Coexpression cluster:C258: Difference between revisions

Revision as of 18:25, 8 August 2012

Full id: C258_hepatoblastoma_hepatocellular_signet_colon_Intestinal_Prostate_gastric

Phase1 CAGE Peaks

Hg19::chr11:61768834..61768840,-	p@chr11:61768834..61768840 -
Hg19::chr11:7625242..7625246,+	p@chr11:7625242..7625246 +
Hg19::chr11:7626993..7627017,+	p9@PPFIBP2
Hg19::chr12:7023055..7023065,+	p30@ENO2
Hg19::chr14:69077243..69077269,-	p@chr14:69077243..69077269 -
Hg19::chr15:65670360..65670378,-	p2@IGDCC3
Hg19::chr17:65241888..65241898,-	p@chr17:65241888..65241898 -
Hg19::chr1:156338993..156339011,+	p1@RHBG
Hg19::chr1:156339014..156339028,+	p2@RHBG
Hg19::chr1:164559591..164559611,+	p@chr1:164559591..164559611 +
Hg19::chr1:182261598..182261603,-	p@chr1:182261598..182261603 -
Hg19::chr1:205902608..205902624,-	p@chr1:205902608..205902624 -
Hg19::chr1:236686717..236686738,+	p7@LGALS8
Hg19::chr1:26552077..26552092,+	p3@ENST00000451482 p3@uc001blq.2
Hg19::chr1:3237334..3237343,+	p@chr1:3237334..3237343 +
Hg19::chr20:3869562..3869580,+	p3@PANK2
Hg19::chr20:52750070..52750079,-	p@chr20:52750070..52750079 -
Hg19::chr20:58615689..58615712,+	p@chr20:58615689..58615712 +
Hg19::chr20:62667528..62667542,+	p1@LINC00176
Hg19::chr20:62667589..62667598,+	p9@LINC00176
Hg19::chr20:9313920..9313929,+	p@chr20:9313920..9313929 +
Hg19::chr20:9313938..9313946,+	p@chr20:9313938..9313946 +
Hg19::chr2:102172717..102172724,-	p@chr2:102172717..102172724 -
Hg19::chr2:171568483..171568494,-	p@chr2:171568483..171568494 -
Hg19::chr2:171568504..171568522,-	p@chr2:171568504..171568522 -
Hg19::chr2:171571909..171571920,+	p9@SP5
Hg19::chr2:171571931..171571959,+	p3@SP5
Hg19::chr2:171572699..171572713,+	p7@SP5
Hg19::chr2:171572729..171572745,+	p10@SP5
Hg19::chr2:171572786..171572840,+	p2@SP5
Hg19::chr2:178129619..178129633,-	p16@NFE2L2
Hg19::chr2:219925416..219925419,-	p2@IHH
Hg19::chr2:242750139..242750158,-	p3@D55640
Hg19::chr2:242750321..242750334,+	p4@NEU4
Hg19::chr3:132004251..132004258,-	p10@CPNE4
Hg19::chr3:197096551..197096578,+	p@chr3:197096551..197096578 +
Hg19::chr3:53878786..53878811,-	p4@CHDH
Hg19::chr6:19806783..19806789,-	p@chr6:19806783..19806789 -
Hg19::chr6:19839318..19839332,-	p@chr6:19839318..19839332 -
Hg19::chr6:34759206..34759244,+	p@chr6:34759206..34759244 +
Hg19::chr7:1017641..1017647,+	p@chr7:1017641..1017647 +
Hg19::chr7:150080907..150080914,-	p1@ENST00000497366
Hg19::chr7:155605098..155605105,-	p6@SHH
Hg19::chr7:20826171..20826190,-	p@chr7:20826171..20826190 -
Hg19::chr7:27180082..27180091,+	p2@LOC100133311
Hg19::chr7:44581054..44581057,+	p@chr7:44581054..44581057 +
Hg19::chr7:7222548..7222558,+	p@chr7:7222548..7222558 +
Hg19::chr8:144816195..144816210,-	p6@FAM83H
Hg19::chr9:132371144..132371159,+	p5@METTL11A
Hg19::chr9:132371162..132371181,+	p6@METTL11A
Hg19::chrX:132670045..132670060,-	p@chrX:132670045..132670060 -

