Coexpression cluster:C1145

Full id: C1145_Hodgkin_chronic_acute_Reticulocytes_lymphoma_diffuse_Hep2

Phase1 CAGE Peaks

Hg19::chr11:61560348..61560419,+	p1@FEN1
Hg19::chr11:65029421..65029459,+	p1@POLA2
Hg19::chr15:48624350..48624425,+	p1@DUT
Hg19::chr20:5100567..5100581,-	p2@PCNA
Hg19::chr20:5100591..5100611,-	p1@PCNA
Hg19::chr6:31126291..31126399,+	p1@TCF19
Hg19::chrX:48555110..48555164,+	p1@SUV39H1

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
0.000180580969984339	0.0127008615555652	2	100	Pyrimidine metabolism (KEGG):00240
3.67416886898525e-08	1.16287444703383e-05	3	36	DNA replication (KEGG):03030
2.05925492603147e-05	0.00260701673635584	2	34	Base excision repair (KEGG):03410
8.58329659590162e-05	0.00679153343150715	2	69	G1 to S cell cycle control (Wikipathways):WP45
3.15809823992966e-05	0.00285582312267925	2	42	DNA Replication (Wikipathways):WP1806
0.000206748318674481	0.0130871685720946	2	107	DNA Repair (Reactome):REACT_216
6.67157721853038e-06	0.00105577709483243	3	200	DNA Replication (Reactome):REACT_383
2.59719623007301e-05	0.00274004202272702	3	315	Cell Cycle, Mitotic (Reactome):REACT_152
3.75206069989847e-07	7.91684807678577e-05	3	77	Chromosome Maintenance (Reactome):REACT_22172
3.07978931231787e-08	1.16287444703383e-05	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:0006260	DNA replication	3.23493187209283e-05
GO:0006259	DNA metabolic process	3.62539169331596e-05
GO:0005657	replication fork	0.00080180884438166
GO:0006139	nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	0.00100012752440769
GO:0003887	DNA-directed DNA polymerase activity	0.00100012752440769
GO:0005634	nucleus	0.00100012752440769
GO:0044427	chromosomal part	0.00131180468070354
GO:0005694	chromosome	0.00175265536069073
GO:0000228	nuclear chromosome	0.00235908563354695
GO:0043283	biopolymer metabolic process	0.00235908563354695
GO:0017108	5'-flap endonuclease activity	0.00235908563354695
GO:0043626	PCNA complex	0.00235908563354695
GO:0004170	dUTP diphosphatase activity	0.00235908563354695
GO:0030337	DNA polymerase processivity factor activity	0.00235908563354695
GO:0048015	phosphoinositide-mediated signaling	0.00264897946591783
GO:0043231	intracellular membrane-bound organelle	0.00300225166600379
GO:0043227	membrane-bound organelle	0.00300225166600379
GO:0047429	nucleoside-triphosphate diphosphatase activity	0.00300225166600379
GO:0048256	flap endonuclease activity	0.00300225166600379
GO:0006287	base-excision repair, gap-filling	0.00300225166600379
GO:0046974	histone lysine N-methyltransferase activity (H3-K9 specific)	0.00300225166600379
GO:0008309	double-stranded DNA specific exodeoxyribonuclease activity	0.00300225166600379
GO:0044428	nuclear part	0.00507998581710691
GO:0016779	nucleotidyltransferase activity	0.00507998581710691
GO:0005652	nuclear lamina	0.00507998581710691
GO:0008409	5'-3' exonuclease activity	0.00507998581710691
GO:0032405	MutLalpha complex binding	0.00608285954516829
GO:0019932	second-messenger-mediated signaling	0.00608285954516829
GO:0043229	intracellular organelle	0.0063152511564931
GO:0043226	organelle	0.0063152511564931
GO:0009650	UV protection	0.00639000930182787
GO:0005663	DNA replication factor C complex	0.00684683280567824
GO:0005658	alpha DNA polymerase:primase complex	0.00684683280567824
GO:0043170	macromolecule metabolic process	0.00684683280567824
GO:0016895	exodeoxyribonuclease activity, producing 5'-phosphomonoesters	0.00686030240274865
GO:0000307	cyclin-dependent protein kinase holoenzyme complex	0.00686030240274865
GO:0032404	mismatch repair complex binding	0.00686030240274865
GO:0004529	exodeoxyribonuclease activity	0.00686030240274865
GO:0003677	DNA binding	0.00686030240274865
GO:0046080	dUTP metabolic process	0.0074267459690403
GO:0006281	DNA repair	0.0088115876286842
GO:0009200	deoxyribonucleoside triphosphate metabolic process	0.0100477932531831
GO:0009211	pyrimidine deoxyribonucleoside triphosphate metabolic process	0.0100477932531831
GO:0000287	magnesium ion binding	0.0100477932531831
GO:0006974	response to DNA damage stimulus	0.0100477932531831
GO:0009120	deoxyribonucleoside metabolic process	0.0100477932531831
GO:0043601	nuclear replisome	0.0100477932531831
GO:0030894	replisome	0.0100477932531831
GO:0046125	pyrimidine deoxyribonucleoside metabolic process	0.0100477932531831
GO:0044237	cellular metabolic process	0.0100477932531831
GO:0044238	primary metabolic process	0.0101510033057196
GO:0016888	endodeoxyribonuclease activity, producing 5'-phosphomonoesters	0.0101510033057196
GO:0043596	nuclear replication fork	0.0105811634345431
GO:0044424	intracellular part	0.0106570737760598
