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Coexpression cluster:C4371: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000475!7.81e-17!365;UBERON:0003102!7.60e-14!95;UBERON:0000914!1.29e-13!83;UBERON:0002329!1.29e-13!83;UBERON:0003077!1.29e-13!83;UBERON:0003059!1.29e-13!83;UBERON:0007282!1.29e-13!83;UBERON:0009618!1.29e-13!83;UBERON:0007285!1.29e-13!83;UBERON:0004290!3.31e-11!70;UBERON:0000468!6.19e-11!659;UBERON:0000481!2.18e-10!347;UBERON:0002199!3.26e-10!45;UBERON:0002416!3.26e-10!45;UBERON:0002385!2.34e-09!63;UBERON:0001015!2.34e-09!63;UBERON:0000383!2.34e-09!63;UBERON:0000486!5.52e-09!82;UBERON:0002097!8.96e-09!40;UBERON:0001134!9.97e-09!61;UBERON:0002036!9.97e-09!61;UBERON:0003082!9.97e-09!61;UBERON:0000033!7.20e-08!123;UBERON:0004121!7.71e-08!169;UBERON:0000924!1.00e-07!173;UBERON:0006601!1.00e-07!173;UBERON:0000153!1.11e-07!129;UBERON:0007811!1.11e-07!129;UBERON:0005256!7.66e-07!143
|ontology_enrichment_uberon=UBERON:0000475!7.81e-17!365;UBERON:0003102!7.60e-14!95;UBERON:0000914!1.29e-13!83;UBERON:0002329!1.29e-13!83;UBERON:0003077!1.29e-13!83;UBERON:0003059!1.29e-13!83;UBERON:0007282!1.29e-13!83;UBERON:0009618!1.29e-13!83;UBERON:0007285!1.29e-13!83;UBERON:0004290!3.31e-11!70;UBERON:0000468!6.19e-11!659;UBERON:0000481!2.18e-10!347;UBERON:0002199!3.26e-10!45;UBERON:0002416!3.26e-10!45;UBERON:0002385!2.34e-09!63;UBERON:0001015!2.34e-09!63;UBERON:0000383!2.34e-09!63;UBERON:0000486!5.52e-09!82;UBERON:0002097!8.96e-09!40;UBERON:0001134!9.97e-09!61;UBERON:0002036!9.97e-09!61;UBERON:0003082!9.97e-09!61;UBERON:0000033!7.20e-08!123;UBERON:0004121!7.71e-08!169;UBERON:0000924!1.00e-07!173;UBERON:0006601!1.00e-07!173;UBERON:0000153!1.11e-07!129;UBERON:0007811!1.11e-07!129;UBERON:0005256!7.66e-07!143
|tf_chipseq_enrich=TRIM28#10155;2:12.3936833635083:0.00836834412943847:0.0329344497318621
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}}
}}

Revision as of 13:51, 5 September 2012


Full id: C4371_Fibroblast_gastric_normal_Mesenchymal_Nucleus_Preadipocyte_mesenchymal



Phase1 CAGE Peaks

Hg19::chr4:138450850..138450867,-p@chr4:138450850..138450867
-
Hg19::chr4:138453559..138453572,-p2@PCDH18
Hg19::chr4:138453606..138453673,-p1@PCDH18


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><br>

Cell Type
Ontology termp-valuen
non-terminally differentiated cell4.86e-33180
fibroblast6.65e-2375
skin fibroblast2.15e-1223
muscle precursor cell2.35e-0857
myoblast2.35e-0857
multi-potent skeletal muscle stem cell2.35e-0857
electrically responsive cell4.51e-0860
electrically active cell4.51e-0860
muscle cell8.64e-0854
fat cell8.99e-0815
contractile cell1.16e-0759
Uber Anatomy
Ontology termp-valuen
organism subdivision7.81e-17365
surface structure7.60e-1495
somite1.29e-1383
paraxial mesoderm1.29e-1383
presomitic mesoderm1.29e-1383
presumptive segmental plate1.29e-1383
trunk paraxial mesoderm1.29e-1383
presumptive paraxial mesoderm1.29e-1383
dermomyotome3.31e-1170
multi-cellular organism6.19e-11659
multi-tissue structure2.18e-10347
integument3.26e-1045
integumental system3.26e-1045
muscle tissue2.34e-0963
musculature2.34e-0963
musculature of body2.34e-0963
multilaminar epithelium5.52e-0982
skin of body8.96e-0940
skeletal muscle tissue9.97e-0961
striated muscle tissue9.97e-0961
myotome9.97e-0961
head7.20e-08123
ectoderm-derived structure7.71e-08169
ectoderm1.00e-07173
presumptive ectoderm1.00e-07173
anterior region of body1.11e-07129
craniocervical region1.11e-07129
trunk mesenchyme7.66e-07143


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
TRIM28#10155212.39368336350830.008368344129438470.0329344497318621



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.

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