Enriched pathways on this co-expression clusterSummary: 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. Analyst: Emmanuel Dimont link to source dataset data

p.value	FDR	nGenes	nPathway	Name
6.75939345257143e-05	0.0213934802773886	2	22	Hedgehog Signaling Pathway (Wikipathways):WP47
2.28911878907859e-05	0.0144901219348675	2	13	{SHH,13} (Static Module):NA

Enriched Gene Ontology terms on this co-expression clusterSummary: 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. Analyst: Erik Arner link to source dataset data

GO ID	GO name	FDR corrected p-value
GO:0030908	protein splicing	1.43290871993427e-05
GO:0005113	patched binding	1.43290871993427e-05
GO:0016539	intein-mediated protein splicing	1.43290871993427e-05
GO:0001569	patterning of blood vessels	0.000590135915578549
GO:0001649	osteoblast differentiation	0.0023106754995096
GO:0009880	embryonic pattern specification	0.0023106754995096
GO:0048754	branching morphogenesis of a tube	0.0023106754995096
GO:0001763	morphogenesis of a branching structure	0.00265112393578677
GO:0045597	positive regulation of cell differentiation	0.00512236837715217
GO:0045596	negative regulation of cell differentiation	0.00671357578165101
GO:0051094	positive regulation of developmental process	0.00671357578165101
GO:0051093	negative regulation of developmental process	0.00671357578165101
GO:0045581	negative regulation of T cell differentiation	0.00671357578165101
GO:0060020	Bergmann glial cell differentiation	0.00671357578165101
GO:0060019	radial glial cell differentiation	0.00671357578165101
GO:0007227	signal transduction downstream of smoothened	0.00671357578165101
GO:0008812	choline dehydrogenase activity	0.00671357578165101
GO:0032435	negative regulation of proteasomal ubiquitin-dependent protein catabolic process	0.00671357578165101
GO:0046639	negative regulation of alpha-beta T cell differentiation	0.00671357578165101
GO:0007228	activation of hh target transcription factor	0.00671357578165101
GO:0046636	negative regulation of alpha-beta T cell activation	0.00671357578165101
GO:0035239	tube morphogenesis	0.00671357578165101
GO:0001503	ossification	0.00675309757192503
GO:0031214	biomineral formation	0.00675309757192503
GO:0046849	bone remodeling	0.00771175918377515
GO:0016485	protein processing	0.00788417781018163
GO:0048771	tissue remodeling	0.00789246122939799
GO:0005615	extracellular space	0.00789246122939799
GO:0035295	tube development	0.00789246122939799
GO:0043587	tongue morphogenesis	0.00789246122939799
GO:0046637	regulation of alpha-beta T cell differentiation	0.00789246122939799
GO:0043586	tongue development	0.00789246122939799
GO:0007435	salivary gland morphogenesis	0.00789246122939799
GO:0022612	gland morphogenesis	0.00789246122939799
GO:0043237	laminin-1 binding	0.00789246122939799
GO:0021978	telencephalon regionalization	0.00789246122939799
GO:0032332	positive regulation of chondrocyte differentiation	0.00789246122939799
GO:0007389	pattern specification process	0.00844294278441691
GO:0001525	angiogenesis	0.00864675372337077
GO:0045944	positive regulation of transcription from RNA polymerase II promoter	0.00864675372337077
GO:0045595	regulation of cell differentiation	0.00864675372337077
GO:0030850	prostate gland development	0.00864675372337077
GO:0045666	positive regulation of neuron differentiation	0.00864675372337077
GO:0021937	Purkinje cell-granule cell precursor cell signaling involved in regulation of granule cell precursor cell proliferation	0.00864675372337077
GO:0032434	regulation of proteasomal ubiquitin-dependent protein catabolic process	0.00864675372337077
GO:0043236	laminin binding	0.00864675372337077
GO:0021938	smoothened signaling pathway in regulation of granule cell precursor cell proliferation	0.00864675372337077
GO:0008519	ammonium transmembrane transporter activity	0.00864675372337077
