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Coexpression cluster:C246: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=1.66371,0.370082,0.636528,0.123984,0.0238115,0.122701,0.1891,0.160144,0.770076,1.31492,1.10123,0.0655002,1.13126,0.178165,0.162422,0.356085,0.147956,0.0938567,0.777455,0.456543,0.109975,0.562989,0.519897,0.0223393,0.318438,1.39464,0.27618,0.821789,1.01404,0.612014,0.216385,0.504336,0.543981,0.91529,0.376265,0.705168,3.41669,0.541984,0.0871582,0.869736,0.115786,0.935587,0.553056,0.00393804,0.910334,0.754947,0.74317,0.716197,0.904129,0.498376,0.273582,0.444974,0.487868,0.617783,0.322362,0.716425,0.0794564,0.151273,0.137757,0.150402,0.563936,0.192447,0.156095,1.33384,0.460899,0.745729,0.390162,0.705585,0.162783,0.561397,0.586451,0.429975,3.56816,0.320875,1.92734,0.113279,0.658273,0.784754,0.160926,0.79036,1.5892,0.132521,0.209902,0.417886,0.283426,1.58863,1.80597,0.577603,1.55853,0.796763,0.465789,0.264421,0.178685,0.0265424,2.07388,0.877439,0.173916,0.204829,0.309297,2.64487,0.0357983,0.520347,0.201323,0.149976,0.355438,0.455165,0.141336,0.698925,0.537465,0.64939,0.438489,0.578937,0.393091,1.14329,0.426436,0.0468794,1.3687,0.214753,0.740564,0.404338,0.314742,0.0897056,0.120566,0.0615179,0.518459,0.124753,0.183026,0.535784,0.346709,0.445752,0.264901,0.421839,0.357714,0.0603443,0.476501,1.87517,0.208306,0.115532,0.44145,1.23091,0.845551,0.41123,0.18467,0.586146,0.357656,0.144037,0.103017,1.07663,0.617159,1.3169,0.289844,2.82816,0.265167,0.943985,0.191975,0.588082,0.596411,0.658064,0.15899,1.73397,0.410256,0.703,0.160476,0.130404,0.118747,0.0573258,0.70856,0.418937,6.35945
|tfbs_overrepresentation_for_novel_motifs=1.66371,0.370082,0.636528,0.123984,0.0238115,0.122701,0.1891,0.160144,0.770076,1.31492,1.10123,0.0655002,1.13126,0.178165,0.162422,0.356085,0.147956,0.0938567,0.777455,0.456543,0.109975,0.562989,0.519897,0.0223393,0.318438,1.39464,0.27618,0.821789,1.01404,0.612014,0.216385,0.504336,0.543981,0.91529,0.376265,0.705168,3.41669,0.541984,0.0871582,0.869736,0.115786,0.935587,0.553056,0.00393804,0.910334,0.754947,0.74317,0.716197,0.904129,0.498376,0.273582,0.444974,0.487868,0.617783,0.322362,0.716425,0.0794564,0.151273,0.137757,0.150402,0.563936,0.192447,0.156095,1.33384,0.460899,0.745729,0.390162,0.705585,0.162783,0.561397,0.586451,0.429975,3.56816,0.320875,1.92734,0.113279,0.658273,0.784754,0.160926,0.79036,1.5892,0.132521,0.209902,0.417886,0.283426,1.58863,1.80597,0.577603,1.55853,0.796763,0.465789,0.264421,0.178685,0.0265424,2.07388,0.877439,0.173916,0.204829,0.309297,2.64487,0.0357983,0.520347,0.201323,0.149976,0.355438,0.455165,0.141336,0.698925,0.537465,0.64939,0.438489,0.578937,0.