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Coexpression cluster:C3260: Difference between revisions

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|ontology_enrichment_disease=DOID:162!6.18e-30!235;DOID:14566!2.57e-29!239;DOID:305!1.45e-18!106;DOID:0050687!1.25e-17!143;DOID:0050686!2.35e-15!137;DOID:2531!3.83e-12!51;DOID:0060083!3.83e-12!51;DOID:1240!3.99e-09!39;DOID:8692!2.29e-07!31
|ontology_enrichment_disease=DOID:162!6.18e-30!235;DOID:14566!2.57e-29!239;DOID:305!1.45e-18!106;DOID:0050687!1.25e-17!143;DOID:0050686!2.35e-15!137;DOID:2531!3.83e-12!51;DOID:0060083!3.83e-12!51;DOID:1240!3.99e-09!39;DOID:8692!2.29e-07!31
|ontology_enrichment_uberon=UBERON:0003104!4.48e-15!238;UBERON:0009142!4.48e-15!238;UBERON:0005177!6.65e-11!107;UBERON:0004119!2.60e-10!169;UBERON:0000925!2.60e-10!169;UBERON:0006595!2.60e-10!169;UBERON:0000077!2.87e-10!130;UBERON:0001041!4.29e-10!98;UBERON:0000072!2.13e-09!46;UBERON:0004921!3.86e-09!129;UBERON:0004185!3.86e-09!129;UBERON:0001007!4.80e-09!155;UBERON:0001555!4.80e-09!155;UBERON:0007026!4.80e-09!155;UBERON:0002100!5.23e-09!216;UBERON:0009569!2.19e-08!113;UBERON:0008947!3.29e-08!38;UBERON:0003258!3.29e-08!38;UBERON:0001048!8.46e-08!168;UBERON:0000490!8.91e-08!138;UBERON:0000065!1.13e-07!53;UBERON:0004211!1.21e-07!16;UBERON:0001285!1.21e-07!16;UBERON:0007684!1.21e-07!16;UBERON:0003220!1.21e-07!16;UBERON:0004208!1.21e-07!16;UBERON:0006554!1.71e-07!44;UBERON:0001851!1.99e-07!16;UBERON:0005172!2.44e-07!55;UBERON:0005173!2.44e-07!55;UBERON:0001004!2.57e-07!72;UBERON:0000466!2.70e-07!126;UBERON:0001008!2.81e-07!45;UBERON:0003914!5.21e-07!118;UBERON:0002113!7.58e-07!27;UBERON:0003918!7.58e-07!27;UBERON:0005095!7.58e-07!27;UBERON:0007687!7.58e-07!27;UBERON:0006555!8.11e-07!17;UBERON:0005103!8.11e-07!17;UBERON:0000083!8.11e-07!17;UBERON:0009201!8.11e-07!17;UBERON:0004819!8.11e-07!17;UBERON:0006553!8.11e-07!17;UBERON:0003074!8.11e-07!17;UBERON:0003060!8.11e-07!17
|ontology_enrichment_uberon=UBERON:0003104!4.48e-15!238;UBERON:0009142!4.48e-15!238;UBERON:0005177!6.65e-11!107;UBERON:0004119!2.60e-10!169;UBERON:0000925!2.60e-10!169;UBERON:0006595!2.60e-10!169;UBERON:0000077!2.87e-10!130;UBERON:0001041!4.29e-10!98;UBERON:0000072!2.13e-09!46;UBERON:0004921!3.86e-09!129;UBERON:0004185!3.86e-09!129;UBERON:0001007!4.80e-09!155;UBERON:0001555!4.80e-09!155;UBERON:0007026!4.80e-09!155;UBERON:0002100!5.23e-09!216;UBERON:0009569!2.19e-08!113;UBERON:0008947!3.29e-08!38;UBERON:0003258!3.29e-08!38;UBERON:0001048!8.46e-08!168;UBERON:0000490!8.91e-08!138;UBERON:0000065!1.13e-07!53;UBERON:0004211!1.21e-07!16;UBERON:0001285!1.21e-07!16;UBERON:0007684!1.21e-07!16;UBERON:0003220!1.21e-07!16;UBERON:0004208!1.21e-07!16;UBERON:0006554!1.71e-07!44;UBERON:0001851!1.99e-07!16;UBERON:0005172!2.44e-07!55;UBERON:0005173!2.44e-07!55;UBERON:0001004!2.57e-07!72;UBERON:0000466!2.70e-07!126;UBERON:0001008!2.81e-07!45;UBERON:0003914!5.21e-07!118;UBERON:0002113!7.58e-07!27;UBERON:0003918!7.58e-07!27;UBERON:0005095!7.58e-07!27;UBERON:0007687!7.58e-07!27;UBERON:0006555!8.11e-07!17;UBERON:0005103!8.11e-07!17;UBERON:0000083!8.11e-07!17;UBERON:0009201!8.11e-07!17;UBERON:0004819!8.11e-07!17;UBERON:0006553!8.11e-07!17;UBERON:0003074!8.11e-07!17;UBERON:0003060!8.11e-07!17
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}}
}}