GO:0007418	ventral midline development	0.00864675372337077
GO:0015696	ammonium transport	0.00864675372337077
GO:0006366	transcription from RNA polymerase II promoter	0.00864675372337077
GO:0048514	blood vessel morphogenesis	0.00864675372337077
GO:0048646	anatomical structure formation	0.00871448100720144
GO:0001568	blood vessel development	0.00871448100720144
GO:0001944	vasculature development	0.00871448100720144
GO:0007439	ectodermal gut development	0.00871448100720144
GO:0045620	negative regulation of lymphocyte differentiation	0.00871448100720144
GO:0021513	spinal cord dorsal/ventral patterning	0.00871448100720144
GO:0002052	positive regulation of neuroblast proliferation	0.00871448100720144
GO:0021871	forebrain regionalization	0.00871448100720144
GO:0050840	extracellular matrix binding	0.00871448100720144
GO:0007442	hindgut morphogenesis	0.00871448100720144
GO:0032330	regulation of chondrocyte differentiation	0.00871448100720144
GO:0046634	regulation of alpha-beta T cell activation	0.00871448100720144
GO:0048567	ectodermal gut morphogenesis	0.00871448100720144
GO:0007431	salivary gland development	0.00871448100720144
GO:0002076	osteoblast development	0.00871448100720144
GO:0048547	gut morphogenesis	0.00923709333081289
GO:0048546	digestive tract morphogenesis	0.00923709333081289
GO:0021930	granule cell precursor proliferation	0.00923709333081289
GO:0021940	positive regulation of granule cell precursor proliferation	0.00923709333081289
GO:0004308	exo-alpha-sialidase activity	0.00923709333081289
GO:0004594	pantothenate kinase activity	0.00923709333081289
GO:0048678	response to axon injury	0.00923709333081289
GO:0021534	cell proliferation in hindbrain	0.00923709333081289
GO:0016997	alpha-sialidase activity	0.00923709333081289
GO:0021511	spinal cord patterning	0.00923709333081289
GO:0021924	cell proliferation in the external granule layer	0.00923709333081289
GO:0021936	regulation of granule cell precursor proliferation	0.00923709333081289
GO:0042177	negative regulation of protein catabolic process	0.0109443447133047
GO:0001501	skeletal development	0.0111212779342219
GO:0015937	coenzyme A biosynthetic process	0.0120391285321079
GO:0030856	regulation of epithelial cell differentiation	0.0120391285321079
GO:0031069	hair follicle morphogenesis	0.0120391285321079
GO:0045893	positive regulation of transcription, DNA-dependent	0.0120391285321079
GO:0008284	positive regulation of cell proliferation	0.012548959196457
GO:0009790	embryonic development	0.012548959196457
GO:0050793	regulation of developmental process	0.012548959196457
GO:0035272	exocrine system development	0.012548959196457
GO:0014003	oligodendrocyte development	0.012548959196457
GO:0042130	negative regulation of T cell proliferation	0.012548959196457
GO:0030901	midbrain development	0.012548959196457
GO:0042733	embryonic digit morphogenesis	0.012548959196457
GO:0044421	extracellular region part	0.0129107769170461
GO:0009895	negative regulation of catabolic process	0.0133953229826029
GO:0002062	chondrocyte differentiation	0.0133953229826029
GO:0030539	male genitalia development	0.0133953229826029
GO:0015695	organic cation transport	0.0133953229826029
GO:0015101	organic cation transmembrane transporter activity	0.0138894019342398
GO:0001755	neural crest cell migration	0.0138894019342398
GO:0000015	phosphopyruvate hydratase complex	0.0138894019342398
GO:0001658	ureteric bud branching	0.0138894019342398
GO:0045580	regulation of T cell differentiation	0.0138894019342398
GO:0021510	spinal cord development	0.0138894019342398
GO:0004634	phosphopyruvate hydratase activity	0.0138894019342398
GO:0045941	positive regulation of transcription	0.0140700865705134
GO:0005737	cytoplasm	0.0140700865705134
GO:0048565	gut development	0.0140700865705134
