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Coexpression cluster:C238: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.0949298,0.0742811,0.0885831,0.104742,0.0573716,0.253743,0.0426289,0.873292,1.09414,0.0015125,0.0186125,0.205231,0.0106854,0.993558,0.247836,1.66495,0.132728,0.822448,0.134736,0.59436,0.347095,0.0801686,0.242634,0.844294,0.27121,0.228315,0.776063,0.0222607,0.0594084,0.163915,0.183691,2.79322,0.0167639,0.29364,0.0922163,0.0254035,0.0102634,0.771712,1.99749,0.00128941,0.179985,0.164026,2.30855,0.404599,0.678258,0.0410822,0.165321,0.197598,2.61845,0.888483,0.0690758,0.0463841,0.0748475,0.197567,0.300571,0.644897,1.21132,0.306276,1.03301,0.0315884,0.175906,0.0436191,1.09838,0.118692,0.183984,0.684725,0.366782,0.677945,0.146783,0.535239,0.0111955,0.350191,0.00316141,0.299123,0.0251676,1.01641,0.888847,0.110499,2.02713,4.80721,0.0803975,0.118163,0.411069,0.0287212,0.262732,0.000739744,0.450686,0.785708,0.0791818,0.768443,0.441004,0.244321,0.48743,0.198965,0.133802,0.540816,0.468009,1.04656,0.0810479,0.646611,0.246787,0.158715,0.540339,0.134639,0.097094,0.0178552,0.126473,0.151276,0.0474206,0.00224124,0.590891,0.181895,0.084004,0.0895378,1.03878,1.19584,0.00436802,0.0149686,0.101237,1.19416,0.293153,0.269164,0.249769,0.755413,0.492871,0.724143,0.65074,0.164766,0.866428,0.129743,0.244786,0.911049,0.33505,1.60894,0.451542,0.206664,0.0142775,0.0223685,0.417082,1.20083,0.816928,0.387425,0.0413267,0.184785,0.0978805,0.293077,0.0905476,1.04698,0.320554,0.0487715,0.0915099,4.22851e-05,0.245043,0.430458,0.379387,0.561603,0.0728126,0.0487284,0.271318,0.00665748,0.38647,1.22477,0.444259,0.225877,0.10523,0.182908,0.0405383,0.371999,0.00172561
|tfbs_overrepresentation_jaspar=MA0003.1;8.14184e-06,MA0004.1;0.218793,MA0006.1;0.130484,MA0007.1;4.37775,MA0009.1;7.23395,MA0014.1;0.000293083,MA0017.1;0.786201,MA0019.1;0.210287,MA0024.1;0.153926,MA0025.1;0.3102,MA0027.1;1.67575,MA0028.1;0.0672484,MA0029.1;0.494881,MA0030.1;1.48766,MA0031.1;0.390791,MA0038.1;0.166846,MA0040.1;0.971444,MA0041.1;0.244832,MA0042.1;0.200853,MA0043.1;0.217679,MA0046.1;6.10396,MA0048.1;0.202882,MA0050.1;0.0173802,MA0051.1;0.0422086,MA0052.1;0.1706,MA0055.1;0.208604,MA0056.1;0,MA0057.1;0.0395139,MA0058.1;0.228214,MA0059.1;0.398553,MA0060.1;0.00202577,MA0061.1;0.490748,MA0063.1;0,MA0066.1;0.167234,MA0067.1;0.454522,MA0068.1;0.0161411,MA0069.1;0.207989,MA0070.1;0.200901,MA0071.1;0.133475,MA0072.1;0.19808,MA0073.1;1.28049e-07,MA0074.1;1.02737,MA0076.1;0.0439914,MA0077.1;0.563808,MA0078.1;0.946655,MA0081.1;0.62421,MA0083.1;2.60044,MA0084.1;2.5366,MA0087.1;1.08484,MA0088.1;0.230784,MA0089.1;0,MA0090.1;1.05431,MA0091.1;0.0885368,MA0092.1;0.0658034,MA0093.1;0.253397,MA0095.1;0,MA0098.1;0,MA0100.1;0.0475732,MA0101.1;1.5275,MA0103.1;0.574744,MA0105.1;0.205057,MA0106.1;0.206361,MA0107.1;1.56128,MA0108.2;0.774493,MA0109.1;0,MA0111.1;0.525433,MA0113.1;1.76622,MA0114.1;0.210103,MA0115.1;0.392652,MA0116.1;0.368149,MA0117.1;0.242391,MA0119.1;0.822541,MA0122.1;0.720853,MA0124.1;0.360154,MA0125.1;0.805219,MA0130.1;0,MA0131.1;0.595204,MA0132.1;0,MA0133.1;0,MA0135.1;1.24305,MA0136.1;0.0455078,MA0139.1;0.0034015,MA0140.1;2.79014,MA0141.1;0.393952,MA0142.1;0.107962,MA0143.1;0.0621685,MA0144.1;2.02845,MA0145.1;0.964485,MA0146.1;0.00117264,MA0147.1;0.0649499,MA0148.1;6.32995,MA0149.1;0.123634,MA0062.2;0.00409761,MA0035.2;3.37578,MA0039.2;5.70861e-05,MA0138.2;0.264886,MA0002.2;0.175819,MA0137.2;0.98521,MA0104.2;0.0603348,MA0047.2;6.27972,MA0112.2;0.715525,MA0065.2;0.0398493,MA0150.1;0.132442,MA0151.1;0,MA0152.1;1.31828,MA0153.1;2.17401,MA0154.1;1.17491,MA0155.1;0.158824,MA0156.1;0.00412532,MA0157.1;0.651833,MA0158.1;0,MA0159.1;0.382473,MA0160.1;0.276825,MA0161.1;0,MA0162.1;7.03442e-05,MA0163.1;0.0018606,MA0164.1;0.236285,MA0080.2;0.058246,MA0018.2;0.207755,MA0099.2;0.13697,MA0079.2;2.45904e-15,MA0102.2;0.64826,MA0258.1;1.58689,MA0259.1;0.2599,MA0442.1;0
}}
}}

