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MCL coexpression mm9:148: Difference between revisions

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{{MCL_coexpression_mm9|gostat_on_MCL_coexpression=GO:0048523;negative regulation of cellular process;0.0188645246761372;21413,12803,20410,110648,50523,16334!GO:0048519;negative regulation of biological process;0.0188645246761372;21413,12803,20410,110648,50523,16334!GO:0000122;negative regulation of transcription from RNA polymerase II promoter;0.0350802163105439;21413,20410,16334!GO:0045892;negative regulation of transcription, DNA-dependent;0.0350802163105439;21413,20410,16334!GO:0050794;regulation of cellular process;0.0350802163105439;16870,101497,14726,16334,21413,12803,20410,110648,50523!GO:0042517;positive regulation of tyrosine phosphorylation of Stat3 protein;0.0350802163105439;12803!GO:0047372;acylglycerol lipase activity;0.0350802163105439;23945!GO:0007243;protein kinase cascade;0.0350802163105439;12803,20410,16334!GO:0042325;regulation of phosphorylation;0.0350802163105439;12803,16334!GO:0051174;regulation of phosphorus metabolic process;0.0350802163105439;12803,16334!GO:0019220;regulation of phosphate metabolic process;0.0350802163105439;12803,16334!GO:0016481;negative regulation of transcription;0.0350802163105439;21413,20410,16334!GO:0045934;negative regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.0350802163105439;21413,20410,16334!GO:0050793;regulation of developmental process;0.0350802163105439;12803,110648,14726!GO:0009967;positive regulation of signal transduction;0.0350802163105439;12803,20410!GO:0046533;negative regulation of photoreceptor cell differentiation;0.0350802163105439;12803!GO:0001946;lymphangiogenesis;0.0350802163105439;14726!GO:0004084;branched-chain-amino-acid transaminase activity;0.0350802163105439;12035!GO:0009082;branched chain family amino acid biosynthetic process;0.0350802163105439;12035!GO:0046532;regulation of photoreceptor cell differentiation;0.0350802163105439;12803!GO:0050789;regulation of biological process;0.0350802163105439;16870,101497,14726,16334,21413,12803,20410,110648,50523!GO:0031324;negative regulation of cellular metabolic process;0.0416813114006787;21413,20410,16334!GO:0045596;negative regulation of cell differentiation;0.0475909014872444;12803,110648!}}
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regulation of cellular process;0.0188645246761372;21413,12803,20410,110648,50523,16334!GO:0048519;negative regulation of biological process;0.0188645246761372;21413,12803,20410,110648,50523,16334!GO:0000122;negative regulation of transcription from RNA polymerase II promoter;0.0350802163105439;21413,20410,16334!GO:0045892;negative regulation of transcription, DNA-dependent;0.0350802163105439;21413,20410,16334!GO:0050794;regulation of cellular process;0.0350802163105439;16870,101497,14726,16334,21413,12803,20410,110648,50523!GO:0042517;positive regulation of tyrosine