GO:0050868	negative regulation of T cell activation	0.0140700865705134
GO:0015936	coenzyme A metabolic process	0.0140700865705134
GO:0050672	negative regulation of lymphocyte proliferation	0.0140700865705134
GO:0008209	androgen metabolic process	0.0140700865705134
GO:0048709	oligodendrocyte differentiation	0.0140700865705134
GO:0032945	negative regulation of mononuclear cell proliferation	0.0140700865705134
GO:0045935	positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	0.0147871953746878
GO:0048806	genitalia development	0.0150823246680163
GO:0044424	intracellular part	0.0156492155543383
GO:0009888	tissue development	0.0159249293429539
GO:0021782	glial cell development	0.0159249293429539
GO:0014032	neural crest cell development	0.0165897615557974
GO:0007224	smoothened signaling pathway	0.0165897615557974
GO:0048663	neuron fate commitment	0.0165897615557974
GO:0014033	neural crest cell differentiation	0.0165897615557974
GO:0001708	cell fate specification	0.0176288057379137
GO:0019866	organelle inner membrane	0.01772162535577
GO:0051146	striated muscle cell differentiation	0.0179335409506194
GO:0001839	neural plate morphogenesis	0.0179335409506194
GO:0045619	regulation of lymphocyte differentiation	0.0179335409506194
GO:0046632	alpha-beta T cell differentiation	0.0179335409506194
GO:0001841	neural tube formation	0.0179335409506194
GO:0030162	regulation of proteolysis	0.0180781453938118
GO:0001840	neural plate development	0.0180781453938118
GO:0007405	neuroblast proliferation	0.0180781453938118
GO:0008907	integrase activity	0.0180781453938118
GO:0042176	regulation of protein catabolic process	0.0180781453938118
GO:0015485	cholesterol binding	0.0180781453938118
GO:0001838	embryonic epithelial tube formation	0.0180781453938118
GO:0050679	positive regulation of epithelial cell proliferation	0.0181778094461828
GO:0022404	molting cycle process	0.0181778094461828
GO:0001942	hair follicle development	0.0181778094461828
GO:0022405	hair cycle process	0.0181778094461828
GO:0042633	hair cycle	0.0181778094461828
GO:0042303	molting cycle	0.0181778094461828
GO:0001570	vasculogenesis	0.0181778094461828
GO:0009887	organ morphogenesis	0.0181778094461828
GO:0031325	positive regulation of cellular metabolic process	0.0182057151642484
GO:0001657	ureteric bud development	0.0182057151642484
GO:0021915	neural tube development	0.0182057151642484
GO:0042475	odontogenesis of dentine-containing teeth	0.0182057151642484
GO:0046631	alpha-beta T cell activation	0.0182057151642484
GO:0030336	negative regulation of cell migration	0.0182057151642484
GO:0051250	negative regulation of lymphocyte activation	0.0182057151642484
GO:0048568	embryonic organ development	0.0190358556751456
GO:0009893	positive regulation of metabolic process	0.0198696412915676
GO:0016331	morphogenesis of embryonic epithelium	0.0206631744665421
GO:0051271	negative regulation of cell motility	0.0211891200991955
GO:0030902	hindbrain development	0.0211891200991955
GO:0043161	proteasomal ubiquitin-dependent protein catabolic process	0.0211891200991955
GO:0040013	negative regulation of locomotion	0.0215612788377167
GO:0014031	mesenchymal cell development	0.0215612788377167
GO:0048762	mesenchymal cell differentiation	0.0215612788377167
GO:0001656	metanephros development	0.0215612788377167
GO:0006357	regulation of transcription from RNA polymerase II promoter	0.021851444770121
GO:0042476	odontogenesis	0.0220480644954898
GO:0009894	regulation of catabolic process	0.0220480644954898
GO:0046546	development of primary male sexual characteristics	0.0226520442942366
GO:0045664	regulation of neuron differentiation	0.0226520442942366
GO:0006066	alcohol metabolic process	0.0232414760306504
GO:0032934	sterol binding	0.0232414760306504
GO:0009953	dorsal/ventral pattern formation	0.0239569694659131
GO:0010001	glial cell differentiation	0.0246638449621801
