Coexpression cluster:C4143

Full id: C4143_Mast_acute_hepatoblastoma_embryonic_rhabdomyosarcoma_testicular_cord

Phase1 CAGE Peaks

Hg19::chr2:170440902..170440927,+	p3@PPIG
Hg19::chr2:71357744..71357791,+	p1@MPHOSPH10
Hg19::chr6:144164455..144164564,+	p1@LTV1

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:0008380	RNA splicing	0.0024019489850783
GO:0006396	RNA processing	0.00566423892359164
GO:0016018	cyclosporin A binding	0.00566423892359164
GO:0031981	nuclear lumen	0.00566423892359164
GO:0031974	membrane-enclosed lumen	0.00693705742595231
GO:0043233	organelle lumen	0.00693705742595231
GO:0005732	small nucleolar ribonucleoprotein complex	0.00693705742595231
GO:0044428	nuclear part	0.00719345594856585
GO:0008144	drug binding	0.00719345594856585
GO:0031202	RNA splicing factor activity, transesterification mechanism	0.00744489806851175
GO:0044452	nucleolar part	0.0120616571778071
GO:0016363	nuclear matrix	0.0126734263056732
GO:0006364	rRNA processing	0.0170965459175916
GO:0016072	rRNA metabolic process	0.0170965459175916
GO:0016607	nuclear speck	0.0176895637176626
GO:0003755	peptidyl-prolyl cis-trans isomerase activity	0.0176895637176626
GO:0016859	cis-trans isomerase activity	0.0176895637176626
GO:0016604	nuclear body	0.018885880737988
GO:0042254	ribosome biogenesis and assembly	0.018885880737988
GO:0005730	nucleolus	0.0266486946639436
GO:0042277	peptide binding	0.0319735175896541
GO:0022613	ribonucleoprotein complex biogenesis and assembly	0.0329026406580026
GO:0044446	intracellular organelle part	0.0329026406580026
GO:0044422	organelle part	0.0329026406580026
GO:0016070	RNA metabolic process	0.0329026406580026
GO:0016853	isomerase activity	0.0389244521400519
GO:0006457	protein folding	0.0411644597921784

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
lymphocyte	1.56e-12	53
common lymphoid progenitor	1.56e-12	53
lymphoid lineage restricted progenitor cell	4.24e-12	52
hematopoietic stem cell	4.70e-08	172
angioblastic mesenchymal cell	4.70e-08	172
hematopoietic cell	5.60e-07	182
lymphocyte of B lineage	8.83e-07	24
pro-B cell	8.83e-07	24

Disease

Ontology term	p-value	n
cancer	7.93e-33	235
disease of cellular proliferation	1.65e-31	239
hematologic cancer	1.02e-20	51
immune system cancer	1.02e-20	51
leukemia	2.03e-18	39
organ system cancer	5.71e-18	137
myeloid leukemia	1.39e-16	31
cell type cancer	5.45e-16	143
carcinoma	2.73e-11	106
germ cell and embryonal cancer	8.61e-07	22
germ cell cancer	8.61e-07	22

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
BCLAF1#9774	2	14.4350984067479	0.00620114743554613	0.0273902151415099
BRCA1#672	2	13.4561537621492	0.00711980771608456	0.0296320075739282
CCNT2#905	3	6.33620157696263	0.00393075003576489	0.0190445167463931
CEBPB#1051	3	7.97114762582482	0.00197418705528856	0.0115449981447607
CHD2#1106	3	10.3440228341169	0.000903370110274688	0.00661434877642864
E2F1#1869	3	4.90738921487932	0.00846098534723939	0.0326156885055304
E2F6#1876	3	5.01715573169739	0.0079176980688633	0.0323064724415539
ELF1#1997	3	4.25809795880754	0.0129517987505461	0.0463371098146164
ELK4#2005	2	10.823787772312	0.0109128471951648	0.0402034233382417
GABPB1#2553	3	7.06768383618217	0.00283221282541742	0.0154429088061904
GTF2F1#2962	3	12.7396608767577	0.000483552504743859	0.004347601587719
IRF1#3659	3	7.6371637535639	0.00224469274729724	0.0128365255344126
JUND#3727	3	6.99466394187103	0.00292184504273499	0.0157069474170372
MAX#4149	3	6.45255550900712	0.00372191383426551	0.0186926164432246
MEF2A#4205	2	12.495487273096	0.00823502947802974	0.0324918112450301
MEF2C#4208	2	27.5409029950827	0.00172911993836969	0.0106491070434835
MXI1#4601	3	9.9615716287593	0.00101147054125902	0.00721317663766139
MYC#4609	3	5.2222818716094	0.00702084375574015	0.0295106009178471
NFKB1#4790	3	5.48806342419384	0.00604938181565543	0.027008865742358
NFYB#4801	2	11.1731955023576	0.0102546713505453	0.0381392265652789
NR3C1#2908	2	9.98201555411536	0.0127847436554717	0.046054975256409
REST#5978	3	9.65002871612802	0.00111263624711459	0.00769095353844733
SETDB1#9869	2	26.880017452007	0.00181446890796441	0.0108958899654379
SIN3A#25942	3	5.40888472681514	0.00631896197799152	0.0277393161287654
SIX5#147912	2	11.391143570306	0.00987382008142903	0.0370806147243569
SP1#6667	3	5.6983813781409	0.00540396270171217	0.0247027820109475
TRIM28#10155	2	12.3936833635083	0.00836834412943847	0.0329245241112987
USF1#7391	3	6.36149927720796	0.0038840405729056	0.0190721384829417

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.