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Difference between revisions of "Coexpression cluster:C4264"

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|ontology_enrichment_disease=DOID:305!6.74e-15!106;DOID:1749!6.46e-12!14;DOID:0050687!3.07e-09!143
 
|ontology_enrichment_disease=DOID:305!6.74e-15!106;DOID:1749!6.46e-12!14;DOID:0050687!3.07e-09!143
 
|ontology_enrichment_uberon=UBERON:0004119!2.94e-23!169;UBERON:0000925!2.94e-23!169;UBERON:0006595!2.94e-23!169;UBERON:0005911!1.05e-19!82;UBERON:0001007!4.58e-19!155;UBERON:0001555!4.58e-19!155;UBERON:0007026!4.58e-19!155;UBERON:0005177!1.40e-17!107;UBERON:0004921!1.54e-17!129;UBERON:0004185!1.54e-17!129;UBERON:0000466!9.51e-15!126;UBERON:0000077!4.65e-14!130;UBERON:0001008!1.48e-12!45;UBERON:0009569!2.61e-12!113;UBERON:0001041!3.48e-12!98;UBERON:0006554!5.54e-12!44;UBERON:0005172!1.91e-11!55;UBERON:0005173!1.91e-11!55;UBERON:0001004!5.11e-11!72;UBERON:0000481!1.08e-10!347;UBERON:0000062!1.51e-10!511;UBERON:0003929!2.91e-10!54;UBERON:0007499!3.15e-10!25;UBERON:0000475!7.83e-10!365;UBERON:0009856!1.34e-09!26;UBERON:0009497!1.53e-09!25;UBERON:0000015!1.53e-09!25;UBERON:0002423!1.53e-09!25;UBERON:0006235!1.53e-09!25;UBERON:0004161!1.53e-09!25;UBERON:0002417!2.65e-09!61;UBERON:0000916!2.65e-09!61;UBERON:0000464!4.17e-09!104;UBERON:0007023!6.99e-09!115;UBERON:0000489!7.21e-09!32;UBERON:0000058!8.69e-09!26;UBERON:0000344!1.15e-08!12;UBERON:0000065!1.29e-08!53;UBERON:0003104!2.20e-08!238;UBERON:0009142!2.20e-08!238;UBERON:0005178!2.91e-08!34;UBERON:0002224!2.91e-08!34;UBERON:0000161!5.67e-08!35;UBERON:0008835!6.82e-08!22;UBERON:0003894!6.82e-08!22;UBERON:0005181!7.65e-08!35;UBERON:0000064!1.07e-07!219;UBERON:0004111!1.25e-07!241;UBERON:0002048!1.83e-07!22;UBERON:0000117!1.83e-07!22;UBERON:0000171!1.83e-07!22;UBERON:0000170!1.83e-07!22;UBERON:0005597!1.83e-07!22;UBERON:0000118!1.83e-07!22;UBERON:0002365!2.08e-07!31;UBERON:0002330!2.08e-07!31;UBERON:0009854!2.40e-07!23;UBERON:0002113!3.35e-07!27;UBERON:0003918!3.35e-07!27;UBERON:0005095!3.35e-07!27;UBERON:0007687!3.35e-07!27;UBERON:0005153!3.97e-07!37;UBERON:0003064!4.20e-07!37;UBERON:0000365!9.53e-07!5;UBERON:0004807!9.66e-07!28;UBERON:0003729!9.86e-07!5
 
|ontology_enrichment_uberon=UBERON:0004119!2.94e-23!169;UBERON:0000925!2.94e-23!169;UBERON:0006595!2.94e-23!169;UBERON:0005911!1.05e-19!82;UBERON:0001007!4.58e-19!155;UBERON:0001555!4.58e-19!155;UBERON:0007026!4.58e-19!155;UBERON:0005177!1.40e-17!107;UBERON:0004921!1.54e-17!129;UBERON:0004185!1.54e-17!129;UBERON:0000466!9.51e-15!126;UBERON:0000077!4.65e-14!130;UBERON:0001008!1.48e-12!45;UBERON:0009569!2.61e-12!113;UBERON:0001041!3.48e-12!98;UBERON:0006554!5.54e-12!44;UBERON:0005172!1.91e-11!55;UBERON:0005173!1.91e-11!55;UBERON:0001004!5.11e-11!72;UBERON:0000481!1.08e-10!347;UBERON:0000062!1.51e-10!511;UBERON:0003929!2.91e-10!54;UBERON:0007499!3.15e-10!25;UBERON:0000475!7.83e-10!365;UBERON:0009856!1.34e-09!26;UBERON:0009497!1.53e-09!25;UBERON:0000015!1.53e-09!25;UBERON:0002423!1.53e-09!25;UBERON:0006235!1.53e-09!25;UBERON:0004161!1.53e-09!25;UBERON:0002417!2.65e-09!61;UBERON:0000916!2.65e-09!61;UBERON:0000464!4.17e-09!104;UBERON:0007023!6.99e-09!115;UBERON:0000489!7.21e-09!32;UBERON:0000058!8.69e-09!26;UBERON:0000344!1.15e-08!12;UBERON:0000065!1.29e-08!53;UBERON:0003104!2.20e-08!238;UBERON:0009142!2.20e-08!238;UBERON:0005178!2.91e-08!34;UBERON:0002224!2.91e-08!34;UBERON:0000161!5.67e-08!35;UBERON:0008835!6.82e-08!22;UBERON:0003894!6.82e-08!22;UBERON:0005181!7.65e-08!35;UBERON:0000064!1.07e-07!219;UBERON:0004111!1.25e-07!241;UBERON:0002048!1.83e-07!22;UBERON:0000117!1.83e-07!22;UBERON:0000171!1.83e-07!22;UBERON:0000170!1.83e-07!22;UBERON:0005597!1.83e-07!22;UBERON:0000118!1.83e-07!22;UBERON:0002365!2.08e-07!31;UBERON:0002330!2.08e-07!31;UBERON:0009854!2.40e-07!23;UBERON:0002113!3.35e-07!27;UBERON:0003918!3.35e-07!27;UBERON:0005095!3.35e-07!27;UBERON:0007687!3.35e-07!27;UBERON:0005153!3.97e-07!37;UBERON:0003064!4.20e-07!37;UBERON:0000365!9.53e-07!5;UBERON:0004807!9.66e-07!28;UBERON:0003729!9.86e-07!5
 +
|tf_chipseq_enrich=FOXA1#3169;3:11.0814197493855:0.00073475527569867:0.00582621716184749!FOXA2#3170;3:24.6304637526652:6.68983856509345e-05:0.00107439650914931!MAFF#23764;2:37.5435709932968:0.000934477401556032:0.00677043949643499!MAFK#7975;2:18.0671554252199:0.00398367474493681:0.0191147205130228
 
