Coexpression cluster:C4457

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

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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

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GO ID	GO name	FDR corrected p-value
GO:0004862	cAMP-dependent protein kinase inhibitor activity	0.00282585658777817
GO:0004860	protein kinase inhibitor activity	0.00463126496330311
GO:0019210	kinase inhibitor activity	0.00463126496330311
GO:0006469	negative regulation of protein kinase activity	0.00463126496330311
GO:0033673	negative regulation of kinase activity	0.00463126496330311
GO:0051348	negative regulation of transferase activity	0.00463126496330311
GO:0043086	negative regulation of catalytic activity	0.00585356007468335
GO:0019887	protein kinase regulator activity	0.00618156128576474
GO:0019207	kinase regulator activity	0.0063843426612766
GO:0045859	regulation of protein kinase activity	0.00969425801640567
GO:0043549	regulation of kinase activity	0.00969425801640567
GO:0051338	regulation of transferase activity	0.00969425801640567
GO:0004857	enzyme inhibitor activity	0.0145278011756288
GO:0050790	regulation of catalytic activity	0.0203528956619737
GO:0065009	regulation of a molecular function	0.0210683307822128

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>

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Cell Type

Ontology term	p-value	n
Langerhans cell	3.47e-16	5
chorionic membrane mesenchymal stem cell	3.19e-12	3
germ line cell	3.93e-11	7
germ cell	3.93e-11	7
conventional dendritic cell	3.18e-09	8
dendritic cell	1.25e-07	10

Uber Anatomy

Ontology term	p-value	n
acellular anatomical structure	3.19e-12	3
egg chorion	3.19e-12	3
chorion	1.41e-11	7
extraembryonic membrane	6.38e-10	14
membranous layer	6.38e-10	14
intralobular bile duct	6.88e-10	1
acinus	6.88e-10	1
intrahepatic bile duct	6.88e-10	1
portal lobule	6.88e-10	1
hepatic acinus	6.88e-10	1

Disease

Ontology term	p-value	n
chondrosarcoma	1.62e-09	1
extraosseous chondrosarcoma	1.62e-09	1
myxoid chondrosarcoma	1.62e-09	1
extraskeletal myxoid chondrosarcoma	1.62e-09	1

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

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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

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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

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This analysis result is provided for C0 - C305 clusters.