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Coexpression cluster:C2854: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000914!1.86e-17!83;UBERON:0002329!1.86e-17!83;UBERON:0003077!1.86e-17!83;UBERON:0003059!1.86e-17!83;UBERON:0007282!1.86e-17!83;UBERON:0009618!1.86e-17!83;UBERON:0007285!1.86e-17!83;UBERON:0004290!2.26e-15!70;UBERON:0000486!1.32e-14!82;UBERON:0001134!3.51e-14!61;UBERON:0002036!3.51e-14!61;UBERON:0003082!3.51e-14!61;UBERON:0002385!1.69e-13!63;UBERON:0001015!1.69e-13!63;UBERON:0000383!1.69e-13!63;UBERON:0001637!2.50e-10!42;UBERON:0003509!2.50e-10!42;UBERON:0004572!2.50e-10!42;UBERON:0004872!3.94e-10!84;UBERON:0004573!1.26e-09!33;UBERON:0004571!1.26e-09!33;UBERON:0000948!6.82e-09!24;UBERON:0005498!6.82e-09!24;UBERON:0004140!6.82e-09!24;UBERON:0009881!6.82e-09!24;UBERON:0004141!6.82e-09!24;UBERON:0003084!6.82e-09!24;UBERON:0007005!6.82e-09!24;UBERON:0004139!6.82e-09!24;UBERON:0004291!6.82e-09!24;UBERON:0007100!2.79e-08!27;UBERON:0005256!6.52e-08!143;UBERON:0002204!1.24e-07!167;UBERON:0003102!1.36e-07!95;UBERON:0002049!2.05e-07!79;UBERON:0007798!2.05e-07!79;UBERON:0001981!3.98e-07!60;UBERON:0007500!3.98e-07!60;UBERON:0004537!3.98e-07!60;UBERON:0006965!3.98e-07!60
|ontology_enrichment_uberon=UBERON:0000914!1.86e-17!83;UBERON:0002329!1.86e-17!83;UBERON:0003077!1.86e-17!83;UBERON:0003059!1.86e-17!83;UBERON:0007282!1.86e-17!83;UBERON:0009618!1.86e-17!83;UBERON:0007285!1.86e-17!83;UBERON:0004290!2.26e-15!70;UBERON:0000486!1.32e-14!82;UBERON:0001134!3.51e-14!61;UBERON:0002036!3.51e-14!61;UBERON:0003082!3.51e-14!61;UBERON:0002385!1.69e-13!63;UBERON:0001015!1.69e-13!63;UBERON:0000383!1.69e-13!63;UBERON:0001637!2.50e-10!42;UBERON:0003509!2.50e-10!42;UBERON:0004572!2.50e-10!42;UBERON:0004872!3.94e-10!84;UBERON:0004573!1.26e-09!33;UBERON:0004571!1.26e-09!33;UBERON:0000948!6.82e-09!24;UBERON:0005498!6.82e-09!24;UBERON:0004140!6.82e-09!24;UBERON:0009881!6.82e-09!24;UBERON:0004141!6.82e-09!24;UBERON:0003084!6.82e-09!24;UBERON:0007005!6.82e-09!24;UBERON:0004139!6.82e-09!24;UBERON:0004291!6.82e-09!24;UBERON:0007100!2.79e-08!27;UBERON:0005256!6.52e-08!143;UBERON:0002204!1.24e-07!167;UBERON:0003102!1.36e-07!95;UBERON:0002049!2.05e-07!79;UBERON:0007798!2.05e-07!79;UBERON:0001981!3.98e-07!60;UBERON:0007500!3.98e-07!60;UBERON:0004537!3.98e-07!60;UBERON:0006965!3.98e-07!60
|tf_chipseq_enrich=JUN#3725;4:12.5128291923363:4.07770316866756e-05:0.000744790558293934!STAT3#6774;4:10.5194649971542:8.16377768286615e-05:0.00123460292125812!TFAP2A#7020;4:16.518634373045:1.34240829060362e-05:0.00032734013416379!TFAP2C#7022;4:10.8092286098602:7.32289634782688e-05:0.00114834229980584
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}}
}}

Revision as of 13:10, 5 September 2012


Full id: C2854_mesothelioma_Smooth_liposarcoma_papillary_mesodermal_mesenchymal_Olfactory



Phase1 CAGE Peaks

Hg19::chr6:169562893..169562942,-p1@ENST00000439703
Hg19::chr6:169562947..169562969,-p6@ENST00000439703
Hg19::chr6:169562989..169563008,-p2@ENST00000439703
Hg19::chr6:169563013..169563043,-p4@ENST00000439703


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>


Uber Anatomy
Ontology termp-valuen
somite1.86e-1783
paraxial mesoderm1.86e-1783
presomitic mesoderm1.86e-1783
presumptive segmental plate1.86e-1783
trunk paraxial mesoderm1.86e-1783
presumptive paraxial mesoderm1.86e-1783
dermomyotome2.26e-1570
multilaminar epithelium1.32e-1482
skeletal muscle tissue3.51e-1461
striated muscle tissue3.51e-1461
myotome3.51e-1461
muscle tissue1.69e-1363
musculature1.69e-1363
musculature of body1.69e-1363
artery2.50e-1042
arterial blood vessel2.50e-1042
arterial system2.50e-1042
splanchnic layer of lateral plate mesoderm3.94e-1084
systemic artery1.26e-0933
systemic arterial system1.26e-0933
heart6.82e-0924
primitive heart tube6.82e-0924
primary heart field6.82e-0924
anterior lateral plate mesoderm6.82e-0924
heart tube6.82e-0924
heart primordium6.82e-0924
cardiac mesoderm6.82e-0924
cardiogenic plate6.82e-0924
heart rudiment6.82e-0924
primary circulatory organ2.79e-0827
trunk mesenchyme6.52e-08143
musculoskeletal system1.24e-07167
surface structure1.36e-0795
vasculature2.05e-0779
vascular system2.05e-0779
blood vessel3.98e-0760
epithelial tube open at both ends3.98e-0760
blood vasculature3.98e-0760
vascular cord3.98e-0760


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
JUN#3725412.51282919233634.07770316866756e-050.000744790558293934
STAT3#6774410.51946499715428.16377768286615e-050.00123460292125812
TFAP2A#7020416.5186343730451.34240829060362e-050.00032734013416379
TFAP2C#7022410.80922860986027.32289634782688e-050.00114834229980584



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.