Coexpression cluster:C3496

Full id: C3496_liver_Hepatocyte_epitheloid_hairy_cord_cervical_non

Phase1 CAGE Peaks

Hg19::chr15:50474385..50474404,+	p2@SLC27A2
Hg19::chr15:50474553..50474562,+	p4@SLC27A2
Hg19::chr15:50474813..50474866,+	p1@CU691220

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:0005782	peroxisomal matrix	0.00309078064288237
GO:0000038	very-long-chain fatty acid metabolic process	0.00309078064288237
GO:0004467	long-chain-fatty-acid-CoA ligase activity	0.00309078064288237
GO:0015645	fatty-acid ligase activity	0.00309078064288237
GO:0016877	ligase activity, forming carbon-sulfur bonds	0.00645629734290984
GO:0031903	microbody membrane	0.00645629734290984
GO:0005778	peroxisomal membrane	0.00645629734290984
GO:0044439	peroxisomal part	0.00645629734290984
GO:0044438	microbody part	0.00645629734290984
GO:0042579	microbody	0.0112392023377541
GO:0005777	peroxisome	0.0112392023377541
GO:0006631	fatty acid metabolic process	0.0196779700930178
GO:0032787	monocarboxylic acid metabolic process	0.0272939706002228
GO:0005789	endoplasmic reticulum membrane	0.0384905216060285
GO:0042175	nuclear envelope-endoplasmic reticulum network	0.0384905216060285
GO:0044432	endoplasmic reticulum part	0.0401801483574708
GO:0016874	ligase activity	0.0470525900222328
GO:0044255	cellular lipid metabolic process	0.0493288590604027
GO:0019752	carboxylic acid metabolic process	0.0493288590604027
GO:0006082	organic acid metabolic process	0.0493288590604027

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>

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Uber Anatomy

Ontology term	p-value	n
larynx	5.62e-11	9
subdivision of digestive tract	1.49e-10	118
organ system subdivision	3.37e-09	223
digestive system	1.97e-07	145
digestive tract	1.97e-07	145
primitive gut	1.97e-07	145
foregut	2.27e-07	87
upper respiratory tract	6.81e-07	19

Disease

Ontology term	p-value	n
cancer	1.49e-17	235
disease of cellular proliferation	1.60e-16	239
carcinoma	4.79e-13	106
leukemia	1.32e-11	39
organ system cancer	7.41e-11	137
myeloid leukemia	9.15e-11	31
hematologic cancer	2.31e-09	51
immune system cancer	2.31e-09	51
cell type cancer	1.51e-08	143

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)
{{{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

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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
CCNT2#905	3	6.33620157696263	0.00393075003576489	0.0189662094241279
CTBP2#1488	3	62.7170003393281	4.049570681927e-06	0.0001293769080605
CTCF#10664	3	5.36025637307503	0.006492509252767	0.0278972753167832
CTCFL#140690	2	13.1643162393162	0.00743336703699601	0.0306742036420572
E2F1#1869	3	4.90738921487932	0.00846098534723939	0.0324527837482219
E2F6#1876	3	5.01715573169739	0.0079176980688633	0.0321407209504825
GATA1#2623	3	13.5603081438004	0.000400961596378263	0.0038741815305902
HMGN3#9324	3	8.17854772335059	0.00182776694216421	0.0108534314119109
MAX#4149	3	6.45255550900712	0.00372191383426551	0.0186218721345624
MYC#4609	3	5.2222818716094	0.00702084375574015	0.0293946643016936
RFX5#5993	3	12.0479108271951	0.000571724605031258	0.00483954822701083
SIN3A#25942	3	5.40888472681514	0.00631896197799152	0.0276024120632171
SMC3#9126	2	10.0299552299552	0.012665637976747	0.0457268585679439
STAT1#6772	3	20.7065874971992	0.000112599244104667	0.00154631853452298
TFAP2A#7020	3	16.518634373045	0.000221803388076634	0.00247779698869778
TFAP2C#7022	3	10.8092286098602	0.000791674657575313	0.00614277188428738
ZNF263#10127	3	8.22184163701068	0.00179904392556587	0.0109168757505185

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.