Coexpression cluster:C4352

Full id: C4352_acute_hepatoblastoma_neuroepithelioma_giant_osteosarcoma_Myoblast_small

Phase1 CAGE Peaks

Hg19::chr3:99536663..99536692,+	p3@C3orf26
Hg19::chr3:99536693..99536718,+	p1@C3orf26
Hg19::chrX:153991088..153991168,+	p1@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

---

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

---

GO ID	GO name	FDR corrected p-value
GO:0003720	telomerase activity	0.00448899093371011
GO:0005697	telomerase holoenzyme complex	0.00448899093371011
GO:0031119	tRNA pseudouridine synthesis	0.00598532124494681
GO:0007004	telomere maintenance via telomerase	0.00650903685387967
GO:0001522	pseudouridine synthesis	0.00650903685387967
GO:0006400	tRNA modification	0.00650903685387967
GO:0032200	telomere organization and biogenesis	0.00650903685387967
GO:0000723	telomere maintenance	0.00650903685387967
GO:0016439	tRNA-pseudouridine synthase activity	0.0065838533694415
GO:0009982	pseudouridine synthase activity	0.00664370658189096
GO:0009451	RNA modification	0.00734562152788927
GO:0003964	RNA-directed DNA polymerase activity	0.00748165155618352
GO:0006278	RNA-dependent DNA replication	0.00830463322736371
GO:0016866	intramolecular transferase activity	0.00830463322736371
GO:0006364	rRNA processing	0.00830463322736371
GO:0016072	rRNA metabolic process	0.00830463322736371
GO:0008033	tRNA processing	0.0097173450800313
GO:0042254	ribosome biogenesis and assembly	0.0110728443031516
GO:0005730	nucleolus	0.0155933369276246
GO:0006399	tRNA metabolic process	0.0195720004709761
GO:0016779	nucleotidyltransferase activity	0.0195805509298974
GO:0022613	ribonucleoprotein complex biogenesis and assembly	0.0200780321762307
GO:0016853	isomerase activity	0.0245137939684343
GO:0006260	DNA replication	0.0265598630244515
GO:0005654	nucleoplasm	0.0356459131921277
GO:0006396	RNA processing	0.0356459131921277
GO:0051276	chromosome organization and biogenesis	0.0356459131921277
GO:0031981	nuclear lumen	0.0442486249179997
GO:0008283	cell proliferation	0.0461282516636419

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>

---

Cell Type

Ontology term	p-value	n
epithelial cell	5.33e-09	254

Uber Anatomy

Ontology term	p-value	n
regional part of nervous system	2.55e-07	94
nervous system	2.55e-07	94

Disease

Ontology term	p-value	n
cancer	3.22e-67	235
disease of cellular proliferation	2.60e-65	239
cell type cancer	1.01e-43	143
carcinoma	2.56e-33	106
organ system cancer	2.01e-29	137
hematologic cancer	2.17e-17	51
immune system cancer	2.17e-17	51
leukemia	1.57e-13	39
myeloid leukemia	9.42e-11	31
germ cell and embryonal cancer	9.22e-09	22
germ cell cancer	9.22e-09	22
respiratory system cancer	1.79e-07	16
lung cancer	7.53e-07	15
adenocarcinoma	9.06e-07	25

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

---

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

---

(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF	#promoters	Enrichment	p-value	q-value
BRCA1#672	2	13.4561537621492	0.00711980771608456	0.0296390943104335
CEBPB#1051	3	7.97114762582482	0.00197418705528856	0.0115553506622923
CTCF#10664	3	5.36025637307503	0.006492509252767	0.028058891576998
E2F1#1869	3	4.90738921487932	0.00846098534723939	0.0326772002322437
E2F4#1874	3	12.6680603152844	0.000491798700629898	0.00438250550299368
E2F6#1876	3	5.01715573169739	0.0079176980688633	0.0323570382146664
ELF1#1997	3	4.25809795880754	0.0129517987505461	0.0463990981960101
FOSL2#2355	2	11.2868004030411	0.010053458697312	0.0376901849697955
GATA3#2625	2	18.1576775714707	0.00394454681927962	0.018955713673158
IRF1#3659	3	7.6371637535639	0.00224469274729724	0.0128498939835001
MAFF#23764	2	37.5435709932968	0.000934477401556032	0.00677137898710264
MAFK#7975	2	18.0671554252199	0.00398367474493681	0.0191164770578228
MAX#4149	3	6.45255550900712	0.00372191383426551	0.0187142149601298
MXI1#4601	3	9.9615716287593	0.00101147054125902	0.00721958528284247
MYC#4609	3	5.2222818716094	0.00702084375574015	0.0295498469011746
NFKB1#4790	3	5.48806342419384	0.00604938181565543	0.0270366050772526
NR3C1#2908	2	9.98201555411536	0.0127847436554717	0.0460629193305209
NRF1#4899	3	12.2102794477109	0.000549217240102001	0.00472563019764483
SETDB1#9869	2	26.880017452007	0.00181446890796441	0.0108977697555291
SIN3A#25942	3	5.40888472681514	0.00631896197799152	0.0277673273875313
SMARCB1#6598	2	12.1684771874383	0.00867500222192174	0.0330045738608898
SP1#6667	3	5.6983813781409	0.00540396270171217	0.0247395985010352
TRIM28#10155	2	12.3936833635083	0.00836834412943847	0.0329332087020282

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

---

This analysis result is provided for C0 - C305 clusters.