;UBERON:0001007!7.70e-10!155;UBERON:0001555!7.70e-10!155;UBERON:0007026!7.70e-10!155;UBERON:0002050!7.98e-10!605;UBERON:0005423!7.98e-10!605;UBERON:0000475!9.05e-10!365;UBERON:0000466!1.64e-09!126;UBERON:0000926!2.30e-09!448;UBERON:0004120!2.30e-09!448;UBERON:0006603!2.30e-09!448;UBERON:0001134!2.61e-09!61;UBERON:0002036!2.61e-09!61;UBERON:0003082!2.61e-09!61;UBERON:0004921!3.12e-09!129;UBERON:0004185!3.12e-09!129;UBERON:0000922!4.13e-09!612;UBERON:0004872!4.21e-09!84;UBERON:0001041!4.80e-09!98;UBERON:0002385!5.87e-09!63;UBERON:0001015!5.87e-09!63;UBERON:0000383!5.87e-09!63;UBERON:0005178!7.91e-09!34;UBERON:0002224!7.91e-09!34;UBERON:0007196!9.55e-09!14;UBERON:0001558!9.55e-09!14;UBERON:0004290!9.95e-09!70;UBERON:0000063!1.56e-08!97;UBERON:0005181!2.80e-08!35;UBERON:0000915!6.08e-08!52;UBERON:0000064!6.24e-08!219;UBERON:0004535!7.81e-08!110;UBERON:0001048!9.83e-08!168;UBERON:0004211!1.18e-07!16;UBERON:0001285!1.18e-07!16;UBERON:0007684!1.18e-07!16;UBERON:0003220!1.18e-07!16;UBERON:0004208!1.18e-07!16;UBERON:0000487!1.56e-07!22;UBERON:0000914!1.72e-07!83;UBERON:0002329!1.72e-07!83;UBERON:0003077!1.72e-07!83;UBERON:0003059!1.72e-07!83;UBERON:0007282!1.72e-07!83;UBERON:0009618!1.72e-07!83;UBERON:0007285!1.72e-07!83;UBERON:0001009!2.09e-07!113;UBERON:0000058!7.15e-07!26;UBERON:0006555!7.41e-07!17;UBERON:0005103!7.41e-07!17;UBERON:0000083!7.41e-07!17;UBERON:0009201!7.41e-07!17;UBERON:0004819!7.41e-07!17;UBERON:0006553!7.41e-07!17;UBERON:0003074!7.41e-07!17;UBERON:0003060!7.41e-07!17;UBERON:0006554!7.68e-07!44;UBERON:0001986!9.84e-07!18;UBERON:0004638!9.84e-07!18;UBERON:0004852!9.84e-07!18
|ontology_enrichment_uberon=UBERON:0000065!2.49e-13!54;UBERON:0001004!3.71e-13!74;UBERON:0000072!4.98e-12!47;UBERON:0008947!5.73e-11!38;UBERON:0003258!5.73e-11!38;UBERON:0004119!1.87e-09!160;UBERON:0000925!1.87e-09!160;UBERON:0006595!1.87e-09!160;UBERON:0007196!1.43e-08!15;UBERON:0001558!1.43e-08!15;UBERON:0000475!3.81e-08!264;UBERON:0001007!1.12e-07!145;UBERON:0001555!1.12e-07!145;UBERON:0007026!1.12e-07!145;UBERON:0000119!1.43e-07!309;UBERON:0000483!1.60e-07!306;UBERON:0001737!3.06e-07!9;UBERON:0001041!3.83e-07!87;UBERON:0002100!7.98e-07!199
|tf_chipseq_enrich=EP300#2033;3:6.7739417262232:0.00321688050010379:0.0168540073517779!FOS#2353;3:8.9979553088944:0.00137249927241713:0.00902148980502061!JUN#3725;3:12.5128291923363:0.000510331399272625:0.00446535698798875!JUND#3727;3:6.99466394187103:0.00292184504273499:0.0157727076248617!NR3C1#2908;3:14.973023331173:0.000297833119467548:0.00310309189585707!STAT3#6774;3:10.5194649971542:0.000858918453041531:0.00645728363930352!TCF7L2#6934;3:10.7701765631373:0.000800318129839838:0.0061758848206253
|tf_chipseq_enrich=EP300#2033;3:6.7739417262232:0.00321688050010379:0.0168540073517779!FOS#2353;3:8.9979553088944:0.00137249927241713:0.00902148980502061!JUN#3725;3:12.5128291923363:0.000510331399272625:0.00446535698798875!JUND#3727;3:6.99466394187103:0.00292184504273499:0.0157727076248617!NR3C1#2908;3:14.973023331173:0.000297833119467548:0.00310309189585707!STAT3#6774;3:10.5194649971542:0.000858918453041531:0.00645728363930352!TCF7L2#6934;3:10.7701765631373:0.000800318129839838:0.0061758848206253
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}}
}}

Revision as of 16:12, 19 October 2012


Full id: C4726_clear_oral_giant_anaplastic_ductal_squamous_serous



Phase1 CAGE Peaks

Hg19::chr8:128306934..128306945,-p@chr8:128306934..128306945
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Hg19::chr8:128306960..128306989,-p@chr8:128306960..128306989
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Hg19::chr8:128306991..128307011,-p@chr8:128306991..128307011
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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
respiratory tract2.49e-1354
respiratory system3.71e-1374
segment of respiratory tract4.98e-1247
respiratory primordium5.73e-1138
endoderm of foregut5.73e-1138
endoderm-derived structure1.87e-09160
endoderm1.87e-09160
presumptive endoderm1.87e-09160
tracheobronchial tree1.43e-0815
lower respiratory tract1.43e-0815
organism subdivision3.81e-08264
digestive system1.12e-07145
digestive tract1.12e-07145
primitive gut1.12e-07145
cell layer1.43e-07309
epithelium1.60e-07306
larynx3.06e-079
foregut3.83e-0787
trunk7.98e-07199
Disease
Ontology termp-valuen
carcinoma3.91e-23106
cell type cancer5.27e-15143
squamous cell carcinoma3.07e-1414
adenocarcinoma4.31e-1225
female reproductive endometrioid cancer6.27e-086


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#203336.77394172622320.003216880500103790.0168540073517779
FOS#235338.99795530889440.001372499272417130.00902148980502061
JUN#3725312.51282919233630.0005103313992726250.00446535698798875
JUND#372736.994663941871030.002921845042734990.0157727076248617
NR3C1#2908314.9730233311730.0002978331194675480.00310309189585707
STAT3#6774310.51946499715420.0008589184530415310.00645728363930352
TCF7L2#6934310.77017656313730.0008003181298398380.0061758848206253



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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