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Coexpression cluster:C4696: Difference between revisions

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|ontology_enrichment_disease=DOID:305!4.48e-29!106;DOID:0050687!2.73e-21!143;DOID:299!6.07e-14!25;DOID:162!1.08e-08!235;DOID:14566!5.78e-08!239
|ontology_enrichment_disease=DOID:305!4.48e-29!106;DOID:0050687!2.73e-21!143;DOID:299!6.07e-14!25;DOID:162!1.08e-08!235;DOID:14566!5.78e-08!239
|ontology_enrichment_uberon=UBERON:0004921!9.63e-17!129;UBERON:0004185!9.63e-17!129;UBERON:0001007!5.68e-15!155;UBERON:0001555!5.68e-15!155;UBERON:0007026!5.68e-15!155;UBERON:0000077!2.53e-14!130;UBERON:0004119!1.18e-13!169;UBERON:0000925!1.18e-13!169;UBERON:0006595!1.18e-13!169;UBERON:0007023!3.07e-13!115;UBERON:0000466!3.71e-13!126;UBERON:0001041!5.16e-11!98;UBERON:0000464!8.65e-11!104;UBERON:0005177!1.19e-10!107;UBERON:0009569!8.36e-10!113;UBERON:0005172!1.70e-09!55;UBERON:0005173!1.70e-09!55;UBERON:0000481!4.45e-09!347;UBERON:0000062!8.97e-09!511;UBERON:0005911!9.77e-09!82;UBERON:0000058!1.41e-08!26;UBERON:0000477!1.73e-08!286;UBERON:0000064!1.94e-08!219;UBERON:0004111!5.97e-08!241;UBERON:0002553!6.41e-08!70;UBERON:0002113!1.04e-07!27;UBERON:0003918!1.04e-07!27;UBERON:0005095!1.04e-07!27;UBERON:0007687!1.04e-07!27;UBERON:0009773!1.31e-07!12;UBERON:0001231!1.31e-07!12;UBERON:0004810!1.31e-07!12;UBERON:0000063!1.33e-07!97;UBERON:0002417!1.87e-07!61;UBERON:0000916!1.87e-07!61;UBERON:0003064!2.17e-07!37;UBERON:0000468!2.26e-07!659;UBERON:0000080!2.36e-07!18;UBERON:0002120!2.36e-07!18;UBERON:0004875!2.36e-07!18;UBERON:0005721!2.36e-07!18;UBERON:0005754!2.36e-07!18;UBERON:0007297!2.36e-07!18;UBERON:0004876!3.47e-07!20;UBERON:0003887!4.14e-07!21;UBERON:0001048!4.49e-07!168;UBERON:0000489!7.08e-07!32;UBERON:0000922!7.56e-07!612;UBERON:0008947!8.55e-07!38;UBERON:0003258!8.55e-07!38;UBERON:0005409!8.71e-07!35;UBERON:0005156!9.36e-07!59;UBERON:0000990!9.36e-07!59
|ontology_enrichment_uberon=UBERON:0004921!9.63e-17!129;UBERON:0004185!9.63e-17!129;UBERON:0001007!5.68e-15!155;UBERON:0001555!5.68e-15!155;UBERON:0007026!5.68e-15!155;UBERON:0000077!2.53e-14!130;UBERON:0004119!1.18e-13!169;UBERON:0000925!1.18e-13!169;UBERON:0006595!1.18e-13!169;UBERON:0007023!3.07e-13!115;UBERON:0000466!3.71e-13!126;UBERON:0001041!5.16e-11!98;UBERON:0000464!8.65e-11!104;UBERON:0005177!1.19e-10!107;UBERON:0009569!8.36e-10!113;UBERON:0005172!1.70e-09!55;UBERON:0005173!1.70e-09!55;UBERON:0000481!4.45e-09!347;UBERON:0000062!8.97e-09!511;UBERON:0005911!9.77e-09!82;UBERON:0000058!1.41e-08!26;UBERON:0000477!1.73e-08!286;UBERON:0000064!1.94e-08!219;UBERON:0004111!5.97e-08!241;UBERON:0002553!6.41e-08!70;UBERON:0002113!1.04e-07!27;UBERON:0003918!1.04e-07!27;UBERON:0005095!1.04e-07!27;UBERON:0007687!1.04e-07!27;UBERON:0009773!1.31e-07!12;UBERON:0001231!1.31e-07!12;UBERON:0004810!1.31e-07!12;UBERON:0000063!1.33e-07!97;UBERON:0002417!1.87e-07!61;UBERON:0000916!1.87e-07!61;UBERON:0003064!2.17e-07!37;UBERON:0000468!2.26e-07!659;UBERON:0000080!2.36e-07!18;UBERON:0002120!2.36e-07!18;UBERON:0004875!2.36e-07!18;UBERON:0005721!2.36e-07!18;UBERON:0005754!2.36e-07!18;UBERON:0007297!2.36e-07!18;UBERON:0004876!3.47e-07!20;UBERON:0003887!4.14e-07!21;UBERON:0001048!4.49e-07!168;UBERON:0000489!7.08e-07!32;UBERON:0000922!7.56e-07!612;UBERON:0008947!8.55e-07!38;UBERON:0003258!8.55e-07!38;UBERON:0005409!8.71e-07!35;UBERON:0005156!9.36e-07!59;UBERON:0000990!9.36e-07!59
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}}
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Revision as of 20:15, 8 August 2012


