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Coexpression cluster:C878: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0003688!9.42e-29!6;UBERON:0002358!9.42e-29!6;UBERON:0003684!9.42e-29!6;UBERON:0001178!9.42e-29!6;UBERON:0002097!9.69e-22!41;UBERON:0002199!5.20e-19!46;UBERON:0002416!5.20e-19!46;UBERON:0004457!4.59e-14!12;UBERON:0000042!4.59e-14!12;UBERON:0000310!2.94e-12!10;UBERON:0001443!4.11e-11!11;UBERON:0003102!3.10e-08!99
|ontology_enrichment_uberon=UBERON:0003688!9.42e-29!6;UBERON:0002358!9.42e-29!6;UBERON:0003684!9.42e-29!6;UBERON:0001178!9.42e-29!6;UBERON:0002097!9.69e-22!41;UBERON:0002199!5.20e-19!46;UBERON:0002416!5.20e-19!46;UBERON:0004457!4.59e-14!12;UBERON:0000042!4.59e-14!12;UBERON:0000310!2.94e-12!10;UBERON:0001443!4.11e-11!11;UBERON:0003102!3.10e-08!99
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}}
}}

Revision as of 14:32, 26 November 2012


Full id: C878_Preadipocyte_Adipocyte_Mast_CD14_CD8_CD4_Fibroblast



Phase1 CAGE Peaks

Hg19::chr11:114167586..114167599,+p16@NNMT
Hg19::chr15:39486361..39486371,-p5@ENST00000560743
Hg19::chr15:39486372..39486387,-p4@ENST00000560743
Hg19::chr15:39486389..39486413,-p1@ENST00000560743
Hg19::chr15:39486417..39486445,-p2@ENST00000560743
Hg19::chr15:39486488..39486494,-p6@ENST00000560743
Hg19::chr15:39486515..39486531,-p3@ENST00000560743
Hg19::chr1:100503682..100503729,+p2@HIAT1
Hg19::chr1:185614334..185614338,-p@chr1:185614334..185614338
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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


GO IDGO nameFDR corrected p-value
GO:0008112nicotinamide N-methyltransferase activity0.00223713646532438
GO:0015904tetracycline transport0.0031954858870987
GO:0015307drug:hydrogen antiporter activity0.0031954858870987
GO:0015520tetracycline:hydrogen antiporter activity0.0031954858870987
GO:0008493tetracycline transporter activity0.0031954858870987
GO:0046677response to antibiotic0.0031954858870987
GO:0042895antibiotic transporter activity0.0031954858870987
GO:0015893drug transport0.0047527954656943
GO:0015238drug transporter activity0.00546686554372937
GO:0015299solute:hydrogen antiporter activity0.0060379569704045
GO:0015298solute:cation antiporter activity0.00876999965365704
GO:0008170N-methyltransferase activity0.00876999965365704
GO:0015300solute:solute antiporter activity0.00876999965365704
GO:0042493response to drug0.0100579274189454
GO:0008757S-adenosylmethionine-dependent methyltransferase activity0.0127068590613247
GO:0015297antiporter activity0.0127068590613247
GO:0008168methyltransferase activity0.0344104638445509
GO:0016741transferase activity, transferring one-carbon groups0.0344104638445509
GO:0015291secondary active transmembrane transporter activity0.0421638748723498



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
skin fibroblast7.25e-3123
fibroblast5.11e-2776
preadipocyte of the breast1.45e-153
omentum preadipocyte2.83e-153
adipocyte of omentum tissue2.97e-153
preadipocyte3.25e-1412
receptor cell3.95e-126
sensory epithelial cell3.95e-126
olfactory epithelial cell3.95e-126
fat cell3.03e-1115
adipocyte of breast5.28e-112
Uber Anatomy
Ontology termp-valuen
omentum9.42e-296
peritoneum9.42e-296
abdominal cavity9.42e-296
visceral peritoneum9.42e-296
skin of body9.69e-2241
integument5.20e-1946
integumental system5.20e-1946
cavity lining4.59e-1412
serous membrane4.59e-1412
breast2.94e-1210
chest4.11e-1111
surface structure3.10e-0899
Disease
Ontology termp-valuen
musculoskeletal system disease5.76e-155
myotonic disease5.76e-155
muscle tissue disease5.76e-155
myopathy5.76e-155
muscular disease5.76e-155
myotonic dystrophy5.76e-155


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.