Revision as of 18:49, 22 January 2013


Full id: C238_stomach_gall_breast_duodenum_temporal_MCF7_smallcell



Phase1 CAGE Peaks

Hg19::chr10:90424196..90424203,+p1@LIPF
Hg19::chr10:90429642..90429650,+p@chr10:90429642..90429650
+
Hg19::chr10:90433455..90433459,+p@chr10:90433455..90433459
+
Hg19::chr10:90438367..90438370,+p@chr10:90438367..90438370
+
Hg19::chr11:1151573..1151590,+p1@MUC5AC
Hg19::chr11:1212843..1212881,+p2@MUC5AC
Hg19::chr11:1213314..1213323,+p7@uc001lsz.2
Hg19::chr11:1213349..1213360,+p4@uc001lsz.2
Hg19::chr11:1213461..1213476,+p1@uc001lsz.2
Hg19::chr11:1213502..1213512,+p6@uc001lsz.2
Hg19::chr11:1213519..1213539,+p3@uc001lsz.2
Hg19::chr11:124622083..124622095,-p1@VSIG2
Hg19::chr11:59612969..59612994,-p1@GIF
Hg19::chr11:60970984..60970989,+p1@PGA3
Hg19::chr13:114312512..114312513,-p1@ATP4B
Hg19::chr17:10707410..10707421,-p2@LOC100289255
Hg19::chr17:33934627..33934631,+p@chr17:33934627..33934631
+
Hg19::chr17:72428429..72428461,+p@chr17:72428429..72428461
+
Hg19::chr18:19748402..19748420,-p@chr18:19748402..19748420
-
Hg19::chr18:19748421..19748445,-p@chr18:19748421..19748445
-
Hg19::chr18:2984886..2984895,-p@chr18:2984886..2984895
-
Hg19::chr19:36054555..36054561,-p1@ATP4A
Hg19::chr1:206317450..206317478,+p2@CTSE
Hg19::chr1:206317482..206317491,+p5@CTSE
Hg19::chr1:206317499..206317506,+p7@CTSE
Hg19::chr1:206317511..206317522,+p4@CTSE
Hg19::chr1:206317523..206317535,+p3@CTSE
Hg19::chr1:206317546..206317580,+p1@CTSE
Hg19::chr1:206317591..206317601,+p6@CTSE
Hg19::chr1:206331238..206331251,+p@chr1:206331238..206331251
+
Hg19::chr1:206331270..206331279,+p@chr1:206331270..206331279
+
Hg19::chr1:230883185..230883196,+p2@CAPN9
Hg19::chr20:52687046..52687058,-p7@BCAS1
Hg19::chr21:35736302..35736315,+p1@KCNE2
Hg19::chr21:43770332..43770340,-p@chr21:43770332..43770340
-
Hg19::chr21:43771096..43771112,-p1@TFF2
Hg19::chr21:43771259..43771274,-p4@TFF2
Hg19::chr21:43786634..43786650,-p1@TFF1
Hg19::chr2:69180018..69180036,-p1@GKN2
Hg19::chr2:69180052..69180063,-p2@GKN2
Hg19::chr2:69201753..69201776,+p1@GKN1
Hg19::chr3:10332416..10332446,-p3@GHRL
Hg19::chr3:109629878..109629886,+p@chr3:109629878..109629886
+
Hg19::chr3:137717571..137717591,+p7@CLDN18
Hg19::chr3:137717649..137717664,+p2@CLDN18
Hg19::chr3:137717669..137717676,+p5@CLDN18
Hg19::chr3:183629904..183629907,-p1@AK057243
Hg19::chr4:169013782..169013786,+p8@ANXA10
Hg19::chr6:30908747..30908757,+p1@DPCR1
Hg19::chr6:31154171..31154185,-p@chr6:31154171..31154185
-
Hg19::chr8:124955722..124955732,+p@chr8:124955722..124955732
+
Hg19::chr8:48911486..48911495,-p@chr8:48911486..48911495
-
Hg19::chr9:6248469..6248472,+p@chr9:6248469..6248472
+
Hg19::chrX:107288164..107288174,+p6@VSIG1
Hg19::chrX:107288197..107288212,+p2@VSIG1
Hg19::chrX:107288280..107288317,+p1@VSIG1
Hg19::chrX:107288318..107288331,+p4@VSIG1
Hg19::chrX:107288353..107288356,+p8@VSIG1


