Coexpression cluster:C3305

Full id: C3305_mesothelioma_Keratocytes_Fibroblast_hepatoma_Trabecular_acute_gastrointestinal

Phase1 CAGE Peaks

Hg19::chr12:57624085..57624106,+	p7@SHMT2
Hg19::chr12:57624119..57624158,+	p3@SHMT2
Hg19::chr12:57624170..57624186,+	p6@SHMT2

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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No GOStat results

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
animal cell	2.42e-23	679
eukaryotic cell	2.42e-23	679
native cell	2.98e-14	722
embryonic cell	8.16e-11	250
fibroblast	6.29e-10	76
epithelial cell	2.12e-08	253
somatic cell	2.46e-08	588
non-terminally differentiated cell	4.86e-08	106

Uber Anatomy

Ontology term	p-value	n
trunk	1.27e-07	199

Disease

Ontology term	p-value	n
cell type cancer	1.50e-09	143
cancer	1.54e-09	235
disease of cellular proliferation	1.73e-09	239

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
ATF3#467	3	22.4631745260087	8.81932387510763e-05	0.00129365360420276
CEBPB#1051	3	7.97114762582482	0.00197418705528856	0.0115024893649808
E2F6#1876	3	5.01715573169739	0.0079176980688633	0.0320983024848231
EGR1#1958	3	4.98817909481014	0.00805648813738344	0.031950315723569
JUND#3727	3	6.99466394187103	0.00292184504273499	0.0156337196791946
MAX#4149	3	6.45255550900712	0.00372191383426551	0.018604047043977
MXI1#4601	3	9.9615716287593	0.00101147054125902	0.00719010154223734
MYC#4609	3	5.2222818716094	0.00702084375574015	0.0293570044843554
SIN3A#25942	3	5.40888472681514	0.00631896197799152	0.0275781893029443
TFAP2A#7020	3	16.518634373045	0.000221803388076634	0.00247620780837366
TFAP2C#7022	3	10.8092286098602	0.000791674657575313	0.00613866727763814
USF1#7391	3	6.36149927720796	0.0038840405729056	0.0189731203645317
USF2#7392	3	12.9921973850696	0.000455897939342781	0.00420800043190638
ZBTB7A#51341	3	7.3519093078759	0.00251625586028227	0.0139784705208521

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.