Full id: C4696_serous_colon_small_MCF7_thyroid_endometrial_choriocarcinoma



Phase1 CAGE Peaks

Hg19::chr7:73183842..73183858,-p@chr7:73183842..73183858
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Hg19::chr7:73184529..73184547,-p2@CLDN3
Hg19::chr7:73184588..73184611,-p1@CLDN3


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 cell3.89e-16254
kidney tubule cell1.31e-0712
nephron tubule epithelial cell1.31e-0712
Uber Anatomy
Ontology termp-valuen
subdivision of digestive tract9.63e-17129
endodermal part of digestive tract9.63e-17129
digestive system5.68e-15155
digestive tract5.68e-15155
primitive gut5.68e-15155
mixed endoderm/mesoderm-derived structure2.53e-14130
endoderm-derived structure1.18e-13169
endoderm1.18e-13169
presumptive endoderm1.18e-13169
adult organism3.07e-13115
immaterial anatomical entity3.71e-13126
foregut5.16e-1198
anatomical space8.65e-11104
trunk region element1.19e-10107
subdivision of trunk8.36e-10113
abdomen element1.70e-0955
abdominal segment element1.70e-0955
multi-tissue structure4.45e-09347
organ8.97e-09511
endo-epithelium9.77e-0982
duct1.41e-0826
anatomical cluster1.73e-08286
organ part1.94e-08219
anatomical conduit5.97e-08241
anatomical cavity6.41e-0870
kidney1.04e-0727
kidney mesenchyme1.04e-0727
kidney rudiment1.04e-0727
kidney field1.04e-0727
renal tubule1.31e-0712
nephron tubule1.31e-0712
nephron tubule epithelium1.31e-0712
organ segment1.33e-0797
abdominal segment of trunk1.87e-0761
abdomen1.87e-0761
intermediate mesoderm2.17e-0737
multi-cellular organism2.26e-07659
mesonephros2.36e-0718
pronephros2.36e-0718
nephrogenic cord2.36e-0718
pronephric mesoderm2.36e-0718
rostral part of nephrogenic cord2.36e-0718
presumptive pronephric mesoderm2.36e-0718
urogenital ridge3.47e-0720
intraembryonic coelom4.14e-0721
primordium4.49e-07168
cavitated compound organ7.08e-0732
embryo7.56e-07612
respiratory primordium8.55e-0738
endoderm of foregut8.55e-0738
gastrointestinal system8.71e-0735
reproductive structure9.36e-0759
reproductive system9.36e-0759
Disease
Ontology termp-valuen
carcinoma4.48e-29106
cell type cancer2.73e-21143
adenocarcinoma6.07e-1425
cancer1.08e-08235
disease of cellular proliferation5.78e-08239


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)

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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


No analysis results for this cluster

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.