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Coexpression cluster:C483: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C483_acute_diffuse_medulloblastoma_hepatocellular_small_mesothelioma_testicular
|full_id=C483_acute_diffuse_medulloblastoma_hepatocellular_small_mesothelioma_testicular
|gostat_on_coexpression_clusters=GO:0005938!cell cortex!0.0238210879547863!4691$GO:0008022!protein C-terminus binding!0.0238210879547863!4691$GO:0001525!angiogenesis!0.0238210879547863!4691$GO:0048514!blood vessel morphogenesis!0.0238210879547863!4691$GO:0048646!anatomical structure formation!0.0238210879547863!4691$GO:0001568!blood vessel development!0.0238210879547863!4691$GO:0005730!nucleolus!0.0238210879547863!4691$GO:0001944!vasculature development!0.0238210879547863!4691$GO:0009887!organ morphogenesis!0.0461752816044586!4691
|gostat_on_coexpression_clusters=GO:0005938!cell cortex!0.0238210879547863!4691$GO:0008022!protein C-terminus binding!0.0238210879547863!4691$GO:0001525!angiogenesis!0.0238210879547863!4691$GO:0048514!blood vessel morphogenesis!0.0238210879547863!4691$GO:0048646!anatomical structure formation!0.0238210879547863!4691$GO:0001568!blood vessel development!0.0238210879547863!4691$GO:0005730!nucleolus!0.0238210879547863!4691$GO:0001944!vasculature development!0.0238210879547863!4691$GO:0009887!organ morphogenesis!0.0461752816044586!4691

Revision as of 17:59, 12 September 2012


Full id: C483_acute_diffuse_medulloblastoma_hepatocellular_small_mesothelioma_testicular



Phase1 CAGE Peaks

Hg19::chr2:203160480..203160512,+p@chr2:203160480..203160512
+
Hg19::chr2:232323777..232323824,-p@chr2:232323777..232323824
-
Hg19::chr2:232324975..232325014,-p@chr2:232324975..232325014
-
Hg19::chr2:232325221..232325253,-p1@SNORD82
Hg19::chr2:232325265..232325286,-p2@SNORD82
Hg19::chr2:232325447..232325475,-p8@NCL
Hg19::chr2:232325476..232325496,-p13@NCL
Hg19::chr2:232325500..232325586,-p3@NCL
Hg19::chr2:232326295..232326310,-p10@NCL
Hg19::chr2:232326319..232326343,-p5@NCL
Hg19::chr2:232326429..232326440,-p11@NCL
Hg19::chr2:232326456..232326471,-p2@NCL
Hg19::chr2:232326479..232326493,-p6@NCL
Hg19::chr2:232326533..232326542,-p15@NCL
Hg19::chr2:232326600..232326609,-p12@NCL
Hg19::chr2:232326643..232326648,-p16@NCL
Hg19::chr2:232326697..232326708,-p9@NCL
Hg19::chr2:232326722..232326727,-p17@NCL
Hg19::chr2:232327965..232327986,-p21@NCL
Hg19::chr2:232327987..232328031,-p14@NCL


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


GO IDGO nameFDR corrected p-value
GO:0005938cell cortex0.0238210879547863
GO:0008022protein C-terminus binding0.0238210879547863
GO:0001525angiogenesis0.0238210879547863
GO:0048514blood vessel morphogenesis0.0238210879547863
GO:0048646anatomical structure formation0.0238210879547863
GO:0001568blood vessel development0.0238210879547863
GO:0005730nucleolus0.0238210879547863
GO:0001944vasculature development0.0238210879547863
GO:0009887organ morphogenesis0.0461752816044586



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><br><br>disease_data<br>


Disease
Ontology termp-valuen
disease of cellular proliferation2.34e-41239
cancer3.10e-41235
cell type cancer4.73e-22143
carcinoma1.74e-16106
organ system cancer5.49e-16137
hematologic cancer3.39e-1451
immune system cancer3.39e-1451
leukemia1.94e-1139
myeloid leukemia8.72e-0931


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
POLR2A#5430192.040080517730175.50039674165619e-060.000166702244719045
SIX5#14791254.271678838864750.005067094740067110.0235945564919465
ZBTB33#1000957.916181257495290.0003267521810830770.00333063351943543
ZNF263#10127114.522012900355875.00671367500679e-060.000154565820131255



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.