Coexpression cluster:C1011

Full id: C1011_acute_granulocyte_Hodgkin_neuroepithelioma_retinoblastoma_hepatoblastoma_merkel

Phase1 CAGE Peaks

Hg19::chr12:133263893..133263986,-	p1@POLE
Hg19::chr19:10305581..10305646,-	p1@DNMT1
Hg19::chr19:4402613..4402658,+	p1@CHAF1A
Hg19::chr19:48673580..48673630,-	p1@LIG1
Hg19::chr19:50887585..50887619,+	p1@POLD1
Hg19::chr8:145669791..145669834,-	p1@TONSL
Hg19::chr8:145743164..145743236,-	p1@RECQL4
Hg19::chr8:145743237..145743261,-	p2@RECQL4

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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p.value	FDR	nGenes	nPathway	Name
0.000478826714662831	0.0233151777216594	2	163	Purine metabolism (KEGG):00230
0.000180580969984339	0.0095256461666739	2	100	Pyrimidine metabolism (KEGG):00240
3.67416886898525e-08	7.75249631355887e-06	3	36	DNA replication (KEGG):03030
3.07978931231787e-08	7.75249631355887e-06	3	34	Base excision repair (KEGG):03410
8.89191667316632e-08	1.40714581352857e-05	3	48	Nucleotide excision repair (KEGG):03420
9.29638856460575e-06	0.000653845995710604	2	23	Mismatch repair (KEGG):03430
3.15809823992966e-05	0.00181734198715952	2	42	DNA Replication (Wikipathways):WP1806
1.32453795997426e-06	0.000119776075523386	2	9	Mismatch repair (Wikipathways):WP531
1.01567335750795e-06	0.000107153539217089	3	107	DNA Repair (Reactome):REACT_216
6.67157721853038e-06	0.000527888547416216	3	200	DNA Replication (Reactome):REACT_383
2.59719623007301e-05	0.00164402521363621	3	315	Cell Cycle, Mitotic (Reactome):REACT_152
3.75206069989847e-07	4.75010884607146e-05	3	77	Chromosome Maintenance (Reactome):REACT_22172
3.07978931231787e-08	7.75249631355887e-06	3	34	{PCNA,34} (Static Module):NA

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:0006281	DNA repair	1.36711281599438e-07
GO:0006974	response to DNA damage stimulus	1.36711281599438e-07
GO:0006259	DNA metabolic process	1.36711281599438e-07
GO:0009719	response to endogenous stimulus	2.2353665367932e-07
GO:0006260	DNA replication	5.81249790921492e-06
GO:0006950	response to stress	9.73788887599282e-06
GO:0000731	DNA synthesis during DNA repair	1.30963982036091e-05
GO:0003682	chromatin binding	1.70270067455608e-05
GO:0007049	cell cycle	9.94130900183607e-05
GO:0006139	nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	0.00043621865655787
GO:0003887	DNA-directed DNA polymerase activity	0.000449255144653721
GO:0005634	nucleus	0.000449255144653721
GO:0051329	interphase of mitotic cell cycle	0.00119150193290442
GO:0051325	interphase	0.00124071983685884
GO:0043283	biopolymer metabolic process	0.00182299496202717
GO:0043231	intracellular membrane-bound organelle	0.00296693105816845
GO:0043227	membrane-bound organelle	0.00296693105816845
GO:0006335	DNA replication-dependent nucleosome assembly	0.00296693105816845
GO:0045875	negative regulation of sister chromatid cohesion	0.00296693105816845
GO:0007063	regulation of sister chromatid cohesion	0.00296693105816845
GO:0006310	DNA recombination	0.0039538293047545
GO:0016779	nucleotidyltransferase activity	0.00494415731932331
GO:0003891	delta DNA polymerase activity	0.00494415731932331
GO:0003910	DNA ligase (ATP) activity	0.00494415731932331
GO:0003886	DNA (cytosine-5-)-methyltransferase activity	0.00549310385928867
GO:0003893	epsilon DNA polymerase activity	0.00549310385928867
GO:0003909	DNA ligase activity	0.00549310385928867
GO:0043229	intracellular organelle	0.00574075701982397
GO:0043226	organelle	0.00574075701982397
GO:0009008	DNA-methyltransferase activity	0.00574075701982397
GO:0005678	chromatin assembly complex	0.00574075701982397
GO:0003676	nucleic acid binding	0.00618596197214122
GO:0043170	macromolecule metabolic process	0.00633756424988399
GO:0000278	mitotic cell cycle	0.00663322789314192
GO:0003677	DNA binding	0.00686763962456978
GO:0007062	sister chromatid cohesion	0.00741350756267838
GO:0022403	cell cycle phase	0.00778579769906605
GO:0016886	ligase activity, forming phosphoric ester bonds	0.0109211497937796
GO:0048705	skeletal morphogenesis	0.0112381757070516
GO:0044237	cellular metabolic process	0.0112381757070516
GO:0008270	zinc ion binding	0.0112381757070516
GO:0044238	primary metabolic process	0.0112443768708326
GO:0000084	S phase of mitotic cell cycle	0.0114891233863831
GO:0000166	nucleotide binding	0.0114891233863831
GO:0044424	intracellular part	0.0114891233863831
GO:0000792	heterochromatin	0.0127739844957742
GO:0051276	chromosome organization and biogenesis	0.0127739844957742
GO:0051320	S phase	0.0129621865307859
GO:0006305	DNA alkylation	0.0136268075946318
GO:0006306	DNA methylation	0.0136268075946318
GO:0022402	cell cycle process	0.0158980673489082
GO:0006304	DNA modification	0.0159452447403155
GO:0046914	transition metal ion binding	0.0161135256749198
GO:0005657	replication fork	0.0175430415041266
GO:0009411	response to UV	0.0177610225540556
GO:0000082	G1/S transition of mitotic cell cycle	0.0179711408745799
GO:0016458	gene silencing	0.0197272102767894
GO:0005622	intracellular	0.0205585703501337
GO:0016585	chromatin remodeling complex	0.0205585703501337
GO:0043414	biopolymer methylation	0.0221816836641472
GO:0003678	DNA helicase activity	0.023750440581921
GO:0007059	chromosome segregation	0.0281155259347484
GO:0040029	regulation of gene expression, epigenetic	0.0304696161599306
GO:0032259	methylation	0.0326956260140766
GO:0004527	exonuclease activity	0.0326956260140766
GO:0009653	anatomical structure morphogenesis	0.0333618840509839
GO:0016740	transferase activity	0.0350776076463905
GO:0009416	response to light stimulus	0.0350776076463905
GO:0043169	cation binding	0.0350776076463905
GO:0008757	S-adenosylmethionine-dependent methyltransferase activity	0.0362262712413766
GO:0046872	metal ion binding	0.0411364456418694
GO:0009314	response to radiation	0.0413173911846125
GO:0043167	ion binding	0.0425175439882766

