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Coexpression cluster:C2854: Difference between revisions

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|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
|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 15:45, 26 November 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
skeletal muscle tissue2.48e-1162
striated muscle tissue2.48e-1162
myotome2.48e-1162
dense mesenchyme tissue3.73e-1173
somite5.00e-1171
presomitic mesoderm5.00e-1171
presumptive segmental plate5.00e-1171
dermomyotome5.00e-1171
trunk paraxial mesoderm5.00e-1171
multilaminar epithelium6.63e-1183
paraxial mesoderm1.16e-1072
presumptive paraxial mesoderm1.16e-1072
muscle tissue1.55e-1064
musculature1.55e-1064
musculature of body1.55e-1064
heart8.55e-1024
primitive heart tube8.55e-1024
primary heart field8.55e-1024
anterior lateral plate mesoderm8.55e-1024
heart tube8.55e-1024
heart primordium8.55e-1024
cardiac mesoderm8.55e-1024
cardiogenic plate8.55e-1024
heart rudiment8.55e-1024
splanchnic layer of lateral plate mesoderm7.31e-0983
primary circulatory organ8.59e-0927
surface structure9.35e-0999
epithelial vesicle1.01e-0878
artery1.22e-0842
arterial blood vessel1.22e-0842
arterial system1.22e-0842
systemic artery5.91e-0833
systemic arterial system5.91e-0833
connective tissue1.66e-07371
integument6.13e-0746
integumental system6.13e-0746


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)

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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.