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Coexpression cluster:C1688: Difference between revisions

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|ontology_enrichment_disease=DOID:305!6.96e-26!106;DOID:0050687!4.10e-25!143;DOID:162!2.68e-14!235;DOID:14566!1.65e-13!239;DOID:7!5.59e-08!39;DOID:299!2.30e-07!25
|ontology_enrichment_disease=DOID:305!6.96e-26!106;DOID:0050687!4.10e-25!143;DOID:162!2.68e-14!235;DOID:14566!1.65e-13!239;DOID:7!5.59e-08!39;DOID:299!2.30e-07!25
|ontology_enrichment_uberon=UBERON:0004119!7.80e-17!169;UBERON:0000925!7.80e-17!169;UBERON:0006595!7.80e-17!169;UBERON:0000466!1.10e-15!126;UBERON:0001007!6.43e-15!155;UBERON:0001555!6.43e-15!155;UBERON:0007026!6.43e-15!155;UBERON:0009569!7.05e-14!113;UBERON:0000464!4.82e-13!104;UBERON:0000077!1.43e-11!130;UBERON:0001048!1.65e-11!168;UBERON:0004921!3.39e-11!129;UBERON:0004185!3.39e-11!129;UBERON:0005911!1.27e-10!82;UBERON:0005177!2.43e-10!107;UBERON:0002553!3.19e-09!70;UBERON:0000475!8.87e-09!365;UBERON:0003886!1.04e-08!63;UBERON:0002100!1.43e-08!216;UBERON:0001041!2.19e-08!98;UBERON:0002417!2.61e-08!61;UBERON:0000916!2.61e-08!61;UBERON:0000481!3.09e-08!347;UBERON:0003104!4.51e-08!238;UBERON:0009142!4.51e-08!238;UBERON:0000468!5.92e-08!659;UBERON:0001004!8.40e-08!72;UBERON:0000477!1.71e-07!286;UBERON:0005153!2.10e-07!37;UBERON:0008947!4.18e-07!38;UBERON:0003258!4.18e-07!38;UBERON:0005172!6.39e-07!55;UBERON:0005173!6.39e-07!55
|ontology_enrichment_uberon=UBERON:0004119!7.80e-17!169;UBERON:0000925!7.80e-17!169;UBERON:0006595!7.80e-17!169;UBERON:0000466!1.10e-15!126;UBERON:0001007!6.43e-15!155;UBERON:0001555!6.43e-15!155;UBERON:0007026!6.43e-15!155;UBERON:0009569!7.05e-14!113;UBERON:0000464!4.82e-13!104;UBERON:0000077!1.43e-11!130;UBERON:0001048!1.65e-11!168;UBERON:0004921!3.39e-11!129;UBERON:0004185!3.39e-11!129;UBERON:0005911!1.27e-10!82;UBERON:0005177!2.43e-10!107;UBERON:0002553!3.19e-09!70;UBERON:0000475!8.87e-09!365;UBERON:0003886!1.04e-08!63;UBERON:0002100!1.43e-08!216;UBERON:0001041!2.19e-08!98;UBERON:0002417!2.61e-08!61;UBERON:0000916!2.61e-08!61;UBERON:0000481!3.09e-08!347;UBERON:0003104!4.51e-08!238;UBERON:0009142!4.51e-08!238;UBERON:0000468!5.92e-08!659;UBERON:0001004!8.40e-08!72;UBERON:0000477!1.71e-07!286;UBERON:0005153!2.10e-07!37;UBERON:0008947!4.18e-07!38;UBERON:0003258!4.18e-07!38;UBERON:0005172!6.39e-07!55;UBERON:0005173!6.39e-07!55
|tf_chipseq_enrich=CTCF#10664;4:4.28820509846002:0.00515201558824328:0.0239270435797109!HEY1#23462;5:4.04011104310571:0.000928885220517799:0.00673786939475333!MYC#4609;5:5.2222818716094:0.000257394484885061:0.00276279780132691!PAX5#5079;4:5.33565242494226:0.00222338958618779:0.0127755603538659!RAD21#5885;3:6.2130203372738:0.00775105506881164:0.0318881446597187!TAF1#6872;5:3.34304628574529:0.00239460009087031:0.0135227446139507!TAF7#6879;5:11.4330694049239:5.11611886715123e-06:0.000157292416357494!ZEB1#6935;5:16.8884320175439:7.27243686732534e-07:3.22927735538517e-05
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}}
}}

Revision as of 14:16, 5 September 2012


Full id: C1688_pancreatic_large_testicular_oral_extraskeletal_mesothelioma_small



Phase1 CAGE Peaks

Hg19::chr12:80084279..80084293,-p8@PAWR
Hg19::chr12:80084303..80084332,-p1@PAWR
Hg19::chr12:80084333..80084380,-p4@PAWR
Hg19::chr12:80084737..80084763,-p3@PAWR
Hg19::chr12:80084768..80084821,-p2@PAWR


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 cell1.44e-49254
embryonic cell1.22e-14248
squamous epithelial cell2.83e-1362
endodermal cell1.56e-1059
endo-epithelial cell2.66e-0943
mesothelial cell7.95e-0919
Uber Anatomy
Ontology termp-valuen
endoderm-derived structure7.80e-17169
endoderm7.80e-17169
presumptive endoderm7.80e-17169
immaterial anatomical entity1.10e-15126
digestive system6.43e-15155
digestive tract6.43e-15155
primitive gut6.43e-15155
subdivision of trunk7.05e-14113
anatomical space4.82e-13104
mixed endoderm/mesoderm-derived structure1.43e-11130
primordium1.65e-11168
subdivision of digestive tract3.39e-11129
endodermal part of digestive tract3.39e-11129
endo-epithelium1.27e-1082
trunk region element2.43e-10107
anatomical cavity3.19e-0970
organism subdivision8.87e-09365
body cavity precursor1.04e-0863
trunk1.43e-08216
foregut2.19e-0898
abdominal segment of trunk2.61e-0861
abdomen2.61e-0861
multi-tissue structure3.09e-08347
mesenchyme4.51e-08238
entire embryonic mesenchyme4.51e-08238
multi-cellular organism5.92e-08659
respiratory system8.40e-0872
anatomical cluster1.71e-07286
epithelial bud2.10e-0737
respiratory primordium4.18e-0738
endoderm of foregut4.18e-0738
abdomen element6.39e-0755
abdominal segment element6.39e-0755
Disease
Ontology termp-valuen
carcinoma6.96e-26106
cell type cancer4.10e-25143
cancer2.68e-14235
disease of cellular proliferation1.65e-13239
disease of anatomical entity5.59e-0839
adenocarcinoma2.30e-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
CTCF#1066444.288205098460020.005152015588243280.0239270435797109
HEY1#2346254.040111043105710.0009288852205177990.00673786939475333
MYC#460955.22228187160940.0002573944848850610.00276279780132691
PAX5#507945.335652424942260.002223389586187790.0127755603538659
RAD21#588536.21302033727380.007751055068811640.0318881446597187
TAF1#687253.343046285745290.002394600090870310.0135227446139507
TAF7#6879511.43306940492395.11611886715123e-060.000157292416357494
ZEB1#6935516.88843201754397.27243686732534e-073.22927735538517e-05



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.