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Coexpression cluster:C4010: Difference between revisions

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|full_id=C4010_ductal_giant_squamous_Tracheal_bronchogenic_Keratinocyte_amniotic
|full_id=C4010_ductal_giant_squamous_Tracheal_bronchogenic_Keratinocyte_amniotic
|id=C4010
|id=C4010
|ontology_enrichment_celltype=CL:0000066!2.54e-44!254;CL:0002076!5.96e-34!43;CL:0000223!3.66e-26!59;CL:0002368!8.62e-16!13;CL:0002251!2.82e-13!21;CL:0002202!9.43e-11!9;CL:0002632!9.43e-11!9;CL:0002159!9.96e-11!13;CL:0000076!5.53e-10!62;CL:0000220!3.04e-09!246;CL:0000063!4.06e-09!578;CL:0002321!4.97e-09!248;CL:0000082!9.46e-09!19;CL:0002077!2.32e-07!33;CL:0000622!3.21e-07!5;CL:0000244!6.77e-07!4;CL:0000731!6.77e-07!4
|ontology_enrichment_celltype=CL:0000066!2.82e-44!253;CL:0002076!5.20e-28!42;CL:0000223!2.94e-21!58;CL:0002368!1.04e-19!13;CL:0002202!2.51e-13!9;CL:0002632!2.51e-13!9;CL:0002159!5.45e-12!14;CL:0000082!1.62e-11!19;CL:0000076!5.55e-11!63;CL:0002251!8.43e-11!20;CL:0002077!2.16e-08!34;CL:0000244!3.40e-08!4;CL:0000731!3.40e-08!4;CL:0000068!3.09e-07!3;CL:0000069!3.09e-07!3;CL:0000307!3.09e-07!3;CL:0000377!3.09e-07!3;CL:0000349!3.27e-07!19;CL:0002328!4.67e-07!3;CL:0002321!4.87e-07!250;CL:0002166!6.75e-07!3
|ontology_enrichment_disease=DOID:305!9.32e-19!106;DOID:0050687!3.43e-14!143;DOID:1749!4.71e-13!14;DOID:162!4.55e-08!235;DOID:14566!1.41e-07!239
|ontology_enrichment_disease=DOID:305!1.08e-17!106;DOID:1749!6.08e-17!14;DOID:0050687!4.16e-13!143
|ontology_enrichment_uberon=UBERON:0004119!7.08e-19!169;UBERON:0000925!7.08e-19!169;UBERON:0006595!7.08e-19!169;UBERON:0001004!2.11e-13!72;UBERON:0005911!1.40e-12!82;UBERON:0001007!1.85e-12!155;UBERON:0001555!1.85e-12!155;UBERON:0007026!1.85e-12!155;UBERON:0005153!3.77e-12!37;UBERON:0000077!1.91e-11!130;UBERON:0004807!1.14e-10!28;UBERON:0005631!3.62e-10!14;UBERON:0000158!3.62e-10!14;UBERON:0000065!3.74e-10!53;UBERON:0005157!5.06e-10!51;UBERON:0004921!2.78e-09!129;UBERON:0004185!2.78e-09!129;UBERON:0000464!5.73e-09!104;UBERON:0004802!9.46e-09!19;UBERON:0000115!9.46e-09!19;UBERON:0001041!9.88e-09!98;UBERON:0005178!1.33e-08!34;UBERON:0002224!1.33e-08!34;UBERON:0000365!2.73e-08!5;UBERON:0005181!3.21e-08!35;UBERON:0000072!4.30e-08!46;UBERON:0008947!7.00e-08!38;UBERON:0003258!7.00e-08!38;UBERON:0003729!9.20e-08!5;UBERON:0000466!9.30e-08!126;UBERON:0007196!9.82e-08!14;UBERON:0001558!9.82e-08!14;UBERON:0000161!1.17e-07!35;UBERON:0000062!1.23e-07!511;UBERON:0002048!4.00e-07!22;UBERON:0000117!4.00e-07!22;UBERON:0000171!4.00e-07!22;UBERON:0000170!4.00e-07!22;UBERON:0005597!4.00e-07!22;UBERON:0000118!4.00e-07!22;UBERON:0001048!6.19e-07!168;UBERON:0000344!7.10e-07!12;UBERON:0003124!8.85e-07!7;UBERON:0005910!8.92e-07!6
|ontology_enrichment_uberon=UBERON:0004119!2.39e-15!160;UBERON:0000925!2.39e-15!160;UBERON:0006595!2.39e-15!160;UBERON:0001004!3.77e-14!74;UBERON:0005153!7.98e-14!37;UBERON:0005631!6.23e-13!14;UBERON:0000158!6.23e-13!14;UBERON:0004807!6.53e-13!28;UBERON:0005911!1.31e-12!82;UBERON:0005157!1.94e-12!47;UBERON:0005178!8.86e-12!34;UBERON:0002224!8.86e-12!34;UBERON:0004802!1.62e-11!19;UBERON:0000115!1.62e-11!19;UBERON:0005181!2.62e-11!35;UBERON:0000065!7.19e-11!54;UBERON:0000464!9.97e-11!95;UBERON:0000365!5.64e-10!5;UBERON:0002048!1.56e-09!22;UBERON:0000117!1.56e-09!22;UBERON:0000171!1.56e-09!22;UBERON:0000170!1.56e-09!22;UBERON:0005597!1.56e-09!22;UBERON:0000118!1.56e-09!22;UBERON:0000466!4.36e-09!117;UBERON:0007196!4.72e-09!15;UBERON:0001558!4.72e-09!15;UBERON:0001007!7.39e-09!145;UBERON:0001555!7.39e-09!145;UBERON:0007026!7.39e-09!145;UBERON:0008947!1.01e-08!38;UBERON:0003258!1.01e-08!38;UBERON:0003124!2.44e-08!7;UBERON:0000072!3.02e-08!47;UBERON:0005910!3.26e-08!6;UBERON:0003729!3.46e-08!13;UBERON:0000344!9.41e-08!20;UBERON:0003343!1.47e-07!4;UBERON:0004785!1.47e-07!4;UBERON:0004923!1.82e-07!66;UBERON:0000161!4.60e-07!36;UBERON:0004815!4.67e-07!3;UBERON:0002031!4.67e-07!3
|tf_chipseq_enrich=CEBPB#1051;3:7.97114762582482:0.00197418705528856:0.0115327285975658!MAX#4149;3:6.45255550900712:0.00372191383426551:0.0186791426687581
|tf_chipseq_enrich=CEBPB#1051;3:7.97114762582482:0.00197418705528856:0.0115327285975658!MAX#4149;3:6.45255550900712:0.00372191383426551:0.0186791426687581
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}}
}}

