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Coexpression cluster:C2329: Difference between revisions

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|ontology_enrichment_disease=DOID:2394!6.61e-08!14
|ontology_enrichment_disease=DOID:2394!6.61e-08!14
|ontology_enrichment_uberon=UBERON:0000486!4.29e-15!82;UBERON:0002199!5.85e-14!45;UBERON:0002416!5.85e-14!45;UBERON:0002097!2.70e-13!40;UBERON:0000914!1.55e-12!83;UBERON:0002329!1.55e-12!83;UBERON:0003077!1.55e-12!83;UBERON:0003059!1.55e-12!83;UBERON:0007282!1.55e-12!83;UBERON:0009618!1.55e-12!83;UBERON:0007285!1.55e-12!83;UBERON:0004290!1.42e-11!70;UBERON:0001134!2.17e-09!61;UBERON:0002036!2.17e-09!61;UBERON:0003082!2.17e-09!61;UBERON:0002204!2.55e-09!167;UBERON:0001637!4.41e-09!42;UBERON:0003509!4.41e-09!42;UBERON:0004572!4.41e-09!42;UBERON:0003102!6.93e-09!95;UBERON:0002385!1.29e-08!63;UBERON:0001015!1.29e-08!63;UBERON:0000383!1.29e-08!63;UBERON:0004573!2.20e-08!33;UBERON:0004571!2.20e-08!33;UBERON:0004237!4.18e-08!10;UBERON:0004695!4.18e-08!10;UBERON:0002111!4.18e-08!10;UBERON:0004178!4.18e-08!10;UBERON:0005256!1.97e-07!143;UBERON:0004872!5.14e-07!84;UBERON:0001981!9.64e-07!60;UBERON:0007500!9.64e-07!60;UBERON:0004537!9.64e-07!60;UBERON:0006965!9.64e-07!60
|ontology_enrichment_uberon=UBERON:0000486!4.29e-15!82;UBERON:0002199!5.85e-14!45;UBERON:0002416!5.85e-14!45;UBERON:0002097!2.70e-13!40;UBERON:0000914!1.55e-12!83;UBERON:0002329!1.55e-12!83;UBERON:0003077!1.55e-12!83;UBERON:0003059!1.55e-12!83;UBERON:0007282!1.55e-12!83;UBERON:0009618!1.55e-12!83;UBERON:0007285!1.55e-12!83;UBERON:0004290!1.42e-11!70;UBERON:0001134!2.17e-09!61;UBERON:0002036!2.17e-09!61;UBERON:0003082!2.17e-09!61;UBERON:0002204!2.55e-09!167;UBERON:0001637!4.41e-09!42;UBERON:0003509!4.41e-09!42;UBERON:0004572!4.41e-09!42;UBERON:0003102!6.93e-09!95;UBERON:0002385!1.29e-08!63;UBERON:0001015!1.29e-08!63;UBERON:0000383!1.29e-08!63;UBERON:0004573!2.20e-08!33;UBERON:0004571!2.20e-08!33;UBERON:0004237!4.18e-08!10;UBERON:0004695!4.18e-08!10;UBERON:0002111!4.18e-08!10;UBERON:0004178!4.18e-08!10;UBERON:0005256!1.97e-07!143;UBERON:0004872!5.14e-07!84;UBERON:0001981!9.64e-07!60;UBERON:0007500!9.64e-07!60;UBERON:0004537!9.64e-07!60;UBERON:0006965!9.64e-07!60
|tf_chipseq_enrich=EP300#2033;3:5.0804562946674:0.0114429840539824:0.0418831503334221!FOS#2353;4:8.9979553088944:0.000152514771116863:0.00194677220492228!MAX#4149;4:6.45255550900712:0.000576761319564549:0.00484994971449291!SPI1#6688;4:8.20432350852273:0.00022066188152768:0.00249331453476895!STAT3#6774;4:10.5194649971542:8.16377768286615e-05:0.00122979486141765!USF1#7391;4:6.36149927720796:0.000610501139914083:0.00507442328304711
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}}
}}

Revision as of 12:51, 5 September 2012


Full id: C2329_cholangiocellular_gall_pagetoid_mesenchymal_bone_Macrophage_Aortic



Phase1 CAGE Peaks

Hg19::chr15:32976499..32976506,+p10@SCG5
Hg19::chr15:32976539..32976558,+p5@SCG5
Hg19::chr15:32976571..32976607,+p3@SCG5
Hg19::chr15:32976620..32976643,+p2@SCG5


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
multilaminar epithelium4.29e-1582
integument5.85e-1445
integumental system5.85e-1445
skin of body2.70e-1340
somite1.55e-1283
paraxial mesoderm1.55e-1283
presomitic mesoderm1.55e-1283
presumptive segmental plate1.55e-1283
trunk paraxial mesoderm1.55e-1283
presumptive paraxial mesoderm1.55e-1283
dermomyotome1.42e-1170
skeletal muscle tissue2.17e-0961
striated muscle tissue2.17e-0961
myotome2.17e-0961
musculoskeletal system2.55e-09167
artery4.41e-0942
arterial blood vessel4.41e-0942
arterial system4.41e-0942
surface structure6.93e-0995
muscle tissue1.29e-0863
musculature1.29e-0863
musculature of body1.29e-0863
systemic artery2.20e-0833
systemic arterial system2.20e-0833
blood vessel smooth muscle4.18e-0810
arterial system smooth muscle4.18e-0810
artery smooth muscle tissue4.18e-0810
aorta smooth muscle tissue4.18e-0810
trunk mesenchyme1.97e-07143
splanchnic layer of lateral plate mesoderm5.14e-0784
blood vessel9.64e-0760
epithelial tube open at both ends9.64e-0760
blood vasculature9.64e-0760
vascular cord9.64e-0760
Disease
Ontology termp-valuen
ovarian cancer6.61e-0814


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
EP300#203335.08045629466740.01144298405398240.0418831503334221
FOS#235348.99795530889440.0001525147711168630.00194677220492228
MAX#414946.452555509007120.0005767613195645490.00484994971449291
SPI1#668848.204323508522730.000220661881527680.00249331453476895
STAT3#6774410.51946499715428.16377768286615e-050.00122979486141765
USF1#739146.361499277207960.0006105011399140830.00507442328304711



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.