Coexpression cluster:C2971

Full id: C2971_Mast_rhabdomyosarcoma_osteosarcoma_hepatoblastoma_malignant_acute_hepatocellular

Phase1 CAGE Peaks

Hg19::chr10:103912137..103912159,+	p1@NOLC1
Hg19::chr2:232329186..232329215,-	p1@NCL
Hg19::chrX:153991175..153991226,+	p2@DKC1

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:0005730	nucleolus	1.09134518659741e-05
GO:0031981	nuclear lumen	0.000340050982291448
GO:0006364	rRNA processing	0.000340050982291448
GO:0016072	rRNA metabolic process	0.000340050982291448
GO:0031974	membrane-enclosed lumen	0.000376365868350794
GO:0043233	organelle lumen	0.000376365868350794
GO:0042254	ribosome biogenesis and assembly	0.000419565009273174
GO:0044428	nuclear part	0.000419565009273174
GO:0022613	ribonucleoprotein complex biogenesis and assembly	0.00168049642567982
GO:0003720	telomerase activity	0.00342604853543545
GO:0005697	telomerase holoenzyme complex	0.00389312236399137
GO:0043232	intracellular non-membrane-bound organelle	0.00473375331587104
GO:0043228	non-membrane-bound organelle	0.00473375331587104
GO:0006396	RNA processing	0.00490394377798006
GO:0031119	tRNA pseudouridine synthesis	0.00570907239064743
GO:0007004	telomere maintenance via telomerase	0.00909695917889302
GO:0001522	pseudouridine synthesis	0.00916701121882851
GO:0044446	intracellular organelle part	0.00916701121882851
GO:0044422	organelle part	0.00916701121882851
GO:0006400	tRNA modification	0.00941664197669587
GO:0003723	RNA binding	0.0107915548678622
GO:0032200	telomere organization and biogenesis	0.0107915548678622
GO:0000723	telomere maintenance	0.0107915548678622
GO:0016439	tRNA-pseudouridine synthase activity	0.011766990608002
GO:0009982	pseudouridine synthase activity	0.0126640690375726
GO:0009451	RNA modification	0.014806363407018
GO:0003964	RNA-directed DNA polymerase activity	0.0158398668910636
GO:0006278	RNA-dependent DNA replication	0.0181666133021973
GO:0005938	cell cortex	0.0181666133021973
GO:0005634	nucleus	0.0181666133021973
GO:0006996	organelle organization and biogenesis	0.0181666133021973
GO:0016866	intramolecular transferase activity	0.0181666133021973
GO:0008022	protein C-terminus binding	0.0191670845322766
GO:0008033	tRNA processing	0.0231162234769279
GO:0001525	angiogenesis	0.0314525679379851
GO:0048514	blood vessel morphogenesis	0.0348272231545753
GO:0048646	anatomical structure formation	0.0352628088452944
GO:0001568	blood vessel development	0.0362830862796039
GO:0001944	vasculature development	0.0362830862796039
GO:0043231	intracellular membrane-bound organelle	0.0414910712264059
GO:0043227	membrane-bound organelle	0.0414910712264059
GO:0006399	tRNA metabolic process	0.0441775786977901
GO:0016779	nucleotidyltransferase activity	0.0453127893723849
GO:0007067	mitosis	0.0462030726886151
GO:0000087	M phase of mitotic cell cycle	0.0463022736324971

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
epithelial cell	4.34e-14	253

Disease

Ontology term	p-value	n
cancer	1.13e-61	235
disease of cellular proliferation	7.55e-61	239
cell type cancer	1.21e-33	143
organ system cancer	3.40e-28	137
carcinoma	1.63e-27	106
hematologic cancer	6.35e-22	51
immune system cancer	6.35e-22	51
leukemia	1.02e-18	39
myeloid leukemia	3.87e-15	31
squamous cell carcinoma	7.64e-07	14
germ cell and embryonal cancer	8.40e-07	22
germ cell cancer	8.40e-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
ATF3#467	2	14.9754496840058	0.00576829454079388	0.0259401874589206
BCLAF1#9774	2	14.4350984067479	0.00620114743554613	0.027369379918903
E2F1#1869	3	4.90738921487932	0.00846098534723939	0.0323281206073145
E2F4#1874	3	12.6680603152844	0.000491798700629898	0.00435021296646786
E2F6#1876	3	5.01715573169739	0.0079176980688633	0.032016279565356
ELF1#1997	3	4.25809795880754	0.0129517987505461	0.045970192343527
FOSL2#2355	2	11.2868004030411	0.010053458697312	0.0376523407046032
IRF1#3659	3	7.6371637535639	0.00224469274729724	0.0127534254071906
MAX#4149	3	6.45255550900712	0.00372191383426551	0.0185614057366467
MYC#4609	3	5.2222818716094	0.00702084375574015	0.0292995245347137
NFKB1#4790	3	5.48806342419384	0.00604938181565543	0.0268401965863137
SIN3A#25942	3	5.40888472681514	0.00631896197799152	0.0275241302089276
SP1#6667	3	5.6983813781409	0.00540396270171217	0.0245288565606553
YY1#7528	3	4.91117074985386	0.00844145534180826	0.0327702172413156

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.