Revision as of 15:36, 19 October 2012


Full id: C4010_ductal_giant_squamous_Tracheal_bronchogenic_Keratinocyte_amniotic



Phase1 CAGE Peaks

Hg19::chr1:94240867..94240875,-p4@uc001dqd.1
Hg19::chr1:94240931..94240955,-p1@uc001dqd.1
Hg19::chr1:94240961..94241024,-p1@ENST00000433544


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>

Uber Anatomy
Ontology termp-valuen
endoderm-derived structure2.39e-15160
endoderm2.39e-15160
presumptive endoderm2.39e-15160
respiratory system3.77e-1474
epithelial bud7.98e-1437
extraembryonic membrane6.23e-1314
membranous layer6.23e-1314
respiratory system epithelium6.53e-1328
endo-epithelium1.31e-1282
epithelial fold1.94e-1247
thoracic cavity element8.86e-1234
thoracic cavity8.86e-1234
respiratory tract epithelium1.62e-1119
lung epithelium1.62e-1119
thoracic segment organ2.62e-1135
respiratory tract7.19e-1154
anatomical space9.97e-1195
urothelium5.64e-105
lung1.56e-0922
respiratory tube1.56e-0922
respiration organ1.56e-0922
pair of lungs1.56e-0922
lung primordium1.56e-0922
lung bud1.56e-0922
immaterial anatomical entity4.36e-09117
tracheobronchial tree4.72e-0915
lower respiratory tract4.72e-0915
digestive system7.39e-09145
digestive tract7.39e-09145
primitive gut7.39e-09145
respiratory primordium1.01e-0838
endoderm of foregut1.01e-0838
chorion2.44e-087
segment of respiratory tract3.02e-0847
transitional epithelium3.26e-086
mouth mucosa3.46e-0813
mucosa9.41e-0820
mucosa of oral region1.47e-074
respiratory system mucosa1.47e-074
organ component layer1.82e-0766
orifice4.60e-0736
lower respiratory tract epithelium4.67e-073
epithelium of bronchus4.67e-073
Disease
Ontology termp-valuen
carcinoma1.08e-17106
squamous cell carcinoma6.08e-1714
cell type cancer4.16e-13143


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
CEBPB#105137.971147625824820.001974187055288560.0115327285975658
MAX#414936.452555509007120.003721913834265510.0186791426687581



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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