Revision as of 19:02, 8 August 2012


Full id: C3260_Alveolar_Renal_hepatoblastoma_Keratinocyte_Bronchial_Endothelial_granulocyte



Phase1 CAGE Peaks

Hg19::chr12:133287378..133287390,+p3@PGAM5
Hg19::chr12:133287392..133287412,+p2@PGAM5
Hg19::chr12:133287419..133287465,+p1@PGAM5


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 cell9.66e-37254
embryonic cell4.96e-21248
animal cell2.16e-16679
eukaryotic cell2.16e-16679
squamous epithelial cell1.52e-1062
endodermal cell3.70e-1059
epithelial cell of nephron1.21e-0716
native cell1.23e-07722
endo-epithelial cell2.65e-0743
kidney cell7.28e-0718
kidney epithelial cell7.28e-0718
meso-epithelial cell8.11e-0744
mesodermal cell9.50e-07119
Uber Anatomy
Ontology termp-valuen
mesenchyme4.48e-15238
entire embryonic mesenchyme4.48e-15238
trunk region element6.65e-11107
endoderm-derived structure2.60e-10169
endoderm2.60e-10169
presumptive endoderm2.60e-10169
mixed endoderm/mesoderm-derived structure2.87e-10130
foregut4.29e-1098
segment of respiratory tract2.13e-0946
subdivision of digestive tract3.86e-09129
endodermal part of digestive tract3.86e-09129
digestive system4.80e-09155
digestive tract4.80e-09155
primitive gut4.80e-09155
trunk5.23e-09216
subdivision of trunk2.19e-08113
respiratory primordium3.29e-0838
endoderm of foregut3.29e-0838
primordium8.46e-08168
unilaminar epithelium8.91e-08138
respiratory tract1.13e-0753
nephron epithelium1.21e-0716
nephron1.21e-0716
uriniferous tubule1.21e-0716
metanephric mesenchyme1.21e-0716
nephrogenic mesenchyme1.21e-0716
urinary system structure1.71e-0744
cortex1.99e-0716
abdomen element2.44e-0755
abdominal segment element2.44e-0755
respiratory system2.57e-0772
immaterial anatomical entity2.70e-07126
renal system2.81e-0745
epithelial tube5.21e-07118
kidney7.58e-0727
kidney mesenchyme7.58e-0727
kidney rudiment7.58e-0727
kidney field7.58e-0727
excretory tube8.11e-0717
mesonephric epithelium8.11e-0717
mesonephric tubule8.11e-0717
nephric duct8.11e-0717
kidney epithelium8.11e-0717
renal duct8.11e-0717
mesonephric duct8.11e-0717
pronephric duct8.11e-0717
Disease
Ontology termp-valuen
cancer6.18e-30235
disease of cellular proliferation2.57e-29239
carcinoma1.45e-18106
cell type cancer1.25e-17143
organ system cancer2.35e-15137
hematologic cancer3.83e-1251
immune system cancer3.83e-1251
leukemia3.99e-0939
myeloid leukemia2.29e-0731


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.

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