phosphorylation of Stat3 protein;0.0350802163105439;12803!GO:0047372;acylglycerol lipase activity;0.0350802163105439;23945!GO:0007243;protein kinase cascade;0.0350802163105439;12803,20410,16334!GO:0042325;regulation of phosphorylation;0.0350802163105439;12803,16334!GO:0051174;regulation of phosphorus metabolic process;0.0350802163105439;12803,16334!GO:0019220;regulation of phosphate metabolic process;0.0350802163105439;12803,16334!GO:0016481;negative regulation of transcription;0.0350802163105439;21413,20410,16334!GO:0045934;negative regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.0350802163105439;21413,20410,16334!GO:0050793;regulation of developmental process;0.0350802163105439;12803,110648,14726!GO:0009967;positive regulation of signal transduction;0.0350802163105439;12803,20410!GO:0046533;negative regulation of photoreceptor cell differentiation;0.0350802163105439;12803!GO:0001946;lymphangiogenesis;0.0350802163105439;14726!GO:0004084;branched-chain-amino-acid transaminase activity;0.0350802163105439;12035!GO:0009082;branched chain family amino acid biosynthetic process;0.0350802163105439;12035!GO:0046532;regulation of photoreceptor cell differentiation;0.0350802163105439;12803!GO:0050789;regulation of biological process;0.0350802163105439;16870,101497,14726,16334,21413,12803,20410,110648,50523!GO:0031324;negative regulation of cellular metabolic process;0.0416813114006787;21413,20410,16334!GO:0045596;negative regulation of cell differentiation;0.0475909014872444;12803,110648!|ontology_enrichment_celltype=CL:0002453!3.02e-24!8;CL:0000333!3.18e-19!10;CL:0000095!3.18e-19!10;CL:0000243!3.18e-19!10;CL:0000123!3.18e-19!10;CL:0000125!3.18e-19!10;CL:0000030!3.18e-19!10;CL:0000339!3.18e-19!10;CL:0000128!5.37e-17!6;CL:0000126!5.37e-17!6;CL:0000127!5.37e-17!6;CL:0002605!2.55e-09!2;CL:0002604!2.55e-09!2;CL:0000878!5.24e-09!2;CL:0000129!5.24e-09!2|ontology_enrichment_disease=|ontology_enrichment_uberon=UBERON:0000947!1.07e-08!4;UBERON:0001637!1.07e-08!4;UBERON:0004573!1.07e-08!4;UBERON:0003509!1.07e-08!4;UBERON:0004571!1.07e-08!4;UBERON:0010191!1.07e-08!4;UBERON:0004572!1.07e-08!4;UBERON:0000055!4.78e-07!5;UBERON:0007500!4.78e-07!5;UBERON:0001981!4.78e-07!5;UBERON:0002049!4.78e-07!5;UBERON:0007798!4.78e-07!5;UBERON:0004537!4.78e-07!5;UBERON:0006965!4.78e-07!5|tfbs_overrepresentation_for_novel_motifs=1.19835,0.627126,0.356127,0.0915758,0.313583,1.20246,0.38887,0.312489,1.251,0.112104,0.302074,0.0714503,0.579131,0.0855507,1.49849,0,0.247937,0.789934,1.96866,0.358371,0.0288233,1.28686,0.0849999,0.308588,0.377016,0.103311,0.316398,0.686592,0.477336,0.4084,0.232033,0.364548,0.775464,1.53875,0.371811,0.107356,0.0434533,0.356818,0.586094,0.20512,0.441483,0.114657,0.439153,1.22849,2.53854,0.181894,0.170455,0.138828,1.55914,0.111208,0.49694,0.292124,1.11184,0.555946,0.200629,0.225427,2.65338,0.338647,1.01208,0.0887041,0.339982,0.561056,0.19294,0.476036,0.0971353,0.0751247,0.291277,0.569799,0.102088