393091,1.14329,0.426436,0.0468794,1.3687,0.214753,0.740564,0.404338,0.314742,0.0897056,0.120566,0.0615179,0.518459,0.124753,0.183026,0.535784,0.346709,0.445752,0.264901,0.421839,0.357714,0.0603443,0.476501,1.87517,0.208306,0.115532,0.44145,1.23091,0.845551,0.41123,0.18467,0.586146,0.357656,0.144037,0.103017,1.07663,0.617159,1.3169,0.289844,2.82816,0.265167,0.943985,0.191975,0.588082,0.596411,0.658064,0.15899,1.73397,0.410256,0.703,0.160476,0.130404,0.118747,0.0573258,0.70856,0.418937,6.35945
|tfbs_overrepresentation_jaspar=MA0003.1;4.40458,MA0004.1;1.12451,MA0006.1;0.711509,MA0007.1;0.433958,MA0009.1;0.236621,MA0014.1;3.41919,MA0017.1;0.62193,MA0019.1;0.512722,MA0024.1;0.50805,MA0025.1;0.332246,MA0027.1;1.70646,MA0028.1;2.20328,MA0029.1;0.181853,MA0030.1;0.998443,MA0031.1;0.428362,MA0038.1;0.426428,MA0040.1;0.185414,MA0041.1;2.124,MA0042.1;2.39906,MA0043.1;0.236833,MA0046.1;0.229332,MA0048.1;1.50961,MA0050.1;0.236451,MA0051.1;1.12988,MA0052.1;0.550571,MA0055.1;1.21376,MA0056.1;0,MA0057.1;1.18916,MA0058.1;1.3728,MA0059.1;0.463899,MA0060.1;1.27527,MA0061.1;0.0532868,MA0063.1;0,MA0066.1;0.192218,MA0067.1;0.479528,MA0068.1;1.13471,MA0069.1;0.643319,MA0070.1;0.625977,MA0071.1;0.357341,MA0072.1;0.216466,MA0073.1;8.88524,MA0074.1;1.58736,MA0076.1;1.10363,MA0077.1;0.211468,MA0078.1;0.0875216,MA0081.1;1.36575,MA0083.1;0.241697,MA0084.1;0.642191,MA0087.1;0.214876,MA0088.1;0.544796,MA0089.1;0,MA0090.1;0.0628294,MA0091.1;0.258639,MA0092.1;0.396383,MA0093.1;1.32367,MA0095.1;0,MA0098.1;0,MA0100.1;0.452318,MA0101.1;0.503042,MA0103.1;0.148295,MA0105.1;0.385157,MA0106.1;0.065918,MA0107.1;0.0780368,MA0108.2;0.13665,MA0109.1;0,MA0111.1;0.898762,MA0113.1;0.252164,MA0114.1;0.827858,MA0115.1;0.41656,MA0116.1;0.643334,MA0117.1;0.262426,MA0119.1;0.65163,MA0122.1;0.280745,MA0124.1;0.38339,MA0125.1;0.318799,MA0130.1;0,MA0131.1;1.60341,MA0132.1;0,MA0133.1;0,MA0135.1;0.257383,MA0136.1;2.1802,MA0139.1;0.249231,MA0140.1;0.352775,MA0141.1;0.0461584,MA0142.1;0.121662,MA0143.1;0.0722469,MA0144.1;0.225073,MA0145.1;0.402364,MA0146.1;3.40008,MA0147.1;0.660855,MA0148.1;0.0298305,MA0149.1;0.0364861,MA0062.2;3.66572,MA0035.2;0.351568,MA0039.2;4.04445,MA0138.2;0.0880528,MA0002.2;0.915965,MA0137.2;0.196936,MA0104.2;0.767436,MA0047.2;0.221346,MA0112.2;0.594057,MA0065.2;1.45423,MA0150.1;0.0123642,MA0151.1;0,MA0152.1;0.04095,MA0153.1;0.306295,MA0154.1;2.20435,MA0155.1;2.10385,MA0156.1;2.74571,MA0157.1;0.350409,MA0158.1;0,MA0159.1;0.295707,MA0160.1;0.135178,MA0161.1;0,MA0162.1;2.12783,MA0163.1;4.43749,MA0164.1;0.0771206,MA0080.2;4.5299,MA0018.2;0.0664342,MA0099.2;0.0410516,MA0079.2;12.3567,MA0102.2;2.73044,MA0258.1;0.327986,MA0259.1;0.0942416,MA0442.1;0
}}
}}

