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Coexpression cluster:C3692: Difference between revisions

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|tf_chipseq_enrich=GATA3#2625;2:18.1576775714707:0.00394454681927962:0.0189478670434525!JUND#3727;3:6.99466394187103:0.00292184504273499:0.0156634110675598!NR3C1#2908;3:14.973023331173:0.000297833119467548:0.00308769040739242!PRDM1#639;2:87.8873038516405:0.000171624884802908:0.00209127655395297!RAD21#5885;3:10.3550338954563:0.000900491207356542:0.0066365394965147!TFAP2A#7020;3:16.518634373045:0.000221803388076634:0.00248098147663442!TFAP2C#7022;3:10.8092286098602:0.000791674657575313:0.00615466053018521
|tf_chipseq_enrich=GATA3#2625;2:18.1576775714707:0.00394454681927962:0.0189478670434525!JUND#3727;3:6.99466394187103:0.00292184504273499:0.0156634110675598!NR3C1#2908;3:14.973023331173:0.000297833119467548:0.00308769040739242!PRDM1#639;2:87.8873038516405:0.000171624884802908:0.00209127655395297!RAD21#5885;3:10.3550338954563:0.000900491207356542:0.0066365394965147!TFAP2A#7020;3:16.518634373045:0.000221803388076634:0.00248098147663442!TFAP2C#7022;3:10.8092286098602:0.000791674657575313:0.00615466053018521
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}}
}}

Revision as of 16:17, 26 November 2012


Full id: C3692_chorionic_Hep2_lens_embryonic_Placental_choriocarcinoma_mesothelioma



Phase1 CAGE Peaks

Hg19::chr17:76677091..76677105,-p12@CYTH1
Hg19::chr17:76677122..76677151,-p8@CYTH1
Hg19::chr19:17422953..17423002,+p@chr19:17422953..17423002
+


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>


Cell Type
Ontology termp-valuen
epithelial cell2.45e-14253
extraembryonic cell7.36e-1219
mesothelial cell9.11e-0719
Uber Anatomy
Ontology termp-valuen
larynx1.78e-159
extraembryonic membrane2.99e-1214
membranous layer2.99e-1214
chorion1.59e-117
extraembryonic structure3.86e-1024
body cavity precursor4.78e-0854
respiratory primordium1.28e-0738
endoderm of foregut1.28e-0738
placenta3.31e-074
allantois3.31e-074
upper respiratory tract4.44e-0719
Disease
Ontology termp-valuen
carcinoma7.64e-09106


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
GATA3#2625218.15767757147070.003944546819279620.0189478670434525
JUND#372736.994663941871030.002921845042734990.0156634110675598
NR3C1#2908314.9730233311730.0002978331194675480.00308769040739242
PRDM1#639287.88730385164050.0001716248848029080.00209127655395297
RAD21#5885310.35503389545630.0009004912073565420.0066365394965147
TFAP2A#7020316.5186343730450.0002218033880766340.00248098147663442
TFAP2C#7022310.80922860986020.0007916746575753130.00615466053018521



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.