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

p.valueFDRnGenesnPathwayName
2.15061658683972e-050.0136134029946954374Gastric acid secretion (KEGG):04971



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 IDGO nameFDR corrected p-value
GO:0007586digestion2.18722116394922e-11
GO:0008900hydrogen:potassium-exchanging ATPase activity0.000185745920106365
GO:0030955potassium ion binding0.00798746707397297
GO:0032501multicellular organismal process0.00798746707397297
GO:0004194pepsin A activity0.00798746707397297
GO:0031420alkali metal ion binding0.0172023480666984
GO:0006813potassium ion transport0.0175242682012079
GO:0022890inorganic cation transmembrane transporter activity0.0175242682012079
GO:0030001metal ion transport0.0175242682012079
GO:0031768ghrelin receptor binding0.0175242682012079
GO:0043400cortisol secretion0.0175242682012079
GO:0004193cathepsin E activity0.0175242682012079
GO:0043062extracellular structure organization and biogenesis0.0175242682012079
GO:0004190aspartic-type endopeptidase activity0.0175242682012079
GO:0006812cation transport0.0175242682012079
GO:0043206fibril organization and biogenesis0.0175242682012079
GO:0051962positive regulation of nervous system development0.0175242682012079
GO:0051965positive regulation of synaptogenesis0.0175242682012079
GO:0019886antigen processing and presentation of exogenous peptide antigen via MHC class II0.0175242682012079
GO:0002495antigen processing and presentation of peptide antigen via MHC class II0.0175242682012079
GO:0046676negative regulation of insulin secretion0.0175242682012079
GO:0060079regulation of excitatory postsynaptic membrane potential0.0175242682012079
GO:0002478antigen processing and presentation of exogenous peptide antigen0.0175242682012079
GO:0051960regulation of nervous system development0.0175242682012079
GO:0032024positive regulation of insulin secretion0.0175242682012079
GO:0008324cation transmembrane transporter activity0.0175242682012079
GO:0006824cobalt ion transport0.0175242682012079
GO:0015087cobalt ion transmembrane transporter activity0.0175242682012079
GO:0032692negative regulation of interleukin-1 production0.0175242682012079
GO:0032100positive regulation of appetite0.0175242682012079
GO:0032106positive regulation of response to extracellular stimulus0.0175242682012079
GO:0032103positive regulation of response to external stimulus0.0175242682012079
GO:0045409negative regulation of interleukin-6 biosynthetic process0.0175242682012079
GO:0032691negative regulation of interleukin-1 beta production0.0175242682012079
GO:0032651regulation of interleukin-1 beta production0.0175242682012079
GO:0046697decidualization0.0175242682012079
GO:0032109positive regulation of response to nutrient levels0.0175242682012079
GO:0051963regulation of synaptogenesis0.0175242682012079
GO:0032097positive regulation of response to food0.0175242682012079
GO:0042536negative regulation of tumor necrosis factor biosynthetic process0.0175242682012079
GO:0019884antigen processing and presentation of exogenous antigen0.0212359104271811
GO:0032652regulation of interleukin-1 production0.0212359104271811
GO:0030252growth hormone secretion0.0212359104271811
GO:0060078regulation of postsynaptic membrane potential0.0212359104271811
GO:0015992proton transport0.0220314283676892
GO:0006818hydrogen transport0.0220314283676892
GO:0032098regulation of appetite0.0220314283676892
GO:0032104regulation of response to extracellular stimulus0.0220314283676892
GO:0032107regulation of response to nutrient levels0.0220314283676892
GO:0016608growth hormone-releasing hormone activity0.0220314283676892
GO:0015889cobalamin transport0.0220314283676892
GO:0032611interleukin-1 beta production0.0220314283676892
GO:0032095regulation of response to food0.0220314283676892
GO:0015662ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism0.0228342053856048
GO:0015672monovalent inorganic cation transport0.0228399978510679
GO:0030296protein tyrosine kinase activator activity0.0241522021383811
GO:0008343adult feeding behavior0.0241522021383811
GO:0032612interleukin-1 production0.0241522021383811
GO:0048584positive regulation of response to stimulus0.0267846915128793
GO:0032094response to food0.0267846915128793
GO:0032101regulation of response to external stimulus0.0267846915128793