,0.44602,0.178527,0.466084,0.00223809,0.631387,0.109388,0.204589,0.726297,0.160545,0.319482,0.621885,0.238244,0.266587,0.128501,0.285671,0.465356,0.0018017,5.79606e-06,0.150669,0.0459912,0.713741,0.342253,0.472159,0.119668,0.0278507,0.0588674,0.467834,0.4201,0.121039,0.0446572,0.761745,0.0884804,0.113379,0.179652,0.856631,2.36163,0.23985,0.0871101,0.475194,0.444253,0.0750426,0.865138,0.533423,0.275298,0.0576475,0.918244,0.803666,1.67386,0.204134,0.532513,0.514289,0.639555,0.0536111,0.25574,0.365461,0.389163,2.87743,2.26165,1.22723,2.20056,0.343175,0.169798,0.0285378,0.269488,0.098794,0.954595,0.00329975,0.280065,0.424577,0.872356,1.05874,0.684967,0.294633,0.112965,0.377654,0.83547,0.0404467,0.173225,1.02077,0.687504,0.118308,0.103428,0.000812287,1.06268,0.358808,0.242573,0.242773,0.293632,0.087576,0.0594604,0.021073,0.334016,0.906021,0.324381,0.243792,0.477917,0.232516,0.25012,0.183815,0.129332|tfbs_overrepresentation_jaspar=MA0003.1;0.12546,MA0004.1;0.199126,MA0006.1;0.030871,MA0007.1;0.516185,MA0009.1;0.126401,MA0014.1;0.0150891,MA0017.1;5.13719,MA0019.1;0.0520677,MA0024.1;0.34325,MA0025.1;0.266379,MA0027.1;1.54541,MA0028.1;0.152858,MA0029.1;0.653803,MA0030.1;0.0986115,MA0031.1;0.0835307,MA0038.1;0.0241079,MA0040.1;0.414229,MA0041.1;0.19915,MA0042.1;0.303297,MA0043.1;0.179063,MA0046.1;0.144981,MA0048.1;0.144507,MA0050.1;0.0453796,MA0051.1;0.0258811,MA0052.1;0.136894,MA0055.1;0.408348,MA0056.1;0,MA0057.1;0.160396,MA0058.1;0.286363,MA0059.1;0.317358,MA0060.1;3.06926e-05,MA0061.1;0.442797,MA0063.1;0,MA0066.1;1.07295,MA0067.1;0.346597,MA0068.1;0.333032,MA0069.1;0.840203,MA0070.1;0.132073,MA0071.1;1.33831,MA0072.1;0.127776,MA0073.1;1.24941,MA0074.1;4.35568,MA0076.1;0.0591105,MA0077.1;0.117104,MA0078.1;1.30246,MA0081.1;0.379658,MA0083.1;0.178598,MA0084.1;0.616887,MA0087.1;0.468122,MA0088.1;0.46871,MA0089.1;0,MA0090.1;1.25071,MA0091.1;0.388577,MA0092.1;0.151222,MA0093.1;0.0901194,MA0095.1;0,MA0098.1;0,MA0100.1;1.22733,MA0101.1;0.103305,MA0103.1;0.49405,MA0105.1;0.411113,MA0106.1;0.327026,MA0107.1;0.313235,MA0108.2;0.0594652,MA0109.1;0,MA0111.1;0.0764388,MA0113.1;0.837078,MA0114.1;1.78587,MA0115.1;0.53344,MA0116.1;0.701759,MA0117.1;0.487992,MA0119.1;0.202507,MA0122.1;0.515783,MA0124.1;0.307255,MA0125.1;0.255313,MA0130.1;0,MA0131.1;0.0506646,MA0132.1;0,MA0133.1;0,MA0135.1;0.200965,MA0136.1;0.216715,MA0139.1;0.202122,MA0140.1;0.350568,MA0141.1;0.392534,MA0142.1;0.267911,MA0143.1;0.308628,MA0144.1;2.14043,MA0145.1;1.74097,MA0146.1;0.0256176,MA0147.1;0.237408,MA0148.1;0.0365899,MA0149.1;0.0456724,MA0062.2;0.102742,MA0035.2;0.183273,MA0039.2;0.114661,MA0138.2;0.181809,MA0002.2;0.428112,MA0137.2;0.563183,MA0104.2;0.105202,MA0047.2;0.0239597,MA0112.2;0.981031,MA0065.2;1.97468,MA0150.1;0.321875,MA0151.1;0,MA0152.1;0.102811,MA0153.1;0.211316,MA0154.1;0.198539,MA0155.1;1.04375,MA0156.1;0.220347,MA0157.1;0.065799,MA0158.1;0,MA0159.1;0.963372,MA0160.1;0.907906,MA0161.1;0,MA0162.1;0.00145342,MA0163.1;0.0983946,MA0164.1;0.0193046,MA0080.2;0.315811,MA0018.2;0.0921331,MA0099.2;0.702314,MA0079.2;0.00341934,MA0102.2;0.663408,MA0258.1;0.515743,MA0259.1;0.208179,MA0442.1;0}}

