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{{Coexpression_clusters
{{Coexpression_clusters
|full_id=C565_CD34_CD133_acute_thymus_Hodgkin_Burkitt_testis
|full_id=C565_CD34_CD133_acute_thymus_Hodgkin_Burkitt_testis
|gostat_on_coexpression_clusters=GO:0045870!positive regulation of retroviral genome replication!0.00479806899799835!7153$GO:0019035!viral integration complex!0.00479806899799835!7153$GO:0009330!DNA topoisomerase complex (ATP-hydrolyzing)!0.00479806899799835!7153$GO:0030263!apoptotic chromosome condensation!0.010278852721011!7153$GO:0045091!regulation of retroviral genome replication!0.010278852721011!7153$GO:0045070!positive regulation of viral genome replication!0.010278852721011!7153$GO:0045090!retroviral genome replication!0.010278852721011!7153$GO:0048524!positive regulation of viral reproduction!0.010278852721011!7153$GO:0005814!centriole!0.010278852721011!7153$GO:0008508!bile acid:sodium symporter activity!0.010278852721011!347051$GO:0006266!DNA ligation!0.010278852721011!7153$GO:0015125!bile acid transmembrane transporter activity!0.010278852721011!347051$GO:0003918!DNA topoisomerase (ATP-hydrolyzing) activity!0.010278852721011!7153$GO:0005080!protein kinase C binding!0.010278852721011!7153$GO:0042826!histone deacetylase binding!0.0115116372212286!7153$GO:0045069!regulation of viral genome replication!0.0116469659001242!7153$GO:0043130!ubiquitin binding!0.0116469659001242!7153$GO:0032182!small conjugating protein binding!0.0116469659001242!7153$GO:0050792!regulation of viral reproduction!0.0116469659001242!7153$GO:0006265!DNA topological change!0.0116469659001242!7153$GO:0003916!DNA topoisomerase activity!0.0116469659001242!7153$GO:0008144!drug binding!0.0126590733377437!7153$GO:0030261!chromosome condensation!0.0126590733377437!7153$GO:0030262!apoptotic nuclear changes!0.0126590733377437!7153$GO:0008028!monocarboxylic acid transmembrane transporter activity!0.0126590733377437!347051$GO:0044450!microtubule organizing center part!0.0127250924038854!7153$GO:0019079!viral genome replication!0.0154477049253973!7153$GO:0006997!nuclear organization and biogenesis!0.0188408388029977!7153$GO:0005343!organic acid:sodium symporter activity!0.0188408388029977!347051$GO:0019058!viral infectious cycle!0.0239557574527735!7153$GO:0022415!viral reproductive process!0.0264231617084463!7153$GO:0007059!chromosome segregation!0.0264940328844091!7153$GO:0008022!protein C-terminus binding!0.0322086059666091!7153$GO:0019901!protein kinase binding!0.0340525037523818!7153$GO:0008094!DNA-dependent ATPase activity!0.0340525037523818!7153$GO:0015370!solute:sodium symporter activity!0.0345342885688741!347051$GO:0008632!apoptotic program!0.0345342885688741!7153$GO:0031402!sodium ion binding!0.0346565724290078!347051$GO:0046943!carboxylic acid transmembrane transporter activity!0.0346565724290078!347051$GO:0005342!organic acid transmembrane transporter activity!0.0346565724290078!347051$GO:0019900!kinase binding!0.0346565724290078!7153$GO:0046982!protein heterodimerization activity!0.03587546151678!7153$GO:0015294!solute:cation symporter activity!0.0380345867309035!347051$GO:0003682!chromatin binding!0.0384698454457164!7153$GO:0048015!phosphoinositide-mediated signaling!0.0402144554204852!7153$GO:0005813!centrosome!0.0402144554204852!7153$GO:0005815!microtubule organizing center!0.0448269676400632!7153$GO:0042803!protein homodimerization activity!0.0471622913629572!7153$GO:0007218!neuropeptide signaling pathway!0.0491093518050705!221395$GO:0006814!sodium ion transport!0.0495522148119735!347051
|id=C565
|id=C565
}}
}}

