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Coexpression cluster:C1244: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters
|full_id=C1244_Smooth_mesenchymal_Fibroblast_mesothelioma_gall_Melanocyte_meningioma
|full_id=C1244_Smooth_mesenchymal_Fibroblast_mesothelioma_gall_Melanocyte_meningioma
|gostat_on_coexpression_clusters=GO:0051902!negative regulation of mitochondrial depolarization!0.0142023708595349!2537$GO:0051900!regulation of mitochondrial depolarization!0.0142023708595349!2537$GO:0051882!mitochondrial depolarization!0.0142023708595349!2537$GO:0043154!negative regulation of caspase activity!0.0142023708595349!2537$GO:0051899!membrane depolarization!0.0142023708595349!2537$GO:0042981!regulation of apoptosis!0.0142023708595349!4599;2537$GO:0043067!regulation of programmed cell death!0.0142023708595349!4599;2537$GO:0051881!regulation of mitochondrial membrane potential!0.0142023708595349!2537$GO:0001836!release of cytochrome c from mitochondria!0.014918783863124!2537$GO:0008637!apoptotic mitochondrial changes!0.0175732208981636!2537$GO:0006915!apoptosis!0.0175732208981636!4599;2537$GO:0012501!programmed cell death!0.0175732208981636!4599;2537$GO:0016265!death!0.0175732208981636!4599;2537$GO:0008219!cell death!0.0175732208981636!4599;2537$GO:0042391!regulation of membrane potential!0.0213340273481574!2537$GO:0048468!cell development!0.0285858889496168!4599;2537$GO:0043281!regulation of caspase activity!0.0364027197571902!2537$GO:0008632!apoptotic program!0.0457389008459905!2537$GO:0007005!mitochondrion organization and biogenesis!0.0457389008459905!2537$GO:0048869!cellular developmental process!0.0457389008459905!4599;2537$GO:0030154!cell differentiation!0.0457389008459905!4599;2537$GO:0009615!response to virus!0.0458932399910274!4599
|id=C1244
|id=C1244
}}
}}

Revision as of 17:34, 18 May 2012


Full id: C1244_Smooth_mesenchymal_Fibroblast_mesothelioma_gall_Melanocyte_meningioma



Phase1 CAGE Peaks

Hg19::chr19:56070737..56070738,-p@chr19:56070737..56070738
-
Hg19::chr1:27992577..27992588,+p@chr1:27992577..27992588
+
Hg19::chr1:27992792..27992807,-p@chr1:27992792..27992807
-
Hg19::chr1:27992888..27992908,+p@chr1:27992888..27992908
+
Hg19::chr1:27998692..27998710,-p1@IFI6
Hg19::chr21:42798552..42798557,+p17@MX1
Hg19::chr22:18632879..18632890,+p4@USP18


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:0051902negative regulation of mitochondrial depolarization0.0142023708595349
GO:0051900regulation of mitochondrial depolarization0.0142023708595349
GO:0051882mitochondrial depolarization0.0142023708595349
GO:0043154negative regulation of caspase activity0.0142023708595349
GO:0051899membrane depolarization0.0142023708595349
GO:0042981regulation of apoptosis0.0142023708595349
GO:0043067regulation of programmed cell death0.0142023708595349
GO:0051881regulation of mitochondrial membrane potential0.0142023708595349
GO:0001836release of cytochrome c from mitochondria0.014918783863124
GO:0008637apoptotic mitochondrial changes0.0175732208981636
GO:0006915apoptosis0.0175732208981636
GO:0012501programmed cell death0.0175732208981636
GO:0016265death0.0175732208981636
GO:0008219cell death0.0175732208981636
GO:0042391regulation of membrane potential0.0213340273481574
GO:0048468cell development0.0285858889496168
GO:0043281regulation of caspase activity0.0364027197571902
GO:0008632apoptotic program0.0457389008459905
GO:0007005mitochondrion organization and biogenesis0.0457389008459905
GO:0048869cellular developmental process0.0457389008459905
GO:0030154cell differentiation0.0457389008459905
GO:0009615response to virus0.0458932399910274



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.