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Coexpression cluster:C2780: Difference between revisions

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|ontology_enrichment_disease=DOID:305!1.53e-20!106;DOID:0050687!4.44e-13!143;DOID:1749!1.22e-07!14;DOID:299!3.64e-07!25
|ontology_enrichment_disease=DOID:305!1.53e-20!106;DOID:0050687!4.44e-13!143;DOID:1749!1.22e-07!14;DOID:299!3.64e-07!25
|ontology_enrichment_uberon=UBERON:0004119!1.74e-14!169;UBERON:0000925!1.74e-14!169;UBERON:0006595!1.74e-14!169;UBERON:0001007!6.21e-12!155;UBERON:0001555!6.21e-12!155;UBERON:0007026!6.21e-12!155;UBERON:0001004!1.10e-11!72;UBERON:0004921!7.93e-10!129;UBERON:0004185!7.93e-10!129;UBERON:0000077!2.28e-09!130;UBERON:0000062!8.77e-09!511;UBERON:0000065!2.03e-08!53;UBERON:0001041!2.47e-07!98;UBERON:0001048!3.37e-07!168;UBERON:0008947!4.76e-07!38;UBERON:0003258!4.76e-07!38
|ontology_enrichment_uberon=UBERON:0004119!1.74e-14!169;UBERON:0000925!1.74e-14!169;UBERON:0006595!1.74e-14!169;UBERON:0001007!6.21e-12!155;UBERON:0001555!6.21e-12!155;UBERON:0007026!6.21e-12!155;UBERON:0001004!1.10e-11!72;UBERON:0004921!7.93e-10!129;UBERON:0004185!7.93e-10!129;UBERON:0000077!2.28e-09!130;UBERON:0000062!8.77e-09!511;UBERON:0000065!2.03e-08!53;UBERON:0001041!2.47e-07!98;UBERON:0001048!3.37e-07!168;UBERON:0008947!4.76e-07!38;UBERON:0003258!4.76e-07!38
|tf_chipseq_enrich=E2F1#1869;4:4.90738921487932:0.00172402235736179:0.010671200793013!E2F6#1876;4:5.01715573169739:0.0015780219347306:0.0099852791785113!FOSL2#2355;3:12.6976504534213:0.00078756857297571:0.00616911979247057!HEY1#23462;4:4.04011104310571:0.0037530463691798:0.0186463255673265!MYC#4609;4:5.2222818716094:0.00134430939527274:0.00889103469906208!NRF1#4899;3:9.15770958578318:0.00206195379173342:0.0119657938575789!RAD21#5885;3:7.76627542159225:0.003341119385872:0.0172727040659878!TAF1#6872;4:3.34304628574529:0.00800566489870165:0.0323007006511687!TBP#6908;4:3.70677068709639:0.00529637781478435:0.0244820927059513!TCF12#6938;4:10.6344649021864:7.8163066689251e-05:0.00120189524763821!ZEB1#6935;3:12.6663240131579:0.00079333607591285:0.00613469764787962
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}}
}}

Revision as of 14:18, 5 September 2012


Full id: C2780_immature_Dendritic_skeletal_renal_tongue_pancreas_amniotic



Phase1 CAGE Peaks

Hg19::chr4:152330321..152330350,+p1@FAM160A1
Hg19::chr4:152330355..152330373,+p2@FAM160A1
Hg19::chr4:152330390..152330405,+p3@FAM160A1
Hg19::chr6:26252009..26252025,+p5@HIST1H2BH


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 cell4.75e-18254
endo-epithelial cell1.53e-1143
endodermal cell1.28e-0959
Uber Anatomy
Ontology termp-valuen
endoderm-derived structure1.74e-14169
endoderm1.74e-14169
presumptive endoderm1.74e-14169
digestive system6.21e-12155
digestive tract6.21e-12155
primitive gut6.21e-12155
respiratory system1.10e-1172
subdivision of digestive tract7.93e-10129
endodermal part of digestive tract7.93e-10129
mixed endoderm/mesoderm-derived structure2.28e-09130
organ8.77e-09511
respiratory tract2.03e-0853
foregut2.47e-0798
primordium3.37e-07168
respiratory primordium4.76e-0738
endoderm of foregut4.76e-0738
Disease
Ontology termp-valuen
carcinoma1.53e-20106
cell type cancer4.44e-13143
squamous cell carcinoma1.22e-0714
adenocarcinoma3.64e-0725


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
E2F1#186944.907389214879320.001724022357361790.010671200793013
E2F6#187645.017155731697390.00157802193473060.0099852791785113
FOSL2#2355312.69765045342130.000787568572975710.00616911979247057
HEY1#2346244.040111043105710.00375304636917980.0186463255673265
MYC#460945.22228187160940.001344309395272740.00889103469906208
NRF1#489939.157709585783180.002061953791733420.0119657938575789
RAD21#588537.766275421592250.0033411193858720.0172727040659878
TAF1#687243.343046285745290.008005664898701650.0323007006511687
TBP#690843.706770687096390.005296377814784350.0244820927059513
TCF12#6938410.63446490218647.8163066689251e-050.00120189524763821
ZEB1#6935312.66632401315790.000793336075912850.00613469764787962



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:C2780&oldid=2133192"