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	2.02e-14	253
migratory neural crest cell	9.42e-07	41

Disease

Ontology term	p-value	n
cancer	1.26e-44	235
disease of cellular proliferation	1.23e-42	239
hematologic cancer	4.11e-25	51
immune system cancer	4.11e-25	51
organ system cancer	1.31e-22	137
leukemia	5.06e-22	39
cell type cancer	1.20e-21	143
myeloid leukemia	1.64e-18	31
carcinoma	1.05e-17	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
ATF3#467	3	8.42369044725328	0.00417116638960993	0.0198701170664327
BRCA1#672	5	12.6151441520149	1.47177326411908e-05	0.000349342108934846
CCNT2#905	8	6.33620157696263	3.84606837428661e-07	1.87437953776071e-05
CHD2#1106	6	7.75801712558764	1.92157406469162e-05	0.000434200073003738
E2F1#1869	8	4.90738921487932	2.97124777369457e-06	0.000101443003019577
E2F4#1874	8	12.6680603152844	1.5050509647149e-09	1.3332147387944e-07
E2F6#1876	8	5.01715573169739	2.48928731545241e-06	8.77713294863383e-05
EGR1#1958	7	4.36465670795887	8.58120841941444e-05	0.00128581467161438
ELF1#1997	8	4.25809795880754	9.24826870984006e-06	0.000246397942802803
HEY1#23462	8	4.04011104310571	1.4081650274634e-05	0.000338864855537443
HMGN3#9324	5	5.11159232709412	0.00110951597588993	0.00770764527111667
IRF1#3659	8	7.6371637535639	8.63190100943299e-08	5.12802678910223e-06
IRF3#3661	2	11.7454880528724	0.0116448804945314	0.0425297130356821
MAX#4149	6	4.83941663175534	0.000291750431370536	0.0030965572461288
MXI1#4601	5	6.22598226797456	0.000439395490353943	0.00409403386716705
MYC#4609	7	4.56949663765823	6.28392411465611e-05	0.00102641030749229
NFYA#4800	3	6.90959276243645	0.00727972723713068	0.030121129627142
NFYB#4801	4	8.37989662676823	0.000729691402927855	0.00581609100437932
NRF1#4899	5	7.63142465481932	0.000166888299471845	0.00204525312233513
PAX5#5079	6	5.00217414838337	0.000241608451547577	0.00262874727275523
PBX3#5090	3	8.21794225752905	0.00447320658280844	0.0211660575526428
POLR2A#5430	8	2.14745317655807	0.00221072578897191	0.0127139862706188
RFX5#5993	4	6.02395541359755	0.0025264968061986	0.0139907104953645
SIN3A#25942	8	5.40888472681514	1.36410592556506e-06	5.34781752102437e-05
SP1#6667	8	5.6983813781409	8.98832477855329e-07	3.86150411989851e-05
SP2#6668	3	9.80757393519174	0.00270718466508561	0.0148855248624237
SRF#6722	4	6.8985891310839	0.00152207190456878	0.00970000412748713
TAF1#6872	8	3.34304628574529	6.40776711117462e-05	0.00104304985867202
TBP#6908	8	3.70677068709639	2.80450451364125e-05	0.000591836021216767
TFAP2A#7020	3	6.19448788989186	0.00986148386238029	0.0370462757851565
YY1#7528	6	3.68337806239039	0.00136063115499274	0.0089564450520791
ZNF143#7702	5	8.43804784514244	0.000103101732172918	0.00144167114826715

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.