GO:0006213	pyrimidine nucleoside metabolic process	0.0113942924920784
GO:0006886	intracellular protein transport	0.0114259662429928
GO:0009719	response to endogenous stimulus	0.0114259662429928
GO:0009219	pyrimidine deoxyribonucleotide metabolic process	0.0118930548377811
GO:0016796	exonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters	0.0118930548377811
GO:0004523	ribonuclease H activity	0.0118930548377811
GO:0000060	protein import into nucleus, translocation	0.0118930548377811
GO:0018024	histone-lysine N-methyltransferase activity	0.0139067156443542
GO:0016278	lysine N-methyltransferase activity	0.0139067156443542
GO:0016279	protein-lysine N-methyltransferase activity	0.0139067156443542
GO:0006275	regulation of DNA replication	0.0141988607925667
GO:0000781	chromosome, telomeric region	0.0150233136872658
GO:0000794	condensed nuclear chromosome	0.0150233136872658
GO:0009262	deoxyribonucleotide metabolic process	0.0150233136872658
GO:0004520	endodeoxyribonuclease activity	0.0152820594469177
GO:0009411	response to UV	0.0155333432796311
GO:0005515	protein binding	0.0157953884552327
GO:0042054	histone methyltransferase activity	0.0157953884552327
GO:0006284	base-excision repair	0.0157953884552327
GO:0006302	double-strand break repair	0.0160259561931682
GO:0008283	cell proliferation	0.016940445835313
GO:0016891	endoribonuclease activity, producing 5'-phosphomonoesters	0.0173199076507755
GO:0005622	intracellular	0.0173199076507755
GO:0008276	protein methyltransferase activity	0.0198242929997908
GO:0051052	regulation of DNA metabolic process	0.0198242929997908
GO:0003684	damaged DNA binding	0.0198242929997908
GO:0008170	N-methyltransferase activity	0.0198242929997908
GO:0009147	pyrimidine nucleoside triphosphate metabolic process	0.0198242929997908
GO:0004536	deoxyribonuclease activity	0.0198242929997908
GO:0015031	protein transport	0.0198951299519024
GO:0000793	condensed chromosome	0.0198951299519024
GO:0009116	nucleoside metabolic process	0.0198951299519024
GO:0016893	endonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters	0.0207964623323496
GO:0046907	intracellular transport	0.0212665692053063
GO:0045184	establishment of protein localization	0.0213738883507893
GO:0043232	intracellular non-membrane-bound organelle	0.0213738883507893
GO:0043228	non-membrane-bound organelle	0.0213738883507893
GO:0008104	protein localization	0.0225955583078951
GO:0044454	nuclear chromosome part	0.0236785144343018
GO:0006220	pyrimidine nucleotide metabolic process	0.0241223676371893
GO:0033036	macromolecule localization	0.0241693364343283
GO:0004527	exonuclease activity	0.024387293458585
GO:0004521	endoribonuclease activity	0.024387293458585
GO:0003676	nucleic acid binding	0.0256838301287325
GO:0016740	transferase activity	0.0263206029691129
GO:0009416	response to light stimulus	0.0263206029691129
GO:0016043	cellular component organization and biogenesis	0.0263206029691129
GO:0051649	establishment of cellular localization	0.0263206029691129
GO:0051641	cellular localization	0.0271406759701018
GO:0008757	S-adenosylmethionine-dependent methyltransferase activity	0.0271406759701018
GO:0006606	protein import into nucleus	0.029831475488504
GO:0051170	nuclear import	0.029831475488504
GO:0046872	metal ion binding	0.029831475488504
GO:0004540	ribonuclease activity	0.029831475488504
GO:0006950	response to stress	0.029831475488504
GO:0009314	response to radiation	0.029831475488504
GO:0032403	protein complex binding	0.029831475488504
GO:0046982	protein heterodimerization activity	0.0305734825634199
GO:0043167	ion binding	0.0305734825634199
GO:0003690	double-stranded DNA binding	0.0310435675766427
GO:0019219	regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	0.0328864569882111
GO:0003682	chromatin binding	0.033308670484058
GO:0017038	protein import	0.034133394260944
GO:0031323	regulation of cellular metabolic process	0.0375000074527852
GO:0030145	manganese ion binding	0.0400260820590306
GO:0009141	nucleoside triphosphate metabolic process	0.0400260820590306
GO:0004519	endonuclease activity	0.0406235751363442
GO:0044446	intracellular organelle part	0.0406235751363442
GO:0006913	nucleocytoplasmic transport	0.0406235751363442
GO:0044422	organelle part	0.0406235751363442
GO:0051169	nuclear transport	0.0406235751363442
GO:0019222	regulation of metabolic process	0.0406235751363442
GO:0043566	structure-specific DNA binding	0.0408711770132874
GO:0006261	DNA-dependent DNA replication	0.0417374929281751
GO:0009628	response to abiotic stimulus	0.0417374929281751
GO:0005635	nuclear envelope	0.0485919622754928