GO:0042127	regulation of cell proliferation	0.0250707327498834
GO:0051091	positive regulation of transcription factor activity	0.0250707327498834
GO:0050678	regulation of epithelial cell proliferation	0.0250707327498834
GO:0044464	cell part	0.0256034667782936
GO:0015074	DNA integration	0.0256082661952266
GO:0044444	cytoplasmic part	0.0260858782406668
GO:0046661	male sex differentiation	0.0261334806487915
GO:0030326	embryonic limb morphogenesis	0.0264995669898537
GO:0035113	embryonic appendage morphogenesis	0.0264995669898537
GO:0050673	epithelial cell proliferation	0.0264995669898537
GO:0043010	camera-type eye development	0.0270002244300642
GO:0042129	regulation of T cell proliferation	0.0270002244300642
GO:0001822	kidney development	0.0278478952098251
GO:0042063	gliogenesis	0.0278478952098251
GO:0051216	cartilage development	0.0278478952098251
GO:0030855	epithelial cell differentiation	0.0278478952098251
GO:0044265	cellular macromolecule catabolic process	0.0278478952098251
GO:0060173	limb development	0.0278478952098251
GO:0035107	appendage morphogenesis	0.0278478952098251
GO:0035108	limb morphogenesis	0.0278478952098251
GO:0048589	developmental growth	0.0278478952098251
GO:0048736	appendage development	0.0278478952098251
GO:0042098	T cell proliferation	0.0291932955248312
GO:0001655	urogenital system development	0.0297839142040696
GO:0030217	T cell differentiation	0.0303682890953978
GO:0032944	regulation of mononuclear cell proliferation	0.0306354950844985
GO:0050670	regulation of lymphocyte proliferation	0.0306354950844985
GO:0030324	lung development	0.0306354950844985
GO:0030323	respiratory tube development	0.0312034992921382
GO:0005622	intracellular	0.0312278993165916
GO:0048469	cell maturation	0.0323220049963033
GO:0030900	forebrain development	0.032393950708822
GO:0045121	lipid raft	0.032393950708822
GO:0042692	muscle cell differentiation	0.032393950708822
GO:0048732	gland development	0.032393950708822
GO:0001654	eye development	0.0329334309438586
GO:0031967	organelle envelope	0.0357199774192478
GO:0031975	envelope	0.0357199774192478
GO:0009057	macromolecule catabolic process	0.0357199774192478
GO:0051090	regulation of transcription factor activity	0.0357199774192478
GO:0032943	mononuclear cell proliferation	0.0358912475091553
GO:0046651	lymphocyte proliferation	0.0358912475091553
GO:0021700	developmental maturation	0.0358912475091553
GO:0007267	cell-cell signaling	0.0365271080616658
GO:0048730	epidermis morphogenesis	0.0367199227902124
GO:0009952	anterior/posterior pattern formation	0.0367199227902124
GO:0006355	regulation of transcription, DNA-dependent	0.0368192780603154
GO:0007411	axon guidance	0.0370406749543051
GO:0050863	regulation of T cell activation	0.0388304880886745
GO:0045137	development of primary sexual characteristics	0.0390393505072002
GO:0030334	regulation of cell migration	0.0390393505072002
GO:0006351	transcription, DNA-dependent	0.0390393505072002
GO:0032774	RNA biosynthetic process	0.0390575131274154
GO:0002009	morphogenesis of an epithelium	0.0405178409584665
GO:0030098	lymphocyte differentiation	0.0409728326599113
GO:0051270	regulation of cell motility	0.0439469432088522
GO:0045165	cell fate commitment	0.045009205564013
GO:0048729	tissue morphogenesis	0.0452313172019513
GO:0040012	regulation of locomotion	0.0452313172019513
GO:0008283	cell proliferation	0.0452313172019513
GO:0040011	locomotion	0.0454658312192687
GO:0045449	regulation of transcription	0.0458650075863592
GO:0051249	regulation of lymphocyte activation	0.046909049259456
GO:0044237	cellular metabolic process	0.046986142197881
GO:0019219	regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	0.0477818211711771
GO:0050865	regulation of cell activation	0.0487242778783049
GO:0007548	sex differentiation	0.0491188347581561

