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Coexpression cluster:C1455: Difference between revisions

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|ontology_enrichment_disease=DOID:305!5.06e-22!106;DOID:0050687!7.41e-14!143;DOID:162!8.62e-12!235;DOID:14566!7.96e-11!239;DOID:1749!1.39e-07!14;DOID:299!2.01e-07!25
|ontology_enrichment_disease=DOID:305!5.06e-22!106;DOID:0050687!7.41e-14!143;DOID:162!8.62e-12!235;DOID:14566!7.96e-11!239;DOID:1749!1.39e-07!14;DOID:299!2.01e-07!25
|ontology_enrichment_uberon=UBERON:0004119!2.09e-20!169;UBERON:0000925!2.09e-20!169;UBERON:0006595!2.09e-20!169;UBERON:0004921!5.80e-16!129;UBERON:0004185!5.80e-16!129;UBERON:0001007!1.22e-15!155;UBERON:0001555!1.22e-15!155;UBERON:0007026!1.22e-15!155;UBERON:0000077!3.26e-14!130;UBERON:0001041!1.09e-12!98;UBERON:0005177!2.65e-11!107;UBERON:0000466!4.10e-11!126;UBERON:0001004!5.92e-11!72;UBERON:0000464!4.39e-10!104;UBERON:0000065!1.74e-09!53;UBERON:0005911!4.72e-09!82;UBERON:0001008!1.27e-08!45;UBERON:0006554!2.10e-08!44;UBERON:0001048!3.06e-08!168;UBERON:0008947!1.33e-07!38;UBERON:0003258!1.33e-07!38;UBERON:0005172!2.86e-07!55;UBERON:0005173!2.86e-07!55;UBERON:0000072!4.40e-07!46;UBERON:0002113!7.43e-07!27;UBERON:0003918!7.43e-07!27;UBERON:0005095!7.43e-07!27;UBERON:0007687!7.43e-07!27
|ontology_enrichment_uberon=UBERON:0004119!2.09e-20!169;UBERON:0000925!2.09e-20!169;UBERON:0006595!2.09e-20!169;UBERON:0004921!5.80e-16!129;UBERON:0004185!5.80e-16!129;UBERON:0001007!1.22e-15!155;UBERON:0001555!1.22e-15!155;UBERON:0007026!1.22e-15!155;UBERON:0000077!3.26e-14!130;UBERON:0001041!1.09e-12!98;UBERON:0005177!2.65e-11!107;UBERON:0000466!4.10e-11!126;UBERON:0001004!5.92e-11!72;UBERON:0000464!4.39e-10!104;UBERON:0000065!1.74e-09!53;UBERON:0005911!4.72e-09!82;UBERON:0001008!1.27e-08!45;UBERON:0006554!2.10e-08!44;UBERON:0001048!3.06e-08!168;UBERON:0008947!1.33e-07!38;UBERON:0003258!1.33e-07!38;UBERON:0005172!2.86e-07!55;UBERON:0005173!2.86e-07!55;UBERON:0000072!4.40e-07!46;UBERON:0002113!7.43e-07!27;UBERON:0003918!7.43e-07!27;UBERON:0005095!7.43e-07!27;UBERON:0007687!7.43e-07!27
|tf_chipseq_enrich=HEY1#23462;5:3.36675920258809:0.00442382704520303:0.0209523410627164!POLR2A#5430;6:2.14745317655807:0.0101957067681878:0.0380336971519365!STAT3#6774;3:5.25973249857712:0.0137766205807855:0.0484743776307749!TAF1#6872;5:2.78587190478774:0.0107863634029041:0.0397950052082767!USF1#7391;4:4.24099951813864:0.00700536775082942:0.0296076080502154!USF2#7392;4:8.66146492337973:0.000463535508143562:0.0042679348439571
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}}
}}

Revision as of 13:31, 5 September 2012


Full id: C1455_Tracheal_Corneal_Keratinocyte_Mammary_Urothelial_Bronchial_Esophageal



Phase1 CAGE Peaks

Hg19::chr19:45281118..45281181,+p1@CBLC
Hg19::chr19:45281215..45281224,+p2@CU688574
Hg19::chr19:45281245..45281260,+p1@CU688574
Hg19::chr1:26856236..26856292,+p2@RPS6KA1
Hg19::chr22:37915562..37915598,-p3@CARD10
Hg19::chr22:40390930..40390994,+p1@FAM83F


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:0007175negative regulation of epidermal growth factor receptor activity0.00847707066194942
GO:0042059negative regulation of epidermal growth factor receptor signaling pathway0.00847707066194942
GO:0032449CBM complex0.00847707066194942
GO:0007176regulation of epidermal growth factor receptor activity0.0158169451647997
GO:0007250activation of NF-kappaB-inducing kinase0.0158169451647997
GO:0042058regulation of epidermal growth factor receptor signaling pathway0.0158169451647997
GO:0065009regulation of a molecular function0.0158169451647997
GO:0030159receptor signaling complex scaffold activity0.0188285090913903
GO:0032947protein complex scaffold0.0188285090913903
GO:0007173epidermal growth factor receptor signaling pathway0.0277273132276541
GO:0006468protein amino acid phosphorylation0.0277273132276541
GO:0007165signal transduction0.0277273132276541
GO:0007154cell communication0.0323588363159623
GO:0016310phosphorylation0.032800513276824
GO:0019538protein metabolic process0.032800513276824
GO:0032147activation of protein kinase activity0.0370140841269794
GO:0006793phosphorus metabolic process0.0385749904955098
GO:0006796phosphate metabolic process0.0385749904955098
GO:0009968negative regulation of signal transduction0.0462629851426927



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 cell1.13e-41254
endodermal cell3.47e-1659
endo-epithelial cell7.96e-1643
respiratory epithelial cell1.43e-0713
epithelial cell of alimentary canal3.83e-0721
Uber Anatomy
Ontology termp-valuen
endoderm-derived structure2.09e-20169
endoderm2.09e-20169
presumptive endoderm2.09e-20169
subdivision of digestive tract5.80e-16129
endodermal part of digestive tract5.80e-16129
digestive system1.22e-15155
digestive tract1.22e-15155
primitive gut1.22e-15155
mixed endoderm/mesoderm-derived structure3.26e-14130
foregut1.09e-1298
trunk region element2.65e-11107
immaterial anatomical entity4.10e-11126
respiratory system5.92e-1172
anatomical space4.39e-10104
respiratory tract1.74e-0953
endo-epithelium4.72e-0982
renal system1.27e-0845
urinary system structure2.10e-0844
primordium3.06e-08168
respiratory primordium1.33e-0738
endoderm of foregut1.33e-0738
abdomen element2.86e-0755
abdominal segment element2.86e-0755
segment of respiratory tract4.40e-0746
kidney7.43e-0727
kidney mesenchyme7.43e-0727
kidney rudiment7.43e-0727
kidney field7.43e-0727
Disease
Ontology termp-valuen
carcinoma5.06e-22106
cell type cancer7.41e-14143
cancer8.62e-12235
disease of cellular proliferation7.96e-11239
squamous cell carcinoma1.39e-0714
adenocarcinoma2.01e-0725


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
HEY1#2346253.366759202588090.004423827045203030.0209523410627164
POLR2A#543062.147453176558070.01019570676818780.0380336971519365
STAT3#677435.259732498577120.01377662058078550.0484743776307749
TAF1#687252.785871904787740.01078636340290410.0397950052082767
USF1#739144.240999518138640.007005367750829420.0296076080502154
USF2#739248.661464923379730.0004635355081435620.0042679348439571



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.