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Coexpression cluster:C2865: Difference between revisions

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|gostat_on_coexpression_clusters=GO:0045104!intermediate filament cytoskeleton organization and biogenesis!0.00772695160720593!667$GO:0045103!intermediate filament-based process!0.00772695160720593!667$GO:0005200!structural constituent of cytoskeleton!0.0260140704109266!667$GO:0007050!cell cycle arrest!0.0260140704109266!667$GO:0045786!negative regulation of progression through cell cycle!0.0463617096432356!667
|gostat_on_coexpression_clusters=GO:0045104!intermediate filament cytoskeleton organization and biogenesis!0.00772695160720593!667$GO:0045103!intermediate filament-based process!0.00772695160720593!667$GO:0005200!structural constituent of cytoskeleton!0.0260140704109266!667$GO:0007050!cell cycle arrest!0.0260140704109266!667$GO:0045786!negative regulation of progression through cell cycle!0.0463617096432356!667
|id=C2865
|id=C2865
|ontology_enrichment_celltype=
|ontology_enrichment_disease=DOID:0050687!5.34e-07!143
|ontology_enrichment_uberon=UBERON:0007023!2.15e-17!115;UBERON:0000468!2.23e-11!659;UBERON:0000062!1.16e-10!511;UBERON:0004921!8.24e-10!129;UBERON:0004185!8.24e-10!129;UBERON:0000477!1.09e-09!286;UBERON:0001007!2.11e-09!155;UBERON:0001555!2.11e-09!155;UBERON:0007026!2.11e-09!155;UBERON:0000480!3.19e-09!626;UBERON:0000467!4.68e-09!625;UBERON:0000481!6.27e-09!347;UBERON:0004111!3.58e-08!241;UBERON:0004119!1.44e-07!169;UBERON:0000925!1.44e-07!169;UBERON:0006595!1.44e-07!169;UBERON:0000077!5.09e-07!130;UBERON:0000922!7.21e-07!612
}}
}}

Revision as of 14:29, 21 May 2012


Full id: C2865_cervix_uterus_lung_rectum_rectal_Prostate_stomach



Phase1 CAGE Peaks

Hg19::chr6:56407223..56407227,-p1@BC038763
Hg19::chr6:56407600..56407638,-p11@DST
Hg19::chr6:56407645..56407662,-p25@DST
Hg19::chr6:56407665..56407745,-p7@DST


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:0045104intermediate filament cytoskeleton organization and biogenesis0.00772695160720593
GO:0045103intermediate filament-based process0.00772695160720593
GO:0005200structural constituent of cytoskeleton0.0260140704109266
GO:0007050cell cycle arrest0.0260140704109266
GO:0045786negative regulation of progression through cell cycle0.0463617096432356



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>uberon_data<br>disease_data<br>


Uber Anatomy
Ontology termp-valuen
adult organism2.15e-17115
multi-cellular organism2.23e-11659
organ1.16e-10511
subdivision of digestive tract8.24e-10129
endodermal part of digestive tract8.24e-10129
anatomical cluster1.09e-09286
digestive system2.11e-09155
digestive tract2.11e-09155
primitive gut2.11e-09155
anatomical group3.19e-09626
anatomical system4.68e-09625
multi-tissue structure6.27e-09347
anatomical conduit3.58e-08241
endoderm-derived structure1.44e-07169
endoderm1.44e-07169
presumptive endoderm1.44e-07169
mixed endoderm/mesoderm-derived structure5.09e-07130
embryo7.21e-07612
Disease
Ontology termp-valuen
cell type cancer5.34e-07143


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.