Latest revision as of 14:46, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr11:102807862..102807882,-p4@C1ql1
Mm9::chr11:65982007..65982020,-p1@Dnahc9
Mm9::chr11:66340488..66340520,-p@chr11:66340488..66340520
-
Mm9::chr11:86449013..86449037,-p@chr11:86449013..86449037
-
Mm9::chr11:94103970..94103978,-p7@Wfikkn2
Mm9::chr12:86222392..86222395,-p@chr12:86222392..86222395
-
Mm9::chr14:58363487..58363492,-p2@Lats2
Mm9::chr14:70584674..70584706,-p@chr14:70584674..70584706
-
Mm9::chr14:70584860..70584873,-p@chr14:70584860..70584873
-
Mm9::chr14:70591272..70591278,-p@chr14:70591272..70591278
-
Mm9::chr14:70592471..70592519,-p@chr14:70592471..70592519
-
Mm9::chr14:70592525..70592545,-p@chr14:70592525..70592545
-
Mm9::chr14:70592586..70592593,-p@chr14:70592586..70592593
-
Mm9::chr14:70592626..70592638,-p@chr14:70592626..70592638
-
Mm9::chr14:70592673..70592699,-p@chr14:70592673..70592699
-
Mm9::chr14:70595792..70595803,-p@chr14:70595792..70595803
-
Mm9::chr14:70595804..70595816,-p@chr14:70595804..70595816
-
Mm9::chr14:70595852..70595906,-p@chr14:70595852..70595906
-
Mm9::chr16:15895800..15895814,-p@chr16:15895800..15895814
-
Mm9::chr16:15895817..15895825,-p@chr16:15895817..15895825
-
Mm9::chr16:15895858..15895888,-p@chr16:15895858..15895888
-
Mm9::chr16:65815522..65815531,+p7@Vgll3
Mm9::chr18:69681575..69681579,+p41@Tcf4
Mm9::chr19:12839908..12839933,-p2@Cntf
Mm9::chr19:12839937..12839975,-p1@Cntf
Mm9::chr19:17030554..17030565,+p5@Prune2
Mm9::chr19:57082667..57082674,-p9@Afap1l2
Mm9::chr19:8788884..8788904,-p11@Slc3a2
Mm9::chr1:135811214..135811246,+p@chr1:135811214..135811246
+
Mm9::chr1:135811313..135811319,-p@chr1:135811313..135811319
-
Mm9::chr1:135811453..135811463,-p@chr1:135811453..135811463
-
Mm9::chr1:135811547..135811559,-p@chr1:135811547..135811559
-
Mm9::chr1:135811595..135811619,-p@chr1:135811595..135811619
-
Mm9::chr1:135811969..135811982,-p@chr1:135811969..135811982
-
Mm9::chr1:135936805..135936816,+p@chr1:135936805..135936816
+
Mm9::chr1:135936829..135936839,+p@chr1:135936829..135936839
+
Mm9::chr1:135936851..135936856,+p@chr1:135936851..135936856
+
Mm9::chr1:135936902..135936908,+p@chr1:135936902..135936908
+
Mm9::chr1:135936916..135936937,+p@chr1:135936916..135936937
+
Mm9::chr1:135936937..135936962,-p@chr1:135936937..135936962
-
Mm9::chr1:135936949..135936959,+p@chr1:135936949..135936959
+
Mm9::chr1:135936966..135936975,-p@chr1:135936966..135936975
-
Mm9::chr1:135936977..135936983,+p@chr1:135936977..135936983
+
Mm9::chr1:135936996..135937007,+p@chr1:135936996..135937007
+
Mm9::chr1:135937391..135937415,+p@chr1:135937391..135937415
+
Mm9::chr1:135937446..135937472,+p@chr1:135937446..135937472
+
Mm9::chr1:135937506..135937517,+p@chr1:135937506..135937517
+
Mm9::chr1:135943255..135943275,+p@chr1:135943255..135943275
+
