Coexpression cluster:C2185

Full id: C2185_mature_Adipocyte_Hepatocyte_skin_liver_skeletal_left

Phase1 CAGE Peaks

Hg19::chr12:109577279..109577289,+	p15@ACACB
Hg19::chr12:109577376..109577404,+	p21@ACACB
Hg19::chr20:33464407..33464423,+	p1@ACSS2
Hg19::chr4:185726631..185726658,-	p@chr4:185726631..185726658 -

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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p.value	FDR	nGenes	nPathway	Name
1.91447319275479e-06	0.000403953843671262	2	40	Pyruvate metabolism (KEGG):00620
1.21740859436715e-06	0.000385309820117203	2	32	Propanoate metabolism (KEGG):00640
5.66978599392766e-07	0.000358897453415621	2	22	Fatty Acid Biosynthesis (Wikipathways):WP357

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:0008610	lipid biosynthetic process	0.00264916256568538
GO:0003989	acetyl-CoA carboxylase activity	0.00264916256568538
GO:0004075	biotin carboxylase activity	0.00264916256568538
GO:0016421	CoA carboxylase activity	0.00298004468581734
GO:0016874	ligase activity	0.00298004468581734
GO:0016885	ligase activity, forming carbon-carbon bonds	0.00298004468581734
GO:0044255	cellular lipid metabolic process	0.00298004468581734
GO:0003987	acetate-CoA ligase activity	0.00298004468581734
GO:0016405	CoA-ligase activity	0.00348582846459488
GO:0006629	lipid metabolic process	0.00348582846459488
GO:0009374	biotin binding	0.00419351958115085
GO:0016878	acid-thiol ligase activity	0.00419351958115085
GO:0016208	AMP binding	0.00427828266515267
GO:0016877	ligase activity, forming carbon-sulfur bonds	0.00529637549745431
GO:0006633	fatty acid biosynthetic process	0.0128793076472514
GO:0046394	carboxylic acid biosynthetic process	0.0129189165628106
GO:0016053	organic acid biosynthetic process	0.0129189165628106
GO:0009058	biosynthetic process	0.0130401524453593
GO:0032559	adenyl ribonucleotide binding	0.0162566837917713
GO:0030554	adenyl nucleotide binding	0.0167888630484699
GO:0030145	manganese ion binding	0.0185048333400419
GO:0032553	ribonucleotide binding	0.0206711729655838
GO:0032555	purine ribonucleotide binding	0.0206711729655838
GO:0006631	fatty acid metabolic process	0.0206711729655838
GO:0017076	purine nucleotide binding	0.0206711729655838
GO:0019842	vitamin binding	0.0248743443344147
GO:0000166	nucleotide binding	0.026251361438029
GO:0032787	monocarboxylic acid metabolic process	0.0270404086116589
GO:0016879	ligase activity, forming carbon-nitrogen bonds	0.0337074386028396

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><br>

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Cell Type

Ontology term	p-value	n
fat cell	1.38e-15	15
stuff accumulating cell	1.01e-07	87

Uber Anatomy

Ontology term	p-value	n
adult organism	2.18e-34	114
neural tube	9.63e-09	56
neural rod	9.63e-09	56
future spinal cord	9.63e-09	56
neural keel	9.63e-09	56
neural plate	2.77e-07	82
presumptive neural plate	2.77e-07	82
regional part of nervous system	8.85e-07	53
regional part of brain	8.85e-07	53

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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(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF	#promoters	Enrichment	p-value	q-value
SREBF1#6720	2	23.5029247202441	0.00263845490076824	0.0145820813558414
SREBF2#6721	1	109.235815602837	0.00912320148412682	0.034514889509553

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.