Enriched sample ontology terms on this co-expression clusterSummary: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. Analyst: Hideya Kawaji links to source dataset uberon_data disease_data

Uber Anatomy
Ontology term	p-value	n
subdivision of digestive tract	6.77e-13	129
endodermal part of digestive tract	6.77e-13	129
digestive system	5.40e-12	155
digestive tract	5.40e-12	155
primitive gut	5.40e-12	155
endoderm-derived structure	1.28e-11	169
endoderm	1.28e-11	169
presumptive endoderm	1.28e-11	169
gastrointestinal system	5.41e-11	35
organ	1.50e-09	511
mixed endoderm/mesoderm-derived structure	2.22e-09	130
intestine	3.72e-09	27
embryo	4.56e-08	612
endo-epithelium	8.15e-08	82
multi-cellular organism	9.68e-08	659
foregut	2.46e-07	98
adult organism	7.10e-07	115

Disease
Ontology term	p-value	n
carcinoma	9.49e-20	106
cell type cancer	1.40e-17	143
cancer	2.85e-13	235
disease of cellular proliferation	3.87e-12	239
adenocarcinoma	4.07e-08	25

Overrepresented TFBS (DNA) motifs on this co-expression clusterSummary: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. Analyst: Michiel de Hoon link to source data Novel motifs data Jaspar motifs data

Novel motifs

JASPAR motifs

Motifs	-log10(p-value)
{{{tfbs_overrepresentation_jaspar}}}

ENCODE TF ChIP-seq peak enrichment analysisSummary: 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. Analyst: Erik Arner link to source dataset data

No analysis results for this cluster

Relative expression of the co-expression clusterSummary:Co-expression clusters are compared against FANTOM5 samples to obtain relative expression. Analyst:NA link to data source data

"{{{coexpression_dpi_cluster_scores_median}}}" is not a number.

@@ Line 7: / Line 7: @@
 |ontology_enrichment_uberon=UBERON:0004921!6.77e-13!129;UBERON:0004185!6.77e-13!129;UBERON:0001007!5.40e-12!155;UBERON:0001555!5.40e-12!155;UBERON:0007026!5.40e-12!155;UBERON:0004119!1.28e-11!169;UBERON:0000925!1.28e-11!169;UBERON:0006595!1.28e-11!169;UBERON:0005409!5.41e-11!35;UBERON:0000062!1.50e-09!511;UBERON:0000077!2.22e-09!130;UBERON:0000160!3.72e-09!27;UBERON:0000922!4.56e-08!612;UBERON:0005911!8.15e-08!82;UBERON:0000468!9.68e-08!659;UBERON:0001041!2.46e-07!98;UBERON:0007023!7.10e-07!115
 |pathway_enrichment=6.75939345257143e-05;0.0213934802773886;2;22;Hedgehog Signaling Pathway (Wikipathways):WP47!2.28911878907859e-05;0.0144901219348675;2;13;{SHH,13} (Static Module):NA
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 }}

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Coexpression cluster:C258: Difference between revisions

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Revision as of 18:25, 8 August 2012

Phase1 CAGE Peaks

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