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{{Coexpression_clusters
{{Coexpression_clusters
|full_id=C3964_chronic_Mesenchymal_hepatocellular_hereditary_acute_rhabdomyosarcoma_Skeletal
|full_id=C3964_chronic_Mesenchymal_hepatocellular_hereditary_acute_rhabdomyosarcoma_Skeletal
|gostat_on_coexpression_clusters=GO:0005083!small GTPase regulator activity!0.00884912319659774!1104;5902$GO:0005087!Ran guanyl-nucleotide exchange factor activity!0.00884912319659774!1104$GO:0030695!GTPase regulator activity!0.00884912319659774!1104;5902$GO:0007090!regulation of S phase of mitotic cell cycle!0.00884912319659774!1104$GO:0007052!mitotic spindle organization and biogenesis!0.00884912319659774!1104$GO:0008536!Ran GTPase binding!0.00884912319659774!5902$GO:0033261!regulation of progression through S phase!0.00904970673294687!1104$GO:0042393!histone binding!0.00904970673294687!1104$GO:0000084!S phase of mitotic cell cycle!0.00911647317396334!1104$GO:0007051!spindle organization and biogenesis!0.00916982948411652!1104$GO:0051320!S phase!0.00921343297182372!1104$GO:0000790!nuclear chromatin!0.00924972184269641!1104$GO:0005092!GDP-dissociation inhibitor activity!0.0102534655193447!5902$GO:0000794!condensed nuclear chromosome!0.0102534655193447!1104$GO:0007346!regulation of progression through mitotic cell cycle!0.0102534655193447!1104$GO:0000082!G1/S transition of mitotic cell cycle!0.0102534655193447!1104$GO:0000793!condensed chromosome!0.0147554015762654!1104$GO:0044454!nuclear chromosome part!0.0170067703933241!1104$GO:0007088!regulation of mitosis!0.0170067703933241!1104$GO:0017016!Ras GTPase binding!0.0185651040629841!5902$GO:0051329!interphase of mitotic cell cycle!0.018628663845914!1104$GO:0031267!small GTPase binding!0.018628663845914!5902$GO:0051325!interphase!0.0188654918799131!1104$GO:0051020!GTPase binding!0.0189105199641022!5902$GO:0000228!nuclear chromosome!0.0189105199641022!1104$GO:0000226!microtubule cytoskeleton organization and biogenesis!0.0189105199641022!1104$GO:0003682!chromatin binding!0.0210616528993315!1104$GO:0016043!cellular component organization and biogenesis!0.0272424842678321!1104;5902$GO:0005088!Ras guanyl-nucleotide exchange factor activity!0.0274005387140235!1104$GO:0007067!mitosis!0.0368278486951195!1104$GO:0000087!M phase of mitotic cell cycle!0.0368278486951195!1104$GO:0051301!cell division!0.0368278486951195!1104$GO:0019899!enzyme binding!0.0412168034622221!5902$GO:0000279!M phase!0.0412168034622221!1104$GO:0005085!guanyl-nucleotide exchange factor activity!0.0412168034622221!1104$GO:0007017!microtubule-based process!0.0412168034622221!1104$GO:0000785!chromatin!0.0412168034622221!1104$GO:0000278!mitotic cell cycle!0.0412168034622221!1104$GO:0005096!GTPase activator activity!0.0420473751475497!5902$GO:0000074!regulation of progression through cell cycle!0.0420473751475497!1104$GO:0051726!regulation of cell cycle!0.0420473751475497!1104$GO:0022403!cell cycle phase!0.0421833541290076!1104$GO:0008047!enzyme activator activity!0.0494377287556743!5902$GO:0006323!DNA packaging!0.0494377287556743!1104$GO:0044427!chromosomal part!0.0494377287556743!1104
|id=C3964
|id=C3964
}}
}}

Revision as of 17:39, 18 May 2012


Full id: C3964_chronic_Mesenchymal_hepatocellular_hereditary_acute_rhabdomyosarcoma_Skeletal



Phase1 CAGE Peaks

Hg19::chr1:28844730..28844776,+p2@RCC1
Hg19::chr1:28844778..28844807,+p3@RCC1
Hg19::chr22:20105012..20105085,+p1@RANBP1


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:0005083small GTPase regulator activity0.00884912319659774
GO:0005087Ran guanyl-nucleotide exchange factor activity0.00884912319659774
GO:0030695GTPase regulator activity0.00884912319659774
GO:0007090regulation of S phase of mitotic cell cycle0.00884912319659774
GO:0007052mitotic spindle organization and biogenesis0.00884912319659774
GO:0008536Ran GTPase binding0.00884912319659774
GO:0033261regulation of progression through S phase0.00904970673294687
GO:0042393histone binding0.00904970673294687
GO:0000084S phase of mitotic cell cycle0.00911647317396334
GO:0007051spindle organization and biogenesis0.00916982948411652
GO:0051320S phase0.00921343297182372
GO:0000790nuclear chromatin0.00924972184269641
GO:0005092GDP-dissociation inhibitor activity0.0102534655193447
GO:0000794condensed nuclear chromosome0.0102534655193447
GO:0007346regulation of progression through mitotic cell cycle0.0102534655193447
GO:0000082G1/S transition of mitotic cell cycle0.0102534655193447
GO:0000793condensed chromosome0.0147554015762654
GO:0044454nuclear chromosome part0.0170067703933241
GO:0007088regulation of mitosis0.0170067703933241
GO:0017016Ras GTPase binding0.0185651040629841
GO:0051329interphase of mitotic cell cycle0.018628663845914
GO:0031267small GTPase binding0.018628663845914
GO:0051325interphase0.0188654918799131
GO:0051020GTPase binding0.0189105199641022
GO:0000228nuclear chromosome0.0189105199641022
GO:0000226microtubule cytoskeleton organization and biogenesis0.0189105199641022
GO:0003682chromatin binding0.0210616528993315
GO:0016043cellular component organization and biogenesis0.0272424842678321
GO:0005088Ras guanyl-nucleotide exchange factor activity0.0274005387140235
GO:0007067mitosis0.0368278486951195
GO:0000087M phase of mitotic cell cycle0.0368278486951195
GO:0051301cell division0.0368278486951195
GO:0019899enzyme binding0.0412168034622221
GO:0000279M phase0.0412168034622221
GO:0005085guanyl-nucleotide exchange factor activity0.0412168034622221
GO:0007017microtubule-based process0.0412168034622221
GO:0000785chromatin0.0412168034622221
GO:0000278mitotic cell cycle0.0412168034622221
GO:0005096GTPase activator activity0.0420473751475497
GO:0000074regulation of progression through cell cycle0.0420473751475497
GO:0051726regulation of cell cycle0.0420473751475497
GO:0022403cell cycle phase0.0421833541290076
GO:0008047enzyme activator activity0.0494377287556743
GO:0006323DNA packaging0.0494377287556743
GO:0044427chromosomal part0.0494377287556743



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.