Coexpression cluster:C3609

Full id: C3609_osteosarcoma_embryonic_Reticulocytes_testicular_chronic_Hep2_teratocarcinoma

Phase1 CAGE Peaks

Hg19::chr17:17184546..17184569,-	p1@COPS3
Hg19::chr17:17184575..17184592,-	p2@COPS3
Hg19::chr17:17184605..17184622,-	p3@COPS3

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><br>uberon_data<br>disease_data<br>

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Uber Anatomy

Ontology term	p-value	n
larynx	2.24e-07	9
upper respiratory tract	6.08e-07	19

Disease

Ontology term	p-value	n
disease of cellular proliferation	5.04e-18	239
cancer	9.63e-17	235
cell type cancer	1.15e-10	143
carcinoma	5.35e-07	106

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
BRCA1#672	3	20.1842306432238	0.000121570486027164	0.00164124870607432
CCNT2#905	3	6.33620157696263	0.00393075003576489	0.0189802396312936
CEBPB#1051	3	7.97114762582482	0.00197418705528856	0.0115121229406634
CHD2#1106	3	10.3440228341169	0.000903370110274688	0.00659815867871726
E2F1#1869	3	4.90738921487932	0.00846098534723939	0.0324802193883825
E2F4#1874	3	12.6680603152844	0.000491798700629898	0.00436611394891924
E2F6#1876	3	5.01715573169739	0.0079176980688633	0.0321619722536663
EGR1#1958	3	4.98817909481014	0.00805648813738344	0.0320147463884099
ELF1#1997	3	4.25809795880754	0.0129517987505461	0.0461584340456674
ELK4#2005	3	16.235681658468	0.000233604395574599	0.00255550533878868
ETS1#2113	3	9.72876092220234	0.00108584009258484	0.00761356518492566
GABPB1#2553	3	7.06768383618217	0.00283221282541742	0.015392281587853
MAX#4149	3	6.45255550900712	0.00372191383426551	0.0186307974950563
MYC#4609	3	5.2222818716094	0.00702084375574015	0.0294123506219714
PAX5#5079	3	6.66956553117783	0.00337029099967726	0.017273878476483
POU2F2#5452	3	9.10612405774252	0.00132416519268213	0.00881305687984508
RFX5#5993	3	12.0479108271951	0.000571724605031258	0.00484111772538183
SIN3A#25942	3	5.40888472681514	0.00631896197799152	0.027626677412067
SP1#6667	3	5.6983813781409	0.00540396270171217	0.0246144385103632
TAF7#6879	3	11.4330694049239	0.000669018198194583	0.0054210250291911
TFAP2A#7020	3	16.518634373045	0.000221803388076634	0.00247938821013974
TFAP2C#7022	3	10.8092286098602	0.000791674657575313	0.00614825323932987
TRIM28#10155	3	18.5905250452625	0.000155596929725528	0.00196878940436205
USF1#7391	3	6.36149927720796	0.0038840405729056	0.0190042311264319
YY1#7528	3	4.91117074985386	0.00844145534180826	0.0328863456596207
ZBTB33#10009	3	31.6647250299812	3.14815888737575e-05	0.00063362992106116
ZNF263#10127	3	8.22184163701068	0.00179904392556587	0.0109283050393866

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.