Mm9::chr1:163171792..163171811,-p@chr1:163171792..163171811
-
Mm9::chr1:169619239..169619257,+p4@Lmx1a
Mm9::chr1:169619683..169619694,+p1@Lmx1a
Mm9::chr1:72827387..72827393,-p@chr1:72827387..72827393
-
Mm9::chr1:72895689..72895698,-p@chr1:72895689..72895698
-
Mm9::chr1:72898995..72899006,+p@chr1:72898995..72899006
+
Mm9::chr2:38207200..38207210,+p13@Lhx2
Mm9::chr4:142857805..142857809,-p@chr4:142857805..142857809
-
Mm9::chr4:142858202..142858210,-p@chr4:142858202..142858210
-
Mm9::chr4:142863932..142863937,-p@chr4:142863932..142863937
-
Mm9::chr4:142889368..142889385,-p1@Pdpn
Mm9::chr4:142889401..142889414,-p2@Pdpn
Mm9::chr4:155213802..155213813,+p4@Mxra8
Mm9::chr5:23932660..23932685,+p6@Slc4a2
Mm9::chr5:23933325..23933336,+p11@Slc4a2
Mm9::chr5:92692680..92692701,-p@chr5:92692680..92692701
-
Mm9::chr6:140668711..140668721,-p@chr6:140668711..140668721
-
Mm9::chr6:144996025..144996043,-p7@Bcat1
Mm9::chr6:82983194..82983205,-p@chr6:82983194..82983205
-
Mm9::chr6:84135739..84135768,+p@chr6:84135739..84135768
+
Mm9::chr6:88777388..88777396,+p@chr6:88777388..88777396
+
Mm9::chr7:149885426..149885434,-p2@Ins2
Mm9::chr7:29157529..29157538,-p11@Plekhg2
Mm9::chr8:13483706..13483711,+p@chr8:13483706..13483711
+
Mm9::chr8:28089083..28089090,+p@chr8:28089083..28089090
+
Mm9::chr8:96676892..96676904,+p@chr8:96676892..96676904
+
Mm9::chr9:122478206..122478208,+p@chr9:122478206..122478208
+
Mm9::chr9:43915826..43915844,+p@chr9:43915826..43915844
+


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

GO IDGO nameFDR corrected p-value
GO:0048523negative regulation of cellular process0.0188645246761372
GO:0048519negative regulation of biological process0.0188645246761372
GO:0000122negative regulation of transcription from RNA polymerase II promoter0.0350802163105439
GO:0045892negative regulation of transcription, DNA-dependent0.0350802163105439
GO:0050794regulation of cellular process0.0350802163105439
GO:0042517positive regulation of tyrosine phosphorylation of Stat3 protein0.0350802163105439
GO:0047372acylglycerol lipase activity0.0350802163105439
GO:0007243protein kinase cascade0.0350802163105439
GO:0042325regulation of phosphorylation0.0350802163105439
GO:0051174regulation of phosphorus metabolic process0.0350802163105439
GO:0019220regulation of phosphate metabolic process0.0350802163105439
GO:0016481negative regulation of transcription0.0350802163105439
GO:0045934negative regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0350802163105439
GO:0050793regulation of developmental process0.0350802163105439
GO:0009967positive regulation of signal transduction0.0350802163105439
GO:0046533negative regulation of photoreceptor cell differentiation0.0350802163105439
GO:0001946lymphangiogenesis0.0350802163105439
GO:0004084branched-chain-amino-acid transaminase activity0.0350802163105439
GO:0009082branched chain family amino acid biosynthetic process0.0350802163105439
GO:0046532regulation of photoreceptor cell differentiation0.0350802163105439