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
 
}}
 
}}

Revision as of 03:34, 5 September 2012


Full id: C4264_Small_oral_malignant_Prostate_epidermoid_argyrophil_Urothelial



Phase1 CAGE Peaks

Hg19::chr3:111451248..111451251,+p6@PLCXD2
Hg19::chr3:111451297..111451320,+p3@PLCXD2
Hg19::chr3:111451321..111451372,+p3@PHLDB2


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:0004629phospholipase C activity0.0377386675552978
GO:0004620phospholipase activity0.0377386675552978
GO:0008081phosphoric diester hydrolase activity0.0377386675552978
GO:0016298lipase activity0.0377386675552978
GO:0016042lipid catabolic process0.0377386675552978
GO:0004091carboxylesterase activity0.0402560676798472



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>


Uber Anatomy
Ontology termp-valuen
endoderm-derived structure2.94e-23169
endoderm2.94e-23169
presumptive endoderm2.94e-23169
endo-epithelium1.05e-1982
digestive system4.58e-19155
digestive tract4.58e-19155
primitive gut4.58e-19155
trunk region element1.40e-17107
subdivision of digestive tract1.54e-17129
endodermal part of digestive tract1.54e-17129
immaterial anatomical entity9.51e-15126
mixed endoderm/mesoderm-derived structure4.65e-14130
renal system1.48e-1245
subdivision of trunk2.61e-12113
foregut3.48e-1298
urinary system structure5.54e-1244
abdomen element1.91e-1155
abdominal segment element1.91e-1155
respiratory system5.11e-1172
multi-tissue structure1.08e-10347
organ1.51e-10511
gut epithelium2.91e-1054
epithelial sac3.15e-1025
organism subdivision7.83e-10365
sac1.34e-0926
epithelium of foregut-midgut junction1.53e-0925
anatomical boundary1.53e-0925
hepatobiliary system1.53e-0925
foregut-midgut junction1.53e-0925
septum transversum1.53e-0925
abdominal segment of trunk2.65e-0961
abdomen2.65e-0961
anatomical space4.17e-09104
adult organism6.99e-09115
cavitated compound organ7.21e-0932
duct8.69e-0926
mucosa1.15e-0812
respiratory tract1.29e-0853
mesenchyme2.20e-08238
entire embryonic mesenchyme2.20e-08238
thoracic cavity element2.91e-0834
thoracic cavity2.91e-0834
orifice5.67e-0835
hepatic diverticulum6.82e-0822
liver primordium6.82e-0822
thoracic segment organ7.65e-0835
organ part1.07e-07219
anatomical conduit1.25e-07241
lung1.83e-0722
respiratory tube1.83e-0722
respiration organ1.83e-0722
pair of lungs1.83e-0722
lung primordium1.83e-0722
lung bud1.83e-0722
exocrine gland2.08e-0731
exocrine system2.08e-0731
digestive tract diverticulum2.40e-0723
kidney3.35e-0727
kidney mesenchyme3.35e-0727
kidney rudiment3.35e-0727
kidney field3.35e-0727
epithelial bud3.97e-0737
intermediate mesoderm4.20e-0737
urothelium9.53e-075
respiratory system epithelium9.66e-0728
mouth mucosa9.86e-075
Disease
Ontology termp-valuen
carcinoma6.74e-15106
squamous cell carcinoma6.46e-1214
cell type cancer3.07e-09143


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
FOXA1#3169311.08141974938550.000734755275698670.00582621716184749
FOXA2#3170324.63046375266526.68983856509345e-050.00107439650914931
MAFF#23764237.54357099329680.0009344774015560320.00677043949643499
MAFK#7975218.06715542521990.003983674744936810.0191147205130228



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.