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Coexpression cluster:C4698: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0007023!8.28e-53!114;UBERON:0003076!5.88e-13!15;UBERON:0003057!5.88e-13!15;UBERON:0000477!9.22e-10!373;UBERON:0011216!9.46e-10!223;UBERON:0003978!1.04e-09!3;UBERON:0009751!1.04e-09!3;UBERON:0000946!1.04e-09!3;UBERON:0002523!1.04e-09!3;UBERON:0005983!1.04e-09!3;UBERON:0002165!1.04e-09!3;UBERON:0002062!1.04e-09!3;UBERON:0007280!1.04e-09!3;UBERON:0002240!1.34e-09!3;UBERON:0005174!1.34e-09!3;UBERON:0001137!1.34e-09!3;UBERON:0001049!4.33e-09!56;UBERON:0005068!4.33e-09!56;UBERON:0006241!4.33e-09!56;UBERON:0007135!4.33e-09!56;UBERON:0001896!5.29e-09!3;UBERON:0005290!5.29e-09!3;UBERON:0010096!5.29e-09!3;UBERON:0006947!5.43e-09!3;UBERON:0004054!5.43e-09!3;UBERON:0003075!7.90e-09!82;UBERON:0007284!7.90e-09!82;UBERON:0000160!1.00e-08!17;UBERON:0003103!1.37e-08!68;UBERON:0005409!1.41e-08!25;UBERON:0010314!2.55e-08!132;UBERON:0003135!2.73e-08!11;UBERON:0000062!3.38e-08!503;UBERON:0002346!3.42e-08!86;UBERON:0000481!4.90e-08!342;UBERON:0001017!2.00e-07!81;UBERON:0002298!2.20e-07!6;UBERON:0004733!3.87e-07!12;UBERON:0002028!3.87e-07!12;UBERON:0007277!3.87e-07!12;UBERON:0002133!4.48e-07!2;UBERON:0002081!6.87e-07!2;UBERON:0010227!6.87e-07!2;UBERON:0003127!7.91e-07!2;UBERON:0005904!8.00e-07!4;UBERON:0010371!9.52e-07!104
|ontology_enrichment_uberon=UBERON:0007023!8.28e-53!114;UBERON:0003076!5.88e-13!15;UBERON:0003057!5.88e-13!15;UBERON:0000477!9.22e-10!373;UBERON:0011216!9.46e-10!223;UBERON:0003978!1.04e-09!3;UBERON:0009751!1.04e-09!3;UBERON:0000946!1.04e-09!3;UBERON:0002523!1.04e-09!3;UBERON:0005983!1.04e-09!3;UBERON:0002165!1.04e-09!3;UBERON:0002062!1.04e-09!3;UBERON:0007280!1.04e-09!3;UBERON:0002240!1.34e-09!3;UBERON:0005174!1.34e-09!3;UBERON:0001137!1.34e-09!3;UBERON:0001049!4.33e-09!56;UBERON:0005068!4.33e-09!56;UBERON:0006241!4.33e-09!56;UBERON:0007135!4.33e-09!56;UBERON:0001896!5.29e-09!3;UBERON:0005290!5.29e-09!3;UBERON:0010096!5.29e-09!3;UBERON:0006947!5.43e-09!3;UBERON:0004054!5.43e-09!3;UBERON:0003075!7.90e-09!82;UBERON:0007284!7.90e-09!82;UBERON:0000160!1.00e-08!17;UBERON:0003103!1.37e-08!68;UBERON:0005409!1.41e-08!25;UBERON:0010314!2.55e-08!132;UBERON:0003135!2.73e-08!11;UBERON:0000062!3.38e-08!503;UBERON:0002346!3.42e-08!86;UBERON:0000481!4.90e-08!342;UBERON:0001017!2.00e-07!81;UBERON:0002298!2.20e-07!6;UBERON:0004733!3.87e-07!12;UBERON:0002028!3.87e-07!12;UBERON:0007277!3.87e-07!12;UBERON:0002133!4.48e-07!2;UBERON:0002081!6.87e-07!2;UBERON:0010227!6.87e-07!2;UBERON:0003127!7.91e-07!2;UBERON:0005904!8.00e-07!4;UBERON:0010371!9.52e-07!104
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}}
}}

Revision as of 16:54, 26 November 2012


Full id: C4698_spinal_heart_esophagus_trachea_duodenum_substantia_penis



Phase1 CAGE Peaks

Hg19::chr7:7575477..7575491,-p2@COL28A1
Hg19::chr7:7575494..7575509,-p1@COL28A1
Hg19::chrX:31526382..31526422,-p10@DMD


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:0043034costamere0.00824159647213382
GO:0043043peptide biosynthetic process0.00824159647213382
GO:0016010dystrophin-associated glycoprotein complex0.0230639023484972
GO:0006518peptide metabolic process0.0230639023484972
GO:0005605basal lamina0.0230639023484972
GO:0008307structural constituent of muscle0.0230639023484972
GO:0030016myofibril0.023422404691628
GO:0044449contractile fiber part0.023422404691628
GO:0043292contractile fiber0.023422404691628
GO:0005604basement membrane0.0243703490898033
GO:0005200structural constituent of cytoskeleton0.0254440286675898
GO:0044420extracellular matrix part0.0353517517207721
GO:0003012muscle system process0.0353517517207721
GO:0006936muscle contraction0.0353517517207721
GO:0004867serine-type endopeptidase inhibitor activity0.0353517517207721
GO:0007517muscle development0.0353517517207721
GO:0004866endopeptidase inhibitor activity0.0485298345557758
GO:0030414protease inhibitor activity0.0485298345557758



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><br>uberon_data<br><br>


Uber Anatomy
Ontology termp-valuen
adult organism8.28e-53114
posterior neural tube5.88e-1315
chordal neural plate5.88e-1315
anatomical cluster9.22e-10373
organ system subdivision9.46e-10223
valve1.04e-093
cardiac mesenchyme1.04e-093
cardial valve1.04e-093
tunica intima1.04e-093
heart layer1.04e-093
endocardium1.04e-093
endocardial cushion1.04e-093
presumptive endocardium1.04e-093
spinal cord1.34e-093
dorsal region element1.34e-093
dorsum1.34e-093
neural tube4.33e-0956
neural rod4.33e-0956
future spinal cord4.33e-0956
neural keel4.33e-0956
medulla oblongata5.29e-093
myelencephalon5.29e-093
future myelencephalon5.29e-093
male genital duct5.43e-093
internal male genitalia5.43e-093
neural plate7.90e-0982
presumptive neural plate7.90e-0982
intestine1.00e-0817
compound organ1.37e-0868
gastrointestinal system1.41e-0825
structure with developmental contribution from neural crest2.55e-08132
male reproductive organ2.73e-0811
organ3.38e-08503
neurectoderm3.42e-0886
multi-tissue structure4.90e-08342
central nervous system2.00e-0781
brainstem2.20e-076
segmental subdivision of hindbrain3.87e-0712
hindbrain3.87e-0712
presumptive hindbrain3.87e-0712
atrioventricular valve4.48e-072
cardiac atrium6.87e-072
future cardiac atrium6.87e-072
open tracheal system trachea7.91e-072
duct of male reproductive system8.00e-074
ecto-epithelium9.52e-07104


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)

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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.