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Coexpression cluster:C594: Difference between revisions

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|gostat_on_coexpression_clusters=GO:0045111!intermediate filament cytoskeleton!0.00086501357605482!286887;3853$GO:0005882!intermediate filament!0.00086501357605482!286887;3853$GO:0044430!cytoskeletal part!0.00875313881962261!286887;3853$GO:0005856!cytoskeleton!0.0156475434545066!286887;3853$GO:0005200!structural constituent of cytoskeleton!0.0359851262584485!3853$GO:0043232!intracellular non-membrane-bound organelle!0.037983235872607!286887;3853$GO:0043228!non-membrane-bound organelle!0.037983235872607!286887;3853$GO:0007398!ectoderm development!0.0385963645451909!3853$GO:0008284!positive regulation of cell proliferation!0.0483587763804884!3853$GO:0044446!intracellular organelle part!0.0483587763804884!286887;3853$GO:0044422!organelle part!0.0483587763804884!286887;3853
|gostat_on_coexpression_clusters=GO:0045111!intermediate filament cytoskeleton!0.00086501357605482!286887;3853$GO:0005882!intermediate filament!0.00086501357605482!286887;3853$GO:0044430!cytoskeletal part!0.00875313881962261!286887;3853$GO:0005856!cytoskeleton!0.0156475434545066!286887;3853$GO:0005200!structural constituent of cytoskeleton!0.0359851262584485!3853$GO:0043232!intracellular non-membrane-bound organelle!0.037983235872607!286887;3853$GO:0043228!non-membrane-bound organelle!0.037983235872607!286887;3853$GO:0007398!ectoderm development!0.0385963645451909!3853$GO:0008284!positive regulation of cell proliferation!0.0483587763804884!3853$GO:0044446!intracellular organelle part!0.0483587763804884!286887;3853$GO:0044422!organelle part!0.0483587763804884!286887;3853
|id=C594
|id=C594
|ontology_enrichment_celltype=CL:0002076!2.57e-19!43;CL:0000066!1.23e-12!254;CL:0000223!1.86e-12!59;CL:0002251!2.96e-10!21;CL:0002368!2.39e-09!13;CL:0002159!1.09e-07!13
|ontology_enrichment_disease=DOID:1749!2.54e-08!14
|ontology_enrichment_uberon=UBERON:0004119!9.54e-17!169;UBERON:0000925!9.54e-17!169;UBERON:0006595!9.54e-17!169;UBERON:0001004!3.34e-14!72;UBERON:0000065!8.53e-11!53;UBERON:0001007!1.21e-10!155;UBERON:0001555!1.21e-10!155;UBERON:0007026!1.21e-10!155;UBERON:0000077!1.63e-10!130;UBERON:0000161!1.83e-10!35;UBERON:0005631!5.11e-10!14;UBERON:0000158!5.11e-10!14;UBERON:0004923!1.81e-09!57;UBERON:0003102!9.47e-09!95;UBERON:0005911!2.28e-08!82;UBERON:0004921!2.78e-08!129;UBERON:0004185!2.78e-08!129;UBERON:0000064!3.84e-08!219;UBERON:0005181!4.24e-08!35;UBERON:0003124!5.38e-08!7;UBERON:0006562!5.87e-08!11;UBERON:0005178!1.10e-07!34;UBERON:0002224!1.10e-07!34;UBERON:0000974!1.12e-07!10;UBERON:0000922!1.64e-07!612;UBERON:0005157!1.87e-07!51;UBERON:0002050!2.14e-07!605;UBERON:0005423!2.14e-07!605;UBERON:0001042!2.31e-07!10;UBERON:0009145!2.31e-07!10;UBERON:0000062!3.02e-07!511;UBERON:0000166!3.09e-07!21;UBERON:0000072!3.38e-07!46;UBERON:0007196!3.65e-07!14;UBERON:0001558!3.65e-07!14;UBERON:0005153!4.45e-07!37;UBERON:0004807!4.67e-07!28;UBERON:0000923!4.72e-07!604;UBERON:0005291!4.72e-07!604;UBERON:0006598!4.72e-07!604;UBERON:0002532!4.72e-07!604
}}
}}

