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Coexpression cluster:C2092: Difference between revisions

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|tf_chipseq_enrich=FOS#2353;3:6.7484664816708:0.00503245277631794:0.0234531162653221!FOSL1#8061;2:19.8567898581865:0.00367705000923323:0.0185547386536363!SETDB1#9869;2:20.1600130890052:0.0035690868540764:0.0180815843780202
|tf_chipseq_enrich=FOS#2353;3:6.7484664816708:0.00503245277631794:0.0234531162653221!FOSL1#8061;2:19.8567898581865:0.00367705000923323:0.0185547386536363!SETDB1#9869;2:20.1600130890052:0.0035690868540764:0.0180815843780202
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}}
}}

Revision as of 15:17, 26 November 2012


Full id: C2092_splenic_Endothelial_Lymphatic_adenocarcinoma_Renal_small_lymphangiectasia



Phase1 CAGE Peaks

Hg19::chr11:108743594..108743616,+p@chr11:108743594..108743616
+
Hg19::chr19:42007093..42007107,-p@chr19:42007093..42007107
-
Hg19::chr19:42007124..42007140,-p@chr19:42007124..42007140
-
Hg19::chr3:11535651..11535655,-p@chr3:11535651..11535655
-


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
blood vessel endothelium2.06e-2418
endothelium2.06e-2418
cardiovascular system endothelium2.06e-2418
simple squamous epithelium2.77e-2222
squamous epithelium4.32e-1925
lymphoid system6.93e-1510
vessel5.89e-1268
lymphatic vessel2.23e-118
lymph vasculature2.23e-118
lymphatic part of lymphoid system2.23e-118
anatomical cluster3.69e-10373
endothelial tube1.28e-099
arterial system endothelium1.28e-099
endothelium of artery1.28e-099
intraembryonic coelom2.83e-0912
anatomical conduit3.96e-09240
vein4.10e-099
venous blood vessel4.10e-099
venous system4.10e-099
microcirculatory vessel6.59e-093
endothelium of capillary6.59e-093
capillary6.59e-093
adult organism1.07e-08114
vasculature1.38e-0878
vascular system1.38e-0878
splanchnic layer of lateral plate mesoderm3.92e-0883
spleen1.07e-073
gastrointestinal system mesentery1.07e-073
stomach region1.07e-073
mesentery1.07e-073
gastrointestinal system serosa1.07e-073
mesentery of stomach1.07e-073
gut mesentery1.07e-073
dorsal mesentery1.07e-073
dorsal mesogastrium1.07e-073
peritoneal cavity1.07e-073
spleen primordium1.07e-073


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
FOS#235336.74846648167080.005032452776317940.0234531162653221
FOSL1#8061219.85678985818650.003677050009233230.0185547386536363
SETDB1#9869220.16001308900520.00356908685407640.0180815843780202



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.