GO:0050789regulation of biological process0.0350802163105439
GO:0031324negative regulation of cellular metabolic process0.0416813114006787
GO:0045596negative regulation of cell differentiation0.0475909014872444



Relative expression of the co-expression cluster over median <br>Analyst:




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><br>

Uber Anatomy
Ontology termp-valuen
aorta1.07e-084
artery1.07e-084
systemic artery1.07e-084
arterial blood vessel1.07e-084
systemic arterial system1.07e-084
aortic system1.07e-084
arterial system1.07e-084
vessel4.78e-075
epithelial tube open at both ends4.78e-075
blood vessel4.78e-075
vasculature4.78e-075
vascular system4.78e-075
blood vasculature4.78e-075
vascular cord4.78e-075


TFBS overrepresentation<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)
MA0003.10.12546
MA0004.10.199126
MA0006.10.030871
MA0007.10.516185
MA0009.10.126401
MA0014.10.0150891
MA0017.15.13719
MA0019.10.0520677
MA0024.10.34325
MA0025.10.266379
MA0027.11.54541
MA0028.10.152858
MA0029.10.653803
MA0030.10.0986115
MA0031.10.0835307
MA0038.10.0241079
MA0040.10.414229
MA0041.10.19915
MA0042.10.303297
MA0043.10.179063
MA0046.10.144981
MA0048.10.144507
MA0050.10.0453796
MA0051.10.0258811
MA0052.10.136894
MA0055.10.408348
MA0056.10
MA0057.10.160396
MA0058.10.286363
MA0059.10.317358
MA0060.13.06926e-05
MA0061.10.442797
MA0063.10
MA0066.11.07295
MA0067.10.346597
MA0068.10.333032
MA0069.10.840203
MA0070.10.132073
MA0071.11.33831
MA0072.10.127776
MA0073.11.24941
MA0074.14.35568
MA0076.10.0591105
MA0077.10.117104
MA0078.11.30246
MA0081.10.379658
MA0083.10.178598
MA0084.10.616887
MA0087.10.468122
MA0088.10.46871
MA0089.10
MA0090.11.25071
MA0091.10.388577
MA0092.10.151222
MA0093.10.0901194
MA0095.10
MA0098.10
MA0100.11.22733
MA0101.10.103305
MA0103.10.49405
MA0105.10.411113
MA0106.10.327026
MA0107.10.313235
MA0108.20.0594652
MA0109.10
MA0111.10.0764388
MA0113.10.837078
MA0114.11.78587
MA0115.10.53344
MA0116.10.701759
MA0117.10.487992
MA0119.10.202507
MA0122.10.515783
MA0124.10.307255
MA0125.10.255313
MA0130.10
MA0131.10.0506646
MA0132.10
MA0133.10
MA0135.10.200965
MA0136.10.216715
MA0139.10.202122
MA0140.10.350568
MA0141.10.392534
MA0142.10.267911
MA0143.10.308628
MA0144.12.14043
MA0145.11.74097
MA0146.10.0256176
MA0147.10.237408
MA0148.10.0365899
MA0149.10.0456724
MA0062.20.102742
MA0035.20.183273
MA0039.20.114661
MA0138.20.181809
MA0002.20.428112
MA0137.20.563183
MA0104.20.105202
MA0047.20.0239597
MA0112.20.981031
MA0065.21.97468
MA0150.10.321875
MA0151.10
MA0152.10.102811
MA0153.10.211316
MA0154.10.198539
MA0155.11.04375
MA0156.10.220347
MA0157.10.065799
MA0158.10
MA0159.10.963372
MA0160.10.907906
MA0161.10
MA0162.10.00145342
MA0163.10.0983946
MA0164.10.0193046
MA0080.20.315811
MA0018.20.0921331
MA0099.20.702314
MA0079.20.00341934
MA0102.20.663408
MA0258.10.515743
MA0259.10.208179
MA0442.10
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