Revision as of 14:55, 21 May 2012


Full id: C594_Keratinocyte_Placental_amniotic_Esophageal_tongue_Corneal_Prostate



Phase1 CAGE Peaks

Hg19::chr12:52867616..52867640,-p2@KRT6C
Hg19::chr12:52881014..52881084,-p@chr12:52881014..52881084
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Hg19::chr12:52881094..52881129,-p@chr12:52881094..52881129
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Hg19::chr12:52881151..52881162,-p@chr12:52881151..52881162
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Hg19::chr12:52881340..52881386,-p@chr12:52881340..52881386
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Hg19::chr12:52881401..52881421,-p@chr12:52881401..52881421
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Hg19::chr12:52881422..52881438,-p@chr12:52881422..52881438
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Hg19::chr12:52881440..52881469,-p@chr12:52881440..52881469
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Hg19::chr12:52881475..52881528,-p@chr12:52881475..52881528
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Hg19::chr12:52884399..52884420,-p7@KRT6A
Hg19::chr12:52885340..52885349,-p10@KRT6A
Hg19::chr12:52885355..52885376,-p2@KRT6A
Hg19::chr12:52886485..52886506,-p6@KRT6A
Hg19::chr12:52886515..52886548,-p4@KRT6A
Hg19::chr12:52887034..52887049,-p1@KRT6A


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


GO IDGO nameFDR corrected p-value
GO:0045111intermediate filament cytoskeleton0.00086501357605482
GO:0005882intermediate filament0.00086501357605482
GO:0044430cytoskeletal part0.00875313881962261
GO:0005856cytoskeleton0.0156475434545066
GO:0005200structural constituent of cytoskeleton0.0359851262584485
GO:0043232intracellular non-membrane-bound organelle0.037983235872607
GO:0043228non-membrane-bound organelle0.037983235872607
GO:0007398ectoderm development0.0385963645451909
GO:0008284positive regulation of cell proliferation0.0483587763804884
GO:0044446intracellular organelle part0.0483587763804884
GO:0044422organelle part0.0483587763804884



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 cell2.57e-1943
epithelial cell1.23e-12254
endodermal cell1.86e-1259
epithelial cell of alimentary canal2.96e-1021
respiratory epithelial cell2.39e-0913
general ecto-epithelial cell1.09e-0713
Uber Anatomy
Ontology termp-valuen
endoderm-derived structure9.54e-17169
endoderm9.54e-17169
presumptive endoderm9.54e-17169
respiratory system3.34e-1472
respiratory tract8.53e-1153
digestive system1.21e-10155
digestive tract1.21e-10155
primitive gut1.21e-10155
mixed endoderm/mesoderm-derived structure1.63e-10130
orifice1.83e-1035
extraembryonic membrane5.11e-1014
membranous layer5.11e-1014
organ component layer1.81e-0957
surface structure9.47e-0995
endo-epithelium2.28e-0882
subdivision of digestive tract2.78e-08129
endodermal part of digestive tract2.78e-08129
organ part3.84e-08219
thoracic segment organ4.24e-0835
chorion5.38e-087
pharynx5.87e-0811
thoracic cavity element1.10e-0734
thoracic cavity1.10e-0734
neck1.12e-0710
embryo1.64e-07612
epithelial fold1.87e-0751
embryonic structure2.14e-07605
developing anatomical structure2.14e-07605
chordate pharynx2.31e-0710
pharyngeal region of foregut2.31e-0710
organ3.02e-07511
oral opening3.09e-0721
segment of respiratory tract3.38e-0746
tracheobronchial tree3.65e-0714
lower respiratory tract3.65e-0714
epithelial bud4.45e-0737
respiratory system epithelium4.67e-0728
germ layer4.72e-07604
embryonic tissue4.72e-07604
presumptive structure4.72e-07604
epiblast (generic)4.72e-07604
Disease
Ontology termp-valuen
squamous cell carcinoma2.54e-0814


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


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.