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>

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Cell Type

Ontology term	p-value	n
animal cell	6.15e-22	679
eukaryotic cell	6.15e-22	679
epithelial cell	1.36e-17	253
native cell	2.19e-16	722
embryonic cell	2.06e-09	250
migratory neural crest cell	8.97e-08	41

Uber Anatomy

Ontology term	p-value	n
larynx	1.62e-07	9

Disease

Ontology term	p-value	n
cancer	1.75e-36	235
disease of cellular proliferation	9.23e-36	239
hematologic cancer	1.38e-19	51
immune system cancer	1.38e-19	51
organ system cancer	5.10e-19	137
leukemia	2.18e-15	39
cell type cancer	4.47e-15	143
carcinoma	6.17e-14	106
myeloid leukemia	2.58e-11	31

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)
MA0003.1	1.35295
MA0004.1	0.502801
MA0006.1	1.62096
MA0007.1	0.483857
MA0009.1	0.973289
MA0014.1	0.367415
MA0017.1	0.380797
MA0019.1	0.652951
MA0024.1	3.33297
MA0025.1	1.10816
MA0027.1	2.59001
MA0028.1	0.35747
MA0029.1	0.886702
MA0030.1	0.875089
MA0031.1	0.809638
MA0038.1	0.60704
MA0040.1	0.892629
MA0041.1	0.521615
MA0042.1	0.48922
MA0043.1	0.973609
MA0046.1	0.962263
MA0048.1	0.120314
MA0050.1	0.490116
MA0051.1	0.602745
MA0052.1	0.896548
MA0055.1	0.649431
MA0056.1	0
MA0057.1	0.744639
MA0058.1	1.04727
MA0059.1	0.404929
MA0060.1	1.86058
MA0061.1	0.198335
MA0063.1	0
MA0066.1	0.607474
MA0067.1	1.29359
MA0068.1	2.88764
MA0069.1	0.958358
MA0070.1	0.947018
MA0071.1	0.567661
MA0072.1	0.942461
MA0073.1	4.03024
MA0074.1	0.60198
MA0076.1	0.422297
MA0077.1	0.934645
MA0078.1	0.703614
MA0081.1	0.405093
MA0083.1	0.980893
MA0084.1	1.48179
MA0087.1	0.939982
MA0088.1	0.252594
MA0089.1	0
MA0090.1	0.436918
MA0091.1	0.505453
MA0092.1	0.467172
MA0093.1	0.9112
MA0095.1	0
MA0098.1	0
MA0100.1	0.621149
MA0101.1	0.918548
MA0103.1	0.332048
MA0105.1	0.104569
MA0106.1	5.14579
MA0107.1	0.752965
MA0108.2	0.806528
MA0109.1	0
MA0111.1	1.14351
MA0113.1	0.665691
MA0114.1	0.269076
MA0115.1	1.21667
MA0116.1	0.760835
MA0117.1	1.01134
MA0119.1	1.00897
MA0122.1	1.03753
MA0124.1	1.17486
MA0125.1	1.0901
MA0130.1	0
MA0131.1	1.71579
MA0132.1	0
MA0133.1	0
MA0135.1	1.00402
MA0136.1	0.614215
MA0139.1	0.547495
MA0140.1	0.564957
MA0141.1	0.403171
MA0142.1	0.777365
MA0143.1	0.66587
MA0144.1	0.254954
MA0145.1	0.276317
MA0146.1	0.547931
MA0147.1	1.40486
MA0148.1	0.528066
MA0149.1	0.555119
MA0062.2	0.563664
MA0035.2	0.564239
MA0039.2	1.82845
MA0138.2	0.704862
MA0002.2	0.213296
MA0137.2	0.36398
MA0104.2	1.19136
MA0047.2	0.636643
MA0112.2	0.944394
MA0065.2	0.0828768
MA0150.1	0.430951
MA0151.1	0
MA0152.1	0.571637
MA0153.1	1.07307
MA0154.1	0.335384
MA0155.1	0.250175
MA0156.1	0.36627
MA0157.1	0.749547
MA0158.1	0
MA0159.1	0.281681
MA0160.1	0.543522
MA0161.1	0
MA0162.1	1.55314
MA0163.1	1.72058
MA0164.1	0.678332
MA0080.2	0.344472
MA0018.2	1.56673
MA0099.2	0.572
MA0079.2	1.1389
MA0102.2	1.51913
MA0258.1	0.245543
MA0259.1	0.787775
MA0442.1	0

