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Coexpression cluster:C4457: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0000476!3.19e-12!3;UBERON:0000920!3.19e-12!3;UBERON:0003124!1.41e-11!7;UBERON:0005631!6.38e-10!14;UBERON:0000158!6.38e-10!14;UBERON:0001282!6.88e-10!1;UBERON:0009842!6.88e-10!1;UBERON:0003704!6.88e-10!1;UBERON:0001171!6.88e-10!1;UBERON:0001172!6.88e-10!1
|ontology_enrichment_uberon=UBERON:0000476!3.19e-12!3;UBERON:0000920!3.19e-12!3;UBERON:0003124!1.41e-11!7;UBERON:0005631!6.38e-10!14;UBERON:0000158!6.38e-10!14;UBERON:0001282!6.88e-10!1;UBERON:0009842!6.88e-10!1;UBERON:0003704!6.88e-10!1;UBERON:0001171!6.88e-10!1;UBERON:0001172!6.88e-10!1
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}}
}}

Revision as of 16:45, 26 November 2012


Full id: C4457_placenta_immature_Mast_breast_colon_small_migratory



Phase1 CAGE Peaks

Hg19::chr5:125695855..125695862,+p40@GRAMD3
Hg19::chr5:125695865..125695875,+p31@GRAMD3
Hg19::chr6:122931366..122931383,+p5@PKIB


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:0004862cAMP-dependent protein kinase inhibitor activity0.00282585658777817
GO:0004860protein kinase inhibitor activity0.00463126496330311
GO:0019210kinase inhibitor activity0.00463126496330311
GO:0006469negative regulation of protein kinase activity0.00463126496330311
GO:0033673negative regulation of kinase activity0.00463126496330311
GO:0051348negative regulation of transferase activity0.00463126496330311
GO:0043086negative regulation of catalytic activity0.00585356007468335
GO:0019887protein kinase regulator activity0.00618156128576474
GO:0019207kinase regulator activity0.0063843426612766
GO:0045859regulation of protein kinase activity0.00969425801640567
GO:0043549regulation of kinase activity0.00969425801640567
GO:0051338regulation of transferase activity0.00969425801640567
GO:0004857enzyme inhibitor activity0.0145278011756288
GO:0050790regulation of catalytic activity0.0203528956619737
GO:0065009regulation of a molecular function0.0210683307822128



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
Langerhans cell3.47e-165
chorionic membrane mesenchymal stem cell3.19e-123
germ line cell3.93e-117
germ cell3.93e-117
conventional dendritic cell3.18e-098
dendritic cell1.25e-0710
Uber Anatomy
Ontology termp-valuen
acellular anatomical structure3.19e-123
egg chorion3.19e-123
chorion1.41e-117
extraembryonic membrane6.38e-1014
membranous layer6.38e-1014
intralobular bile duct6.88e-101
acinus6.88e-101
intrahepatic bile duct6.88e-101
portal lobule6.88e-101
hepatic acinus6.88e-101
Disease
Ontology termp-valuen
chondrosarcoma1.62e-091
extraosseous chondrosarcoma1.62e-091
myxoid chondrosarcoma1.62e-091
extraskeletal myxoid chondrosarcoma1.62e-091


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)

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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.