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Coexpression cluster:C1394: Difference between revisions

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|full_id=C1394_large_bronchioalveolar_prostate_nonsmall_papillary_small_Alveolar
|full_id=C1394_large_bronchioalveolar_prostate_nonsmall_papillary_small_Alveolar
|id=C1394
|id=C1394
|ontology_enrichment_celltype=CL:0002076!1.50e-13!43;CL:0002368!2.16e-11!13;CL:0000223!4.64e-10!59;CL:0000066!1.36e-08!254;CL:0000082!1.60e-08!19
|ontology_enrichment_celltype=CL:0002076!6.89e-11!42;CL:0000223!4.57e-08!58;CL:0002368!1.33e-07!13
|ontology_enrichment_disease=DOID:305!9.08e-17!106;DOID:0050687!3.07e-15!143;DOID:162!1.30e-11!235;DOID:14566!5.00e-11!239;DOID:1749!1.95e-09!14
|ontology_enrichment_disease=DOID:305!9.90e-12!106;DOID:0050687!1.21e-08!143;DOID:162!2.42e-07!235;DOID:14566!5.14e-07!239
|ontology_enrichment_uberon=UBERON:0008947!3.88e-23!38;UBERON:0003258!3.88e-23!38;UBERON:0000065!4.86e-22!53;UBERON:0001004!1.54e-17!72;UBERON:0002780!5.85e-15!41;UBERON:0001890!5.85e-15!41;UBERON:0006240!5.85e-15!41;UBERON:0003080!1.89e-14!42;UBERON:0001737!5.49e-14!9;UBERON:0000072!5.60e-14!46;UBERON:0002791!3.44e-13!33;UBERON:0001893!1.18e-12!34;UBERON:0001869!2.07e-12!32;UBERON:0002048!2.47e-12!22;UBERON:0000117!2.47e-12!22;UBERON:0000171!2.47e-12!22;UBERON:0000170!2.47e-12!22;UBERON:0005597!2.47e-12!22;UBERON:0000118!2.47e-12!22;UBERON:0004119!6.79e-12!169;UBERON:0000925!6.79e-12!169;UBERON:0006595!6.79e-12!169;UBERON:0005178!1.57e-11!34;UBERON:0002224!1.57e-11!34;UBERON:0002020!2.11e-11!34;UBERON:0003528!2.11e-11!34;UBERON:0005181!4.69e-11!35;UBERON:0001007!6.08e-11!155;UBERON:0001555!6.08e-11!155;UBERON:0007026!6.08e-11!155;UBERON:0001049!7.11e-10!57;UBERON:0005068!7.11e-10!57;UBERON:0006241!7.11e-10!57;UBERON:0007135!7.11e-10!57;UBERON:0001041!8.85e-10!98;UBERON:0000064!1.40e-09!219;UBERON:0004921!1.77e-09!129;UBERON:0004185!1.77e-09!129;UBERON:0002616!2.50e-09!59;UBERON:0000077!7.18e-09!130;UBERON:0000955!1.24e-08!69;UBERON:0006238!1.24e-08!69;UBERON:0004802!1.60e-08!19;UBERON:0000115!1.60e-08!19;UBERON:0003056!4.77e-08!61;UBERON:0005153!4.89e-08!37;UBERON:0009663!7.50e-08!7;UBERON:0001017!1.05e-07!82;UBERON:0000956!2.55e-07!25;UBERON:0000203!2.55e-07!25;UBERON:0005743!4.87e-07!86;UBERON:0000369!5.07e-07!4;UBERON:0002435!5.07e-07!4;UBERON:0000204!5.07e-07!4;UBERON:0010082!5.07e-07!4
|ontology_enrichment_uberon=UBERON:0000065!5.17e-16!54;UBERON:0008947!2.31e-15!38;UBERON:0003258!2.31e-15!38;UBERON:0001004!2.69e-14!74;UBERON:0004119!2.62e-12!160;UBERON:0000925!2.62e-12!160;UBERON:0006595!2.62e-12!160;UBERON:0000369!6.19e-11!4;UBERON:0002435!6.19e-11!4;UBERON:0000204!6.19e-11!4;UBERON:0010082!6.19e-11!4;UBERON:0001007!2.05e-10!145;UBERON:0001555!2.05e-10!145;UBERON:0007026!2.05e-10!145;UBERON:0002046!2.58e-10!5;UBERON:0004117!2.58e-10!5;UBERON:0007689!2.58e-10!5;UBERON:0007123!2.58e-10!5;UBERON:0003091!2.58e-10!5;UBERON:0001737!3.91e-10!9;UBERON:0002048!1.41e-09!22;UBERON:0000117!1.41e-09!22;UBERON:0000171!1.41e-09!22;UBERON:0000170!1.41e-09!22;UBERON:0005597!1.41e-09!22;UBERON:0000118!1.41e-09!22;UBERON:0005383!7.87e-09!3;UBERON:0005382!7.87e-09!3;UBERON:0005178!3.33e-08!34;UBERON:0002224!3.33e-08!34;UBERON:0005181!6.69e-08!35;UBERON:0005153!1.79e-07!37;UBERON:0004921!2.59e-07!118;UBERON:0000072!3.28e-07!47;UBERON:0005911!3.47e-07!82;UBERON:0011216!3.80e-07!223;UBERON:0001041!5.81e-07!87;UBERON:0000341!6.60e-07!2
|tf_chipseq_enrich=CTBP2#1488;6:62.7170003393281:1.6349770986689e-11:1.98783903618022e-09!CTCF#10664;6:5.36025637307503:4.21437267579784e-05:0.000755094986940557!SUZ12#23512;6:50.1157809110629:6.2866744827465e-11:6.97740697453307e-09
|tf_chipseq_enrich=CTBP2#1488;6:62.7170003393281:1.6349770986689e-11:1.98783903618022e-09!CTCF#10664;6:5.36025637307503:4.21437267579784e-05:0.000755094986940557!SUZ12#23512;6:50.1157809110629:6.2866744827465e-11:6.97740697453307e-09
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}}
}}

