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Coexpression cluster:C4282: Difference between revisions

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|tf_chipseq_enrich=TFAP2C#7022;3:10.8092286098602:0.000791674657575313:0.00617304088117875!ZNF263#10127;3:8.22184163701068:0.00179904392556587:0.0109710585391904
|tf_chipseq_enrich=TFAP2C#7022;3:10.8092286098602:0.000791674657575313:0.00617304088117875!ZNF263#10127;3:8.22184163701068:0.00179904392556587:0.0109710585391904
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}}
}}

Revision as of 16:39, 26 November 2012


Full id: C4282_Mallassezderived_Small_Gingival_Urothelial_papillotubular_Sebocyte_transitionalcell



Phase1 CAGE Peaks

Hg19::chr3:129513355..129513392,-p6@TMCC1
Hg19::chr3:129513407..129513425,-p10@TMCC1
Hg19::chr3:129513434..129513460,-p8@TMCC1


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
endoderm-derived structure7.69e-11160
endoderm7.69e-11160
presumptive endoderm7.69e-11160
extraembryonic membrane8.53e-0914
membranous layer8.53e-0914
respiratory system1.26e-0874
chorion2.88e-087
urinary system structure9.57e-0847
epithelial bud9.83e-0837
respiratory tract9.99e-0854
endo-epithelium1.59e-0782
renal system1.93e-0748
anatomical system2.50e-07624
anatomical group2.98e-07625
urothelium3.17e-075
female organism5.50e-0741
reproductive structure9.71e-0759
reproductive system9.71e-0759
Disease
Ontology termp-valuen
squamous cell carcinoma1.14e-0914
carcinoma1.96e-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)

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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
TFAP2C#7022310.80922860986020.0007916746575753130.00617304088117875
ZNF263#1012738.221841637010680.001799043925565870.0109710585391904



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.