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{{Coexpression_clusters
{{Coexpression_clusters
|full_id=C2138_Smooth_CD14_mesothelioma_Hair_meningioma_normal_mesenchymal
|full_id=C2138_Smooth_CD14_mesothelioma_Hair_meningioma_normal_mesenchymal
|gostat_on_coexpression_clusters=GO:0031571!G1 DNA damage checkpoint!0.0286350242431562!5371$GO:0006977!DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest!0.0286350242431562!5371$GO:0042771!DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis!0.0286350242431562!5371$GO:0031575!G1/S transition checkpoint!0.0286350242431562!5371$GO:0016605!PML body!0.0286350242431562!5371$GO:0030330!DNA damage response, signal transduction by p53 class mediator!0.0286350242431562!5371$GO:0016525!negative regulation of angiogenesis!0.0286350242431562!5371$GO:0008630!DNA damage response, signal transduction resulting in induction of apoptosis!0.0286350242431562!5371$GO:0005626!insoluble fraction!0.0286350242431562!5371$GO:0000077!DNA damage checkpoint!0.0300596940472044!5371$GO:0007093!mitotic cell cycle checkpoint!0.0300596940472044!5371$GO:0031570!DNA integrity checkpoint!0.0300596940472044!5371$GO:0008629!induction of apoptosis by intracellular signals!0.0349571040718196!5371$GO:0045765!regulation of angiogenesis!0.0349571040718196!5371$GO:0042770!DNA damage response, signal transduction!0.0369141724117895!5371$GO:0001666!response to hypoxia!0.0379388436354144!5371$GO:0030308!negative regulation of cell growth!0.0379388436354144!5371$GO:0045792!negative regulation of cell size!0.0379388436354144!5371$GO:0000075!cell cycle checkpoint!0.0379388436354144!5371$GO:0045926!negative regulation of growth!0.0392541470303728!5371$GO:0007088!regulation of mitosis!0.0410548490495792!5371
|id=C2138
|id=C2138
}}
}}

Revision as of 17:36, 18 May 2012


Full id: C2138_Smooth_CD14_mesothelioma_Hair_meningioma_normal_mesenchymal



Phase1 CAGE Peaks

Hg19::chr11:57335090..57335155,-p1@UBE2L6
Hg19::chr15:74287118..74287142,+p2@PML
Hg19::chr17:41158760..41158822,+p1@IFI35
Hg19::chr17:41158825..41158847,+p2@IFI35


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:0031571G1 DNA damage checkpoint0.0286350242431562
GO:0006977DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest0.0286350242431562
GO:0042771DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis0.0286350242431562
GO:0031575G1/S transition checkpoint0.0286350242431562
GO:0016605PML body0.0286350242431562
GO:0030330DNA damage response, signal transduction by p53 class mediator0.0286350242431562
GO:0016525negative regulation of angiogenesis0.0286350242431562
GO:0008630DNA damage response, signal transduction resulting in induction of apoptosis0.0286350242431562
GO:0005626insoluble fraction0.0286350242431562
GO:0000077DNA damage checkpoint0.0300596940472044
GO:0007093mitotic cell cycle checkpoint0.0300596940472044
GO:0031570DNA integrity checkpoint0.0300596940472044
GO:0008629induction of apoptosis by intracellular signals0.0349571040718196
GO:0045765regulation of angiogenesis0.0349571040718196
GO:0042770DNA damage response, signal transduction0.0369141724117895
GO:0001666response to hypoxia0.0379388436354144
GO:0030308negative regulation of cell growth0.0379388436354144
GO:0045792negative regulation of cell size0.0379388436354144
GO:0000075cell cycle checkpoint0.0379388436354144
GO:0045926negative regulation of growth0.0392541470303728
GO:0007088regulation of mitosis0.0410548490495792



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.