Revision as of 11:13, 19 October 2012


Full id: C1394_large_bronchioalveolar_prostate_nonsmall_papillary_small_Alveolar



Phase1 CAGE Peaks

Hg19::chr14:36989336..36989354,-p5@NKX2-1
Hg19::chr14:36989358..36989378,-p3@NKX2-1
Hg19::chr14:36989379..36989390,-p8@NKX2-1
Hg19::chr14:36989407..36989410,-p15@NKX2-1
Hg19::chr14:36989412..36989423,-p12@NKX2-1
Hg19::chr14:36989427..36989442,-p1@NKX2-1


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
endo-epithelial cell6.89e-1142
endodermal cell4.57e-0858
respiratory epithelial cell1.33e-0713
Uber Anatomy
Ontology termp-valuen
respiratory tract5.17e-1654
respiratory primordium2.31e-1538
endoderm of foregut2.31e-1538
respiratory system2.69e-1474
endoderm-derived structure2.62e-12160
endoderm2.62e-12160
presumptive endoderm2.62e-12160
corpus striatum6.19e-114
striatum6.19e-114
ventral part of telencephalon6.19e-114
future corpus striatum6.19e-114
digestive system2.05e-10145
digestive tract2.05e-10145
primitive gut2.05e-10145
thyroid gland2.58e-105
pharyngeal pouch2.58e-105
thyroid diverticulum2.58e-105
pharyngeal pouch 22.58e-105
thyroid primordium2.58e-105
larynx3.91e-109
lung1.41e-0922
respiratory tube1.41e-0922
respiration organ1.41e-0922
pair of lungs1.41e-0922
lung primordium1.41e-0922
lung bud1.41e-0922
caudate-putamen7.87e-093
dorsal striatum7.87e-093
thoracic cavity element3.33e-0834
thoracic cavity3.33e-0834
thoracic segment organ6.69e-0835
epithelial bud1.79e-0737
subdivision of digestive tract2.59e-07118
segment of respiratory tract3.28e-0747
endo-epithelium3.47e-0782
organ system subdivision3.80e-07223
foregut5.81e-0787
throat6.60e-072
Disease
Ontology termp-valuen
carcinoma9.90e-12106
cell type cancer1.21e-08143
cancer2.42e-07235
disease of cellular proliferation5.14e-07239


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
CTBP2#1488662.71700033932811.6349770986689e-111.98783903618022e-09
CTCF#1066465.360256373075034.21437267579784e-050.000755094986940557
SUZ12#23512650.11578091106296.2866744827465e-116.97740697453307e-09



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.