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Coexpression cluster:C3583: Difference between revisions

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|full_id=C3583_large_mature_amniotic_heart_renal_Esophageal_breast
|full_id=C3583_large_mature_amniotic_heart_renal_Esophageal_breast
|id=C3583
|id=C3583
|ontology_enrichment_celltype=CL:0000066!7.15e-13!254;CL:0002076!7.32e-08!43
|ontology_enrichment_celltype=CL:0000066!1.60e-09!253;CL:0002076!5.46e-07!42
|ontology_enrichment_disease=DOID:305!9.64e-09!106;DOID:0050687!1.99e-07!143
|ontology_enrichment_disease=DOID:305!2.78e-07!106
|ontology_enrichment_uberon=UBERON:0000475!6.22e-21!365;UBERON:0000481!2.49e-19!347;UBERON:0000468!2.92e-18!659;UBERON:0000064!1.93e-17!219;UBERON:0007023!1.42e-15!115;UBERON:0000062!1.55e-15!511;UBERON:0000477!1.40e-14!286;UBERON:0000467!1.99e-14!625;UBERON:0000480!2.62e-14!626;UBERON:0002050!2.89e-13!605;UBERON:0005423!2.89e-13!605;UBERON:0000922!5.37e-13!612;UBERON:0000923!5.42e-13!604;UBERON:0005291!5.42e-13!604;UBERON:0006598!5.42e-13!604;UBERON:0002532!5.42e-13!604;UBERON:0004111!6.66e-13!241;UBERON:0004121!1.02e-11!169;UBERON:0000483!1.79e-11!309;UBERON:0001004!2.37e-11!72;UBERON:0000924!3.85e-11!173;UBERON:0006601!3.85e-11!173;UBERON:0000119!9.32e-11!312;UBERON:0000033!1.61e-10!123;UBERON:0004119!2.16e-10!169;UBERON:0000925!2.16e-10!169;UBERON:0006595!2.16e-10!169;UBERON:0000025!2.49e-10!194;UBERON:0001049!2.96e-10!57;UBERON:0005068!2.96e-10!57;UBERON:0006241!2.96e-10!57;UBERON:0007135!2.96e-10!57;UBERON:0003104!6.55e-10!238;UBERON:0009142!6.55e-10!238;UBERON:0000153!1.21e-09!129;UBERON:0007811!1.21e-09!129;UBERON:0008947!1.45e-09!38;UBERON:0003258!1.45e-09!38;UBERON:0000065!2.76e-09!53;UBERON:0003075!1.38e-08!86;UBERON:0007284!1.38e-08!86;UBERON:0002100!2.84e-08!216;UBERON:0002616!4.45e-08!59;UBERON:0000955!4.48e-08!69;UBERON:0006238!4.48e-08!69;UBERON:0000077!5.74e-08!130;UBERON:0000072!7.00e-08!46;UBERON:0002346!7.05e-08!90;UBERON:0001007!7.95e-08!155;UBERON:0001555!7.95e-08!155;UBERON:0007026!7.95e-08!155;UBERON:0002780!1.02e-07!41;UBERON:0001890!1.02e-07!41;UBERON:0006240!1.02e-07!41;UBERON:0003080!1.39e-07!42;UBERON:0000915!1.81e-07!52;UBERON:0001041!4.53e-07!98;UBERON:0001737!7.87e-07!9;UBERON:0002020!8.66e-07!34;UBERON:0003528!8.66e-07!34
|ontology_enrichment_uberon=UBERON:0007023!4.05e-17!114;UBERON:0000481!2.64e-16!342;UBERON:0000064!1.02e-15!218;UBERON:0000062!7.27e-14!503;UBERON:0000468!2.23e-13!656;UBERON:0011216!4.13e-12!223;UBERON:0001004!1.09e-11!74;UBERON:0000477!1.61e-11!373;UBERON:0004119!2.82e-11!160;UBERON:0000925!2.82e-11!160;UBERON:0006595!2.82e-11!160;UBERON:0000480!3.29e-11!625;UBERON:0000467!3.79e-11!624;UBERON:0004121!4.10e-10!171;UBERON:0000924!4.10e-10!171;UBERON:0006601!4.10e-10!171;UBERON:0008947!5.61e-10!38;UBERON:0003258!5.61e-10!38;UBERON:0000065!7.05e-10!54;UBERON:0010371!7.90e-10!104;UBERON:0004111!1.55e-09!240;UBERON:0001049!1.91e-09!56;UBERON:0005068!1.91e-09!56;UBERON:0006241!1.91e-09!56;UBERON:0007135!1.91e-09!56;UBERON:0000483!3.47e-09!306;UBERON:0005423!4.21e-09!581;UBERON:0000922!5.84e-09!592;UBERON:0000073!1.32e-08!53;UBERON:0002616!1.32e-08!53;UBERON:0000119!1.50e-08!309;UBERON:0001007!2.14e-08!145;UBERON:0001555!2.14e-08!145;UBERON:0007026!2.14e-08!145;UBERON:0010314!2.44e-08!132;UBERON:0000072!3.23e-08!47;UBERON:0001041!4.02e-08!87;UBERON:0000475!4.78e-08!264;UBERON:0002050!5.34e-08!564;UBERON:0003075!7.47e-08!82;UBERON:0007284!7.47e-08!82;UBERON:0000923!1.69e-07!560;UBERON:0010316!1.69e-07!560;UBERON:0005291!1.69e-07!560;UBERON:0006598!1.69e-07!560;UBERON:0010317!1.69e-07!560;UBERON:0002532!1.69e-07!560;UBERON:0000025!2.79e-07!192;UBERON:0002780!3.62e-07!41;UBERON:0001890!3.62e-07!41;UBERON:0003080!3.62e-07!41;UBERON:0006240!3.62e-07!41;UBERON:0002346!3.70e-07!86;UBERON:0000955!6.19e-07!68;UBERON:0006238!6.19e-07!68;UBERON:0001737!6.36e-07!9
|tf_chipseq_enrich=MYC#4609;3:5.2222818716094:0.00702084375574015:0.0294052735404935!NR3C1#2908;3:14.973023331173:0.000297833119467548:0.00308554639064292!SUZ12#23512;2:33.4105206073753:0.0011782676453603:0.00799747154180698!ZNF263#10127;3:8.22184163701068:0.00179904392556587:0.0109270339367359
|tf_chipseq_enrich=MYC#4609;3:5.2222818716094:0.00702084375574015:0.0294052735404935!NR3C1#2908;3:14.973023331173:0.000297833119467548:0.00308554639064292!SUZ12#23512;2:33.4105206073753:0.0011782676453603:0.00799747154180698!ZNF263#10127;3:8.22184163701068:0.00179904392556587:0.0109270339367359
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}}
}}

