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Coexpression cluster:C2379: Difference between revisions

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|full_id=C2379_smallcell_maxillary_malignant_kidney_pancreatic_signet_bronchioalveolar
|full_id=C2379_smallcell_maxillary_malignant_kidney_pancreatic_signet_bronchioalveolar
|id=C2379
|id=C2379
|ontology_enrichment_celltype=CL:0000066!1.14e-39!254;CL:0002076!9.31e-25!43;CL:0000223!9.46e-22!59;CL:0002251!1.96e-12!21;CL:0002368!9.65e-10!13;CL:0002159!2.17e-07!13
|ontology_enrichment_disease=DOID:305!6.52e-28!106;DOID:0050687!5.78e-19!143;DOID:299!9.59e-11!25;DOID:1749!3.23e-10!14;DOID:162!1.05e-07!235;DOID:14566!4.47e-07!239
|ontology_enrichment_uberon=UBERON:0004119!1.58e-32!169;UBERON:0000925!1.58e-32!169;UBERON:0006595!1.58e-32!169;UBERON:0001007!1.46e-25!155;UBERON:0001555!1.46e-25!155;UBERON:0007026!1.46e-25!155;UBERON:0004921!1.88e-22!129;UBERON:0004185!1.88e-22!129;UBERON:0000077!1.72e-21!130;UBERON:0001004!1.18e-19!72;UBERON:0001041!7.66e-16!98;UBERON:0000466!1.22e-15!126;UBERON:0000464!6.45e-15!104;UBERON:0000065!9.81e-15!53;UBERON:0005911!1.19e-13!82;UBERON:0000062!6.49e-12!511;UBERON:0008947!9.33e-12!38;UBERON:0003258!9.33e-12!38;UBERON:0001008!1.98e-11!45;UBERON:0005177!2.61e-11!107;UBERON:0006554!5.05e-11!44;UBERON:0000072!5.93e-11!46;UBERON:0003104!6.20e-10!238;UBERON:0009142!6.20e-10!238;UBERON:0009569!1.76e-09!113;UBERON:0005153!2.89e-09!37;UBERON:0000161!4.01e-09!35;UBERON:0000064!6.29e-09!219;UBERON:0004175!1.19e-08!25;UBERON:0001048!1.55e-08!168;UBERON:0005178!1.86e-08!34;UBERON:0002224!1.86e-08!34;UBERON:0005156!2.31e-08!59;UBERON:0000990!2.31e-08!59;UBERON:0000344!2.57e-08!12;UBERON:0000058!2.59e-08!26;UBERON:0000481!4.95e-08!347;UBERON:0000166!4.97e-08!21;UBERON:0005181!5.27e-08!35;UBERON:0003133!5.57e-08!48;UBERON:0002553!6.56e-08!70;UBERON:0000922!8.51e-08!612;UBERON:0000063!1.94e-07!97;UBERON:0002113!2.65e-07!27;UBERON:0003918!2.65e-07!27;UBERON:0005095!2.65e-07!27;UBERON:0007687!2.65e-07!27;UBERON:0000468!2.89e-07!659;UBERON:0002048!4.87e-07!22;UBERON:0000117!4.87e-07!22;UBERON:0000171!4.87e-07!22;UBERON:0000170!4.87e-07!22;UBERON:0005597!4.87e-07!22;UBERON:0000118!4.87e-07!22;UBERON:0003100!5.28e-07!41;UBERON:0000489!6.45e-07!32;UBERON:0000467!9.80e-07!625
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Revision as of 14:23, 21 May 2012


Full id: C2379_smallcell_maxillary_malignant_kidney_pancreatic_signet_bronchioalveolar



Phase1 CAGE Peaks

Hg19::chr16:57653596..57653610,+p10@GPR56
Hg19::chr16:57653625..57653669,+p3@GPR56
Hg19::chr16:57653946..57653968,+p4@GPR56
Hg19::chr16:57653997..57654022,+p7@GPR56


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
epithelial cell1.14e-39254
endo-epithelial cell9.31e-2543
endodermal cell9.46e-2259
epithelial cell of alimentary canal1.96e-1221
respiratory epithelial cell9.65e-1013
general ecto-epithelial cell2.17e-0713
Uber Anatomy
Ontology termp-valuen
endoderm-derived structure1.58e-32169
endoderm1.58e-32169
presumptive endoderm1.58e-32169
digestive system1.46e-25155
digestive tract1.46e-25155
primitive gut1.46e-25155
subdivision of digestive tract1.88e-22129
endodermal part of digestive tract1.88e-22129
mixed endoderm/mesoderm-derived structure1.72e-21130
respiratory system1.18e-1972
foregut7.66e-1698
immaterial anatomical entity1.22e-15126
anatomical space6.45e-15104
respiratory tract9.81e-1553
endo-epithelium1.19e-1382
organ6.49e-12511
respiratory primordium9.33e-1238
endoderm of foregut9.33e-1238
renal system1.98e-1145
trunk region element2.61e-11107
urinary system structure5.05e-1144
segment of respiratory tract5.93e-1146
mesenchyme6.20e-10238
entire embryonic mesenchyme6.20e-10238
subdivision of trunk1.76e-09113
epithelial bud2.89e-0937
orifice4.01e-0935
organ part6.29e-09219
internal genitalia1.19e-0825
primordium1.55e-08168
thoracic cavity element1.86e-0834
thoracic cavity1.86e-0834
reproductive structure2.31e-0859
reproductive system2.31e-0859
mucosa2.57e-0812
duct2.59e-0826
multi-tissue structure4.95e-08347
oral opening4.97e-0821
thoracic segment organ5.27e-0835
reproductive organ5.57e-0848
anatomical cavity6.56e-0870
embryo8.51e-08612
organ segment1.94e-0797
kidney2.65e-0727
kidney mesenchyme2.65e-0727
kidney rudiment2.65e-0727
kidney field2.65e-0727
multi-cellular organism2.89e-07659
lung4.87e-0722
respiratory tube4.87e-0722
respiration organ4.87e-0722
pair of lungs4.87e-0722
lung primordium4.87e-0722
lung bud4.87e-0722
female organism5.28e-0741
cavitated compound organ6.45e-0732
anatomical system9.80e-07625
Disease
Ontology termp-valuen
carcinoma6.52e-28106
cell type cancer5.78e-19143
adenocarcinoma9.59e-1125
squamous cell carcinoma3.23e-1014
cancer1.05e-07235
disease of cellular proliferation4.47e-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


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.