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Coexpression cluster:C1048: Difference between revisions

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|ontology_enrichment_disease=DOID:305!3.67e-14!106;DOID:0050687!1.43e-09!143
|ontology_enrichment_disease=DOID:305!3.67e-14!106;DOID:0050687!1.43e-09!143
|ontology_enrichment_uberon=UBERON:0004119!1.84e-23!169;UBERON:0000925!1.84e-23!169;UBERON:0006595!1.84e-23!169;UBERON:0001007!2.17e-21!155;UBERON:0001555!2.17e-21!155;UBERON:0007026!2.17e-21!155;UBERON:0004921!5.80e-21!129;UBERON:0004185!5.80e-21!129;UBERON:0000077!2.47e-16!130;UBERON:0005911!1.13e-13!82;UBERON:0000466!3.19e-12!126;UBERON:0001041!3.63e-12!98;UBERON:0005177!1.88e-10!107;UBERON:0005153!9.44e-10!37;UBERON:0001004!1.14e-09!72;UBERON:0000464!3.25e-09!104;UBERON:0000062!7.41e-09!511;UBERON:0005409!4.40e-08!35;UBERON:0009569!6.58e-08!113;UBERON:0005178!8.25e-08!34;UBERON:0002224!8.25e-08!34;UBERON:0005181!2.03e-07!35;UBERON:0000161!2.85e-07!35;UBERON:0000065!2.96e-07!53;UBERON:0005157!3.81e-07!51;UBERON:0008947!7.47e-07!38;UBERON:0003258!7.47e-07!38;UBERON:0003104!9.16e-07!238;UBERON:0009142!9.16e-07!238
|ontology_enrichment_uberon=UBERON:0004119!1.84e-23!169;UBERON:0000925!1.84e-23!169;UBERON:0006595!1.84e-23!169;UBERON:0001007!2.17e-21!155;UBERON:0001555!2.17e-21!155;UBERON:0007026!2.17e-21!155;UBERON:0004921!5.80e-21!129;UBERON:0004185!5.80e-21!129;UBERON:0000077!2.47e-16!130;UBERON:0005911!1.13e-13!82;UBERON:0000466!3.19e-12!126;UBERON:0001041!3.63e-12!98;UBERON:0005177!1.88e-10!107;UBERON:0005153!9.44e-10!37;UBERON:0001004!1.14e-09!72;UBERON:0000464!3.25e-09!104;UBERON:0000062!7.41e-09!511;UBERON:0005409!4.40e-08!35;UBERON:0009569!6.58e-08!113;UBERON:0005178!8.25e-08!34;UBERON:0002224!8.25e-08!34;UBERON:0005181!2.03e-07!35;UBERON:0000161!2.85e-07!35;UBERON:0000065!2.96e-07!53;UBERON:0005157!3.81e-07!51;UBERON:0008947!7.47e-07!38;UBERON:0003258!7.47e-07!38;UBERON:0003104!9.16e-07!238;UBERON:0009142!9.16e-07!238
|tf_chipseq_enrich=FOXA1#3169;4:5.54070987469273:0.00344427292594616:0.0175223547232155!GATA3#2625;4:13.618258178603:0.000112839652281084:0.00154677260068042
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}}
}}

Revision as of 11:57, 5 September 2012


Full id: C1048_signet_small_colon_duodenum_temporal_trachea_gall



Phase1 CAGE Peaks

Hg19::chr17:34328588..34328597,-p2@CCL15
Hg19::chr2:201242699..201242710,+p23@SPATS2L
Hg19::chr2:201242715..201242739,+p12@SPATS2L
Hg19::chr2:27669034..27669075,-p3@IFT172
Hg19::chr4:165675319..165675335,+p1@LOC100505989
Hg19::chr4:165675340..165675345,+p5@LOC100505989
Hg19::chr4:165675379..165675390,+p4@LOC100505989
Hg19::chr4:165675511..165675518,+p6@LOC100505989


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:0008201heparin binding0.0273314247674389
GO:0008009chemokine activity0.0273314247674389
GO:0042379chemokine receptor binding0.0273314247674389
GO:0001664G-protein-coupled receptor binding0.0273314247674389
GO:0005539glycosaminoglycan binding0.0273314247674389
GO:0006874cellular calcium ion homeostasis0.0273314247674389
GO:0030247polysaccharide binding0.0273314247674389
GO:0055074calcium ion homeostasis0.0273314247674389
GO:0006875cellular metal ion homeostasis0.0273314247674389
GO:0055065metal ion homeostasis0.0273314247674389
GO:0001871pattern binding0.0273314247674389
GO:0042330taxis0.0273314247674389
GO:0006935chemotaxis0.0273314247674389
GO:0030005cellular di-, tri-valent inorganic cation homeostasis0.0278028021233909
GO:0007626locomotory behavior0.0278028021233909
GO:0055066di-, tri-valent inorganic cation homeostasis0.0278028021233909
GO:0030003cellular cation homeostasis0.0278028021233909
GO:0055080cation homeostasis0.0278028021233909
GO:0055082cellular chemical homeostasis0.0291988233652572
GO:0006873cellular ion homeostasis0.0291988233652572
GO:0050801ion homeostasis0.0313145728501302
GO:0007610behavior0.031792812417562
GO:0048878chemical homeostasis0.031792812417562
GO:0005125cytokine activity0.031792812417562
GO:0019725cellular homeostasis0.036885202050857
GO:0030246carbohydrate binding0.0436478611125488
GO:0042592homeostatic process0.0436478611125488
GO:0005615extracellular space0.046264968808301
GO:0042221response to chemical stimulus0.0497852317519475



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
endodermal cell1.08e-1559
epithelial cell9.36e-15254
endo-epithelial cell3.30e-1343
respiratory epithelial cell9.12e-0713
Uber Anatomy
Ontology termp-valuen
endoderm-derived structure1.84e-23169
endoderm1.84e-23169
presumptive endoderm1.84e-23169
digestive system2.17e-21155
digestive tract2.17e-21155
primitive gut2.17e-21155
subdivision of digestive tract5.80e-21129
endodermal part of digestive tract5.80e-21129
mixed endoderm/mesoderm-derived structure2.47e-16130
endo-epithelium1.13e-1382
immaterial anatomical entity3.19e-12126
foregut3.63e-1298
trunk region element1.88e-10107
epithelial bud9.44e-1037
respiratory system1.14e-0972
anatomical space3.25e-09104
organ7.41e-09511
gastrointestinal system4.40e-0835
subdivision of trunk6.58e-08113
thoracic cavity element8.25e-0834
thoracic cavity8.25e-0834
thoracic segment organ2.03e-0735
orifice2.85e-0735
respiratory tract2.96e-0753
epithelial fold3.81e-0751
respiratory primordium7.47e-0738
endoderm of foregut7.47e-0738
mesenchyme9.16e-07238
entire embryonic mesenchyme9.16e-07238
Disease
Ontology termp-valuen
carcinoma3.67e-14106
cell type cancer1.43e-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#316945.540709874692730.003444272925946160.0175223547232155
GATA3#2625413.6182581786030.0001128396522810840.00154677260068042



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.