Revision as of 15:13, 19 October 2012


Full id: C3583_large_mature_amniotic_heart_renal_Esophageal_breast



Phase1 CAGE Peaks

Hg19::chr16:67207821..67207836,+p5@NOL3
Hg19::chr16:67207838..67207870,+p2@NOL3
Hg19::chr16:67207872..67207900,+p4@NOL3


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
epithelial cell1.60e-09253
endo-epithelial cell5.46e-0742
Uber Anatomy
Ontology termp-valuen
adult organism4.05e-17114
multi-tissue structure2.64e-16342
organ part1.02e-15218
organ7.27e-14503
multi-cellular organism2.23e-13656
organ system subdivision4.13e-12223
respiratory system1.09e-1174
anatomical cluster1.61e-11373
endoderm-derived structure2.82e-11160
endoderm2.82e-11160
presumptive endoderm2.82e-11160
anatomical group3.29e-11625
anatomical system3.79e-11624
ectoderm-derived structure4.10e-10171
ectoderm4.10e-10171
presumptive ectoderm4.10e-10171
respiratory primordium5.61e-1038
endoderm of foregut5.61e-1038
respiratory tract7.05e-1054
ecto-epithelium7.90e-10104
anatomical conduit1.55e-09240
neural tube1.91e-0956
neural rod1.91e-0956
future spinal cord1.91e-0956
neural keel1.91e-0956
epithelium3.47e-09306
developing anatomical structure4.21e-09581
embryo5.84e-09592
regional part of nervous system1.32e-0853
regional part of brain1.32e-0853
cell layer1.50e-08309
digestive system2.14e-08145
digestive tract2.14e-08145
primitive gut2.14e-08145
structure with developmental contribution from neural crest2.44e-08132
segment of respiratory tract3.23e-0847
foregut4.02e-0887
organism subdivision4.78e-08264
embryonic structure5.34e-08564
neural plate7.47e-0882
presumptive neural plate7.47e-0882
germ layer1.69e-07560
germ layer / neural crest1.69e-07560
embryonic tissue1.69e-07560
presumptive structure1.69e-07560
germ layer / neural crest derived structure1.69e-07560
epiblast (generic)1.69e-07560
tube2.79e-07192
regional part of forebrain3.62e-0741
forebrain3.62e-0741
anterior neural tube3.62e-0741
future forebrain3.62e-0741
neurectoderm3.70e-0786
brain6.19e-0768
future brain6.19e-0768
larynx6.36e-079
Disease
Ontology termp-valuen
carcinoma2.78e-07106


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
MYC#460935.22228187160940.007020843755740150.0294052735404935
NR3C1#2908314.9730233311730.0002978331194675480.00308554639064292
SUZ12#23512233.41052060737530.00117826764536030.00799747154180698
ZNF263#1012738.221841637010680.001799043925565870.0109270339367359



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.

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=Coexpression_cluster:C3583&oldid=2249820"