GO:0006952defense response0.0268938422781071
GO:0050796regulation of insulin secretion0.0287197098478608
GO:0042534regulation of tumor necrosis factor biosynthetic process0.0287197098478608
GO:0042533tumor necrosis factor biosynthetic process0.0287197098478608
GO:0031348negative regulation of defense response0.0304285892654746
GO:0031419cobalamin binding0.0304285892654746
GO:0051899membrane depolarization0.0304285892654746
GO:0050728negative regulation of inflammatory response0.0304285892654746
GO:0015075ion transmembrane transporter activity0.0319485041327731
GO:0045408regulation of interleukin-6 biosynthetic process0.0319485041327731
GO:0001818negative regulation of cytokine production0.0319485041327731
GO:0009755hormone-mediated signaling0.0319485041327731
GO:0015078hydrogen ion transmembrane transporter activity0.0320987977032904
GO:0042625ATPase activity, coupled to transmembrane movement of ions0.032727017974858
GO:0030197extracellular matrix constituent, lubricant activity0.032727017974858
GO:0046888negative regulation of hormone secretion0.032727017974858
GO:0043205fibril0.032727017974858
GO:0006811ion transport0.032727017974858
GO:0015077monovalent inorganic cation transmembrane transporter activity0.0329083200346653
GO:0001937negative regulation of endothelial cell proliferation0.0329083200346653
GO:0040018positive regulation of multicellular organism growth0.0329083200346653
GO:0016358dendrite development0.0329083200346653
GO:0030295protein kinase activator activity0.0329083200346653
GO:0042226interleukin-6 biosynthetic process0.0329083200346653
GO:0032640tumor necrosis factor production0.0352268091308551
GO:0032635interleukin-6 production0.0397015116088441
GO:0030073insulin secretion0.0397015116088441
GO:0008083growth factor activity0.0407986436183481
GO:0051180vitamin transport0.0407986436183481
GO:0042036negative regulation of cytokine biosynthetic process0.0407986436183481
GO:0022891substrate-specific transmembrane transporter activity0.0407986436183481
GO:0016525negative regulation of angiogenesis0.0407986436183481
GO:0001936regulation of endothelial cell proliferation0.0407986436183481
GO:0051048negative regulation of secretion0.0407986436183481
GO:0004806triacylglycerol lipase activity0.0407986436183481
GO:0005391sodium:potassium-exchanging ATPase activity0.0407986436183481
GO:0004175endopeptidase activity0.0409325213519086
GO:0006641triacylglycerol metabolic process0.0409325213519086
GO:0050897cobalt ion binding0.0409325213519086
GO:0019209kinase activator activity0.0409325213519086
GO:0015459potassium channel regulator activity0.0409325213519086
GO:0042626ATPase activity, coupled to transmembrane movement of substances0.0409325213519086
GO:0043492ATPase activity, coupled to movement of substances0.0409325213519086
GO:0002790peptide secretion0.0409325213519086
GO:0046883regulation of hormone secretion0.0409325213519086
GO:0001935endothelial cell proliferation0.0409325213519086
GO:0030072peptide hormone secretion0.0409325213519086
GO:0016820hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances0.0415786889852224
GO:0022857transmembrane transporter activity0.0439951814301084
GO:0040014regulation of multicellular organism growth0.0439951814301084
GO:0045927positive regulation of growth0.044202531091155
GO:0016338calcium-independent cell-cell adhesion0.044202531091155
GO:0043627response to estrogen stimulus0.044202531091155
GO:0015399primary active transmembrane transporter activity0.044202531091155
GO:0015405P-P-bond-hydrolysis-driven transmembrane transporter activity0.044202531091155
GO:0006638neutral lipid metabolic process0.0453027747526112
GO:0006639acylglycerol metabolic process0.0453027747526112
GO:0040013negative regulation of locomotion0.0460882211474788
GO:0046486glycerolipid metabolic process0.0460882211474788
GO:0035264multicellular organism growth0.0460882211474788
GO:0044421extracellular region part0.0460912670108073
GO:0031347regulation of defense response0.0460912670108073
GO:0050727regulation of inflammatory response0.0460912670108073
GO:0007416synaptogenesis0.0460912670108073
GO:0006662glycerol ether metabolic process0.0460912670108073
GO:0030534adult behavior0.049201892712604
GO:0022892substrate-specific transporter activity0.049201892712604



