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Coexpression cluster:C3076: Difference between revisions

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|full_id=C3076_Astrocyte_Preadipocyte_mesenchymal_Fibroblast_Neural_Adipocyte_Neurons
|full_id=C3076_Astrocyte_Preadipocyte_mesenchymal_Fibroblast_Neural_Adipocyte_Neurons
|id=C3076
|id=C3076
|ontology_enrichment_celltype=CL:0002494!2.71e-14!16;CL:0002548!3.40e-11!6;CL:0000057!1.61e-10!75;CL:0000055!2.46e-09!180;CL:0000569!4.02e-08!4;CL:0000011!4.02e-08!4;CL:1000306!5.16e-08!4;CL:0002547!5.16e-08!4;CL:0002605!5.25e-07!3;CL:0002334!6.18e-07!12;CL:0002580!9.19e-07!3
|ontology_enrichment_celltype=CL:0002494!6.31e-17!16;CL:0000057!4.59e-13!76;CL:0000569!1.56e-12!4;CL:0000011!1.56e-12!4;CL:1000306!1.65e-12!4;CL:0002547!1.65e-12!4;CL:0002605!1.44e-10!3;CL:0002580!3.20e-10!3;CL:0000047!7.02e-10!8;CL:0002579!1.20e-09!3;CL:0002334!1.09e-08!12;CL:0002548!1.16e-08!6;CL:0002617!1.67e-07!2
|ontology_enrichment_disease=DOID:2394!1.74e-10!14
|ontology_enrichment_disease=DOID:2394!4.78e-07!14
|ontology_enrichment_uberon=UBERON:0007100!7.66e-19!27;UBERON:0000948!1.10e-17!24;UBERON:0005498!1.10e-17!24;UBERON:0004140!1.10e-17!24;UBERON:0009881!1.10e-17!24;UBERON:0004141!1.10e-17!24;UBERON:0003084!1.10e-17!24;UBERON:0007005!1.10e-17!24;UBERON:0004139!1.10e-17!24;UBERON:0004291!1.10e-17!24;UBERON:0004872!1.64e-15!84;UBERON:0003103!2.52e-10!69;UBERON:0001009!1.49e-09!113;UBERON:0003914!2.16e-09!118;UBERON:0002118!5.12e-09!5;UBERON:0004532!5.12e-09!5;UBERON:0004535!1.09e-08!110;UBERON:0001637!1.40e-08!42;UBERON:0003509!1.40e-08!42;UBERON:0004572!1.40e-08!42;UBERON:0000415!5.16e-08!4;UBERON:0007240!5.16e-08!4;UBERON:0005742!5.16e-08!4;UBERON:0005734!5.16e-08!4;UBERON:0004664!5.16e-08!4;UBERON:0004663!5.16e-08!4;UBERON:0004573!6.16e-08!33;UBERON:0004571!6.16e-08!33;UBERON:0003688!9.72e-08!6;UBERON:0002358!9.72e-08!6;UBERON:0003684!9.72e-08!6;UBERON:0001178!9.72e-08!6;UBERON:0000992!1.60e-07!13;UBERON:0001981!5.41e-07!60;UBERON:0007500!5.41e-07!60;UBERON:0004537!5.41e-07!60;UBERON:0006965!5.41e-07!60
|ontology_enrichment_uberon=UBERON:0000948!1.80e-15!24;UBERON:0005498!1.80e-15!24;UBERON:0004140!1.80e-15!24;UBERON:0009881!1.80e-15!24;UBERON:0004141!1.80e-15!24;UBERON:0003084!1.80e-15!24;UBERON:0007005!1.80e-15!24;UBERON:0004139!1.80e-15!24;UBERON:0004291!1.80e-15!24;UBERON:0007100!1.94e-13!27;UBERON:0000415!1.65e-12!4;UBERON:0007240!1.65e-12!4;UBERON:0005742!1.65e-12!4;UBERON:0005734!1.65e-12!4;UBERON:0004664!1.65e-12!4;UBERON:0004663!1.65e-12!4;UBERON:0004872!1.92e-10!83;UBERON:0003688!3.11e-08!6;UBERON:0002358!3.11e-08!6;UBERON:0003684!3.11e-08!6;UBERON:0001178!3.11e-08!6;UBERON:0000310!8.55e-08!10;UBERON:0003103!3.08e-07!68;UBERON:0004797!3.89e-07!7;UBERON:0000078!4.19e-07!2;UBERON:0007497!4.19e-07!2;UBERON:0003643!4.19e-07!2;UBERON:0003504!4.19e-07!2;UBERON:0003469!4.19e-07!2;UBERON:0003496!4.19e-07!2;UBERON:0002012!4.19e-07!2;UBERON:0008886!4.19e-07!2;UBERON:0007303!4.19e-07!2;UBERON:0002061!4.19e-07!2;UBERON:0005432!4.19e-07!2;UBERON:0004363!4.19e-07!2;UBERON:0001443!4.81e-07!11
|tf_chipseq_enrich=FOS#2353;3:8.9979553088944:0.00137249927241713:0.00894771857128418
|tf_chipseq_enrich=FOS#2353;3:8.9979553088944:0.00137249927241713:0.00894771857128418
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}}
}}

Revision as of 14:46, 19 October 2012


Full id: C3076_Astrocyte_Preadipocyte_mesenchymal_Fibroblast_Neural_Adipocyte_Neurons



Phase1 CAGE Peaks

Hg19::chr11:103673814..103673817,-p@chr11:103673814..103673817
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Hg19::chr11:103673856..103673877,-p@chr11:103673856..103673877
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Hg19::chr11:103673881..103673894,-p@chr11:103673881..103673894
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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
heart1.80e-1524
primitive heart tube1.80e-1524
primary heart field1.80e-1524
anterior lateral plate mesoderm1.80e-1524
heart tube1.80e-1524
heart primordium1.80e-1524
cardiac mesoderm1.80e-1524
cardiogenic plate1.80e-1524
heart rudiment1.80e-1524
primary circulatory organ1.94e-1327
artery wall1.65e-124
tunica adventitia of artery1.65e-124
adventitia1.65e-124
tunica adventitia of blood vessel1.65e-124
aorta tunica adventitia1.65e-124
aorta wall1.65e-124
splanchnic layer of lateral plate mesoderm1.92e-1083
omentum3.11e-086
peritoneum3.11e-086
abdominal cavity3.11e-086
visceral peritoneum3.11e-086
breast8.55e-0810
compound organ3.08e-0768
blood vessel layer3.89e-077
mixed ectoderm/mesoderm/endoderm-derived structure4.19e-072
developing epithelial placode4.19e-072
respiratory system arterial blood vessel4.19e-072
respiratory system blood vessel4.19e-072
respiratory system artery4.19e-072
head blood vessel4.19e-072
pulmonary artery4.19e-072
pulmonary vascular system4.19e-072
pharyngeal vasculature4.19e-072
truncus arteriosus4.19e-072
aortic sac4.19e-072
pharyngeal arch artery4.19e-072
chest4.81e-0711
Disease
Ontology termp-valuen
ovarian cancer4.78e-0714


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
FOS#235338.99795530889440.001372499272417130.00894771857128418



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.