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	8.65038456138161	0.00365929333120223	0.0184731697707574
CCNT2#905	6	5.43102992311083	9.35028339706757e-05	0.00135780623985865
E2F1#1869	7	4.90738921487932	1.45832274679793e-05	0.000346701045647232
E2F4#1874	7	12.6680603152844	1.90745058834676e-08	1.36633903975547e-06
E2F6#1876	7	5.01715573169739	1.24910426162553e-05	0.000308040613884082
EGR1#1958	6	4.27558208126583	0.000376213061986645	0.0037359813616833
ELF1#1997	5	3.04149854200538	0.00971956226937075	0.0365604669134094
GABPB1#2553	4	4.03867647781838	0.0098011349469615	0.0368434198152004
GATA1#2623	3	5.81156063305733	0.0111931160082029	0.0411256936774213
GTF2B#2959	3	13.6902128289961	0.000976196317024572	0.0070152733195988
HDAC2#3066	3	5.74955152998268	0.0115304170404053	0.0421691783199528
HEY1#23462	7	4.04011104310571	5.68979821988558e-05	0.000949563496782727
HMGN3#9324	5	5.84181980239328	0.000462918719129959	0.00426300750438354
HNF4A#3172	3	9.91383872698015	0.00247865482166154	0.0139213891325361
IRF1#3659	6	6.54614036019763	3.13027310449255e-05	0.000631734478763474
MAX#4149	5	4.60896822071937	0.00142433701403361	0.0091779573919457
MYC#4609	5	3.73020133686386	0.00382194422230669	0.0188692461299749
NFKB1#4790	5	3.9200453029956	0.00303658142448461	0.0161163495981171
NFYA#4800	4	10.528903257046	0.000265728718323708	0.00284436216183353
NFYB#4801	4	9.57702471630654	0.000383006171601648	0.00376017875126006
NRF1#4899	5	8.72162817693636	6.71450045004423e-05	0.00107324106596598
POLR2A#5430	7	2.14745317655807	0.00474763644761028	0.02232701742399
POU2F2#5452	4	5.20349946156716	0.00386671431017981	0.0190623448591394
PRDM1#639	2	37.6659873649888	0.001177328194587	0.00799837242662277
RFX5#5993	4	6.88452047268291	0.00135220703152858	0.00890267604903318
SIN3A#25942	7	5.40888472681514	7.3795239773719e-06	0.000211443101419134
SMARCB1#6598	4	10.4301233035185	0.000275586383300937	0.00293633608300006
SP1#6667	5	4.07027241295778	0.00254920612899158	0.014108236919387
SP2#6668	3	11.2086559259334	0.00174151533091611	0.0107165990835227
SREBF1#6720	3	20.1453640459236	0.000315801026139468	0.00323606194750587
SRF#6722	3	5.91307639807192	0.0106686813016745	0.0393900521959057
TAF1#6872	7	3.34304628574529	0.000214233631962245	0.0024646779344024
TAF7#6879	4	6.53318251709938	0.0016484941094751	0.0103106405736897
TBP#6908	7	3.70677068709639	0.000103967209750511	0.00145047173645921
YY1#7528	5	3.50797910703847	0.00507257067280898	0.0236126853493269

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.