Revision as of 17:40, 18 May 2012


Full id: C565_CD34_CD133_acute_thymus_Hodgkin_Burkitt_testis



Phase1 CAGE Peaks

Hg19::chr12:58329819..58329867,-p1@ENST00000547492
p1@ENST00000551421
p1@ENST00000553102
p1@uc001sqo.2
Hg19::chr15:50367664..50367673,-p@chr15:50367664..50367673
-
Hg19::chr15:51295063..51295067,-p@chr15:51295063..51295067
-
Hg19::chr17:38545799..38545823,-p4@TOP2A
Hg19::chr18:36894194..36894210,+p@chr18:36894194..36894210
+
Hg19::chr19:3479160..3479176,-p7@C19orf77
Hg19::chr21:16816472..16816488,-p@chr21:16816472..16816488
-
Hg19::chr22:43660399..43660404,+p@chr22:43660399..43660404
+
Hg19::chr2:16659873..16659891,-p@chr2:16659873..16659891
-
Hg19::chr2:207565092..207565103,-p@chr2:207565092..207565103
-
Hg19::chr3:87841949..87841976,+p@chr3:87841949..87841976
+
Hg19::chr4:75196177..75196198,-p1@ENST00000513776
p1@uc003hhv.1
Hg19::chr5:146864161..146864177,+p@chr5:146864161..146864177
+
Hg19::chr6:130834916..130834919,-p@chr6:130834916..130834919
-
Hg19::chr6:46847996..46847997,-p12@GPR116
Hg19::chr8:82607407..82607417,-p2@SLC10A5


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:0045870positive regulation of retroviral genome replication0.00479806899799835
GO:0019035viral integration complex0.00479806899799835
GO:0009330DNA topoisomerase complex (ATP-hydrolyzing)0.00479806899799835
GO:0030263apoptotic chromosome condensation0.010278852721011
GO:0045091regulation of retroviral genome replication0.010278852721011
GO:0045070positive regulation of viral genome replication0.010278852721011
GO:0045090retroviral genome replication0.010278852721011
GO:0048524positive regulation of viral reproduction0.010278852721011
GO:0005814centriole0.010278852721011
GO:0008508bile acid:sodium symporter activity0.010278852721011
GO:0006266DNA ligation0.010278852721011
GO:0015125bile acid transmembrane transporter activity0.010278852721011
GO:0003918DNA topoisomerase (ATP-hydrolyzing) activity0.010278852721011
GO:0005080protein kinase C binding0.010278852721011
GO:0042826histone deacetylase binding0.0115116372212286
GO:0045069regulation of viral genome replication0.0116469659001242
GO:0043130ubiquitin binding0.0116469659001242
GO:0032182small conjugating protein binding0.0116469659001242
GO:0050792regulation of viral reproduction0.0116469659001242
GO:0006265DNA topological change0.0116469659001242
GO:0003916DNA topoisomerase activity0.0116469659001242
GO:0008144drug binding0.0126590733377437
GO:0030261chromosome condensation0.0126590733377437
GO:0030262apoptotic nuclear changes0.0126590733377437
GO:0008028monocarboxylic acid transmembrane transporter activity0.0126590733377437
GO:0044450microtubule organizing center part0.0127250924038854
GO:0019079viral genome replication0.0154477049253973
GO:0006997nuclear organization and biogenesis0.0188408388029977
GO:0005343organic acid:sodium symporter activity0.0188408388029977
GO:0019058viral infectious cycle0.0239557574527735
GO:0022415viral reproductive process0.0264231617084463
GO:0007059chromosome segregation0.0264940328844091
GO:0008022protein C-terminus binding0.0322086059666091
GO:0019901protein kinase binding0.0340525037523818
GO:0008094DNA-dependent ATPase activity0.0340525037523818
GO:0015370solute:sodium symporter activity0.0345342885688741
GO:0008632apoptotic program0.0345342885688741
GO:0031402sodium ion binding0.0346565724290078
GO:0046943carboxylic acid transmembrane transporter activity0.0346565724290078
GO:0005342organic acid transmembrane transporter activity0.0346565724290078
GO:0019900kinase binding0.0346565724290078
GO:0046982protein heterodimerization activity0.03587546151678
GO:0015294solute:cation symporter activity0.0380345867309035
GO:0003682chromatin binding0.0384698454457164
GO:0048015phosphoinositide-mediated signaling0.0402144554204852
GO:0005813centrosome0.0402144554204852
GO:0005815microtubule organizing center0.0448269676400632
GO:0042803protein homodimerization activity0.0471622913629572
GO:0007218neuropeptide signaling pathway0.0491093518050705
GO:0006814sodium ion transport0.0495522148119735



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

Uber Anatomy
Ontology termp-valuen

Disease
Ontology termp-valuen


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

No analysis results for this cluster

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.

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