Coexpression cluster:C3137

Full id: C3137_gastric_chronic_mycosis_acute_teratocarcinoma_mesenchymal_hepatocellular

Phase1 CAGE Peaks

Hg19::chr11:27384634..27384656,-	p4@CCDC34
Hg19::chr11:27384671..27384693,-	p3@CCDC34
Hg19::chr11:27384695..27384718,-	p2@CCDC34

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><br>disease_data<br>

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Cell Type

Ontology term	p-value	n
non-terminally differentiated cell	8.20e-08	180

Disease

Ontology term	p-value	n
disease of cellular proliferation	3.44e-18	239
cancer	1.94e-17	235
organ system cancer	1.05e-09	137
cell type cancer	1.01e-07	143
hematologic cancer	3.92e-07	51
immune system cancer	3.92e-07	51

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	0.0189198821543575
CHD2#1106	3	10.3440228341169	0.000903370110274688	0.00658526355461563
E2F1#1869	3	4.90738921487932	0.00846098534723939	0.0323683827355434
E2F4#1874	3	12.6680603152844	0.000491798700629898	0.00435574664985464
E2F6#1876	3	5.01715573169739	0.0079176980688633	0.0320485415322073
EGR1#1958	3	4.98817909481014	0.00805648813738344	0.0319127499271861
ELF1#1997	3	4.25809795880754	0.0129517987505461	0.046013977947011
EP300#2033	3	6.7739417262232	0.00321688050010379	0.0166882466993016
FOSL2#2355	3	16.9302006045617	0.000206016205317162	0.00242271438656898
HMGN3#9324	3	8.17854772335059	0.00182776694216421	0.0108324907316246
HNF4A#3172	3	23.1322903629537	8.07584663437677e-05	0.0012248523767756
MAX#4149	3	6.45255550900712	0.00372191383426551	0.0185782611927953
MXI1#4601	3	9.9615716287593	0.00101147054125902	0.00718276819599857
MYC#4609	3	5.2222818716094	0.00702084375574015	0.029324131213987
NANOG#79923	3	29.2447784810127	3.99627955670032e-05	0.000734026452026425
REST#5978	3	9.65002871612802	0.00111263624711459	0.00765346881462166
RFX5#5993	3	12.0479108271951	0.000571724605031258	0.00483093414440611
SIN3A#25942	3	5.40888472681514	0.00631896197799152	0.0275494080575853
SMARCB1#6598	3	18.2527157811574	0.00016439776067989	0.00202590415665452
SMARCC1#6599	3	43.6633593196315	1.20046018043203e-05	0.000300875595834271
SREBF1#6720	3	47.0058494404883	9.62099323994382e-06	0.000254124156041096
STAT1#6772	3	20.7065874971992	0.000112599244104667	0.00154428791267857
TCF7L2#6934	3	10.7701765631373	0.000800318129839838	0.00611802262936194
USF1#7391	3	6.36149927720796	0.0038840405729056	0.018957160173553
YY1#7528	3	4.91117074985386	0.00844145534180826	0.0328019181621131
ZNF143#7702	3	13.5008765522279	0.000406280496299717	0.00387750422672449
ZNF263#10127	3	8.22184163701068	0.00179904392556587	0.0108947204303708

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.