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><br>uberon_data<br>disease_data<br>

Disease
Ontology termp-valuen
signet ring cell adenocarcinoma2.59e-122


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)
MA0003.18.14184e-06
MA0004.10.218793
MA0006.10.130484
MA0007.14.37775
MA0009.17.23395
MA0014.10.000293083
MA0017.10.786201
MA0019.10.210287
MA0024.10.153926
MA0025.10.3102
MA0027.11.67575
MA0028.10.0672484
MA0029.10.494881
MA0030.11.48766
MA0031.10.390791
MA0038.10.166846
MA0040.10.971444
MA0041.10.244832
MA0042.10.200853
MA0043.10.217679
MA0046.16.10396
MA0048.10.202882
MA0050.10.0173802
MA0051.10.0422086
MA0052.10.1706
MA0055.10.208604
MA0056.10
MA0057.10.0395139
MA0058.10.228214
MA0059.10.398553
MA0060.10.00202577
MA0061.10.490748
MA0063.10
MA0066.10.167234
MA0067.10.454522
MA0068.10.0161411
MA0069.10.207989
MA0070.10.200901
MA0071.10.133475
MA0072.10.19808
MA0073.11.28049e-07
MA0074.11.02737
MA0076.10.0439914
MA0077.10.563808
MA0078.10.946655
MA0081.10.62421
MA0083.12.60044
MA0084.12.5366
MA0087.11.08484
MA0088.10.230784
MA0089.10
MA0090.11.05431
MA0091.10.0885368
MA0092.10.0658034
MA0093.10.253397
MA0095.10
MA0098.10
MA0100.10.0475732
MA0101.11.5275
MA0103.10.574744
MA0105.10.205057
MA0106.10.206361
MA0107.11.56128
MA0108.20.774493
MA0109.10
MA0111.10.525433
MA0113.11.76622
MA0114.10.210103
MA0115.10.392652
MA0116.10.368149
MA0117.10.242391
MA0119.10.822541
MA0122.10.720853
MA0124.10.360154
MA0125.10.805219
MA0130.10
MA0131.10.595204
MA0132.10
MA0133.10
MA0135.11.24305
MA0136.10.0455078
MA0139.10.0034015
MA0140.12.79014
MA0141.10.393952
MA0142.10.107962
MA0143.10.0621685
MA0144.12.02845
MA0145.10.964485
MA0146.10.00117264
MA0147.10.0649499
MA0148.16.32995
MA0149.10.123634
MA0062.20.00409761
MA0035.23.37578
MA0039.25.70861e-05
MA0138.20.264886
MA0002.20.175819
MA0137.20.98521
MA0104.20.0603348
MA0047.26.27972
MA0112.20.715525
MA0065.20.0398493
MA0150.10.132442
MA0151.10
MA0152.11.31828
MA0153.12.17401
MA0154.11.17491
MA0155.10.158824
MA0156.10.00412532
MA0157.10.651833
MA0158.10
MA0159.10.382473
MA0160.10.276825
MA0161.10
MA0162.17.03442e-05
MA0163.10.0018606
MA0164.10.236285
MA0080.20.058246
MA0018.20.207755
MA0099.20.13697
MA0079.22.45904e-15
MA0102.20.64826
MA0258.11.58689
MA0259.10.2599
MA0442.10



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#promotersEnrichmentp-valueq-value
MAFF#2376454.854772111202170.003698320632130460.0186566636960379



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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