Revision as of 18:51, 22 January 2013


Full id: C246_Neutrophils_Eosinophils_Whole_CD14_CD14CD16_Basophils_migratory



Phase1 CAGE Peaks

Hg19::chr10:11207438..11207455,+p1@CELF2
Hg19::chr10:12391685..12391734,+p2@CAMK1D
Hg19::chr11:61722670..61722712,+p2@BEST1
Hg19::chr11:65408273..65408341,+p3@SIPA1
Hg19::chr12:51717949..51717976,-p4@BIN2
Hg19::chr12:53835508..53835533,+p1@PRR13
p2@PCBP2
Hg19::chr13:46753825..46753846,-p@chr13:46753825..46753846
-
Hg19::chr13:46756271..46756348,-p1@LCP1
Hg19::chr13:50699661..50699695,-p1@DLEU2
Hg19::chr14:93118543..93118570,+p4@RIN3
Hg19::chr14:93155682..93155685,+p@chr14:93155682..93155685
+
Hg19::chr15:69958901..69958913,-p@chr15:69958901..69958913
-
Hg19::chr15:85259768..85259799,+p@chr15:85259768..85259799
+
Hg19::chr16:69796212..69796275,+p1@WWP2
Hg19::chr17:61699766..61699826,+p1@MAP3K3
Hg19::chr17:73840423..73840499,-p1@UNC13D
Hg19::chr18:74208364..74208381,-p@chr18:74208364..74208381
-
Hg19::chr18:74844727..74844747,-p2@MBP
Hg19::chr19:1067043..1067054,+p9@HMHA1
Hg19::chr19:14492247..14492264,+p1@CD97
Hg19::chr19:2085323..2085357,-p2@MOB3A
Hg19::chr19:38916839..38916871,-p1@RASGRP4
Hg19::chr1:161039597..161039625,-p2@ARHGAP30
Hg19::chr1:198608152..198608247,+p1@PTPRC
Hg19::chr1:26869597..26869637,+p3@RPS6KA1
Hg19::chr21:30671189..30671207,+p4@BACH1
Hg19::chr22:17565841..17565896,+p1@IL17RA
Hg19::chr22:17565903..17565929,+p2@IL17RA
Hg19::chr22:37678505..37678563,+p1@CYTH4
Hg19::chr22:51021397..51021434,-p2@CHKB-CPT1B
p2@CHKB
Hg19::chr2:175499294..175499339,-p4@WIPF1
Hg19::chr2:231084659..231084721,-p1@SP110
Hg19::chr2:32289003..32289089,+p1@AB384105
Hg19::chr3:121379739..121379771,-p1@HCLS1
Hg19::chr3:122512619..122512690,-p1@HSPBAP1
Hg19::chr3:129158715..129158766,-p2@MBD4
Hg19::chr4:88312301..88312375,-p1@HSD17B11
Hg19::chr5:100238920..100238949,-p2@ST8SIA4
Hg19::chr5:100238956..100238994,-p1@ST8SIA4
Hg19::chr5:100239086..100239122,+p1@AK055485
Hg19::chr5:154238052..154238091,+p2@CNOT8
Hg19::chr5:175085039..175085106,+p1@HRH2
Hg19::chr5:176853702..176853742,+p2@GRK6
Hg19::chr5:95157986..95158004,-p2@GLRX
Hg19::chr6:33266687..33266728,-p1@RGL2
Hg19::chr7:106505696..106505798,+p1@PIK3CG
Hg19::chr7:26332645..26332661,+p8@SNX10
Hg19::chr7:36763985..36764000,-p4@AOAH
Hg19::chr8:103251611..103251667,+p2@ENST00000520820
Hg19::chr8:67579326..67579368,-p2@VCPIP1
Hg19::chr9:115095883..115095932,-p1@PTBP3
Hg19::chr9:95726554..95726616,+p1@FGD3
Hg19::chrX:48542169..48542241,+p1@WAS
Hg19::chrX:71321022..71321043,+p@chrX:71321022..71321043
+


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
0.0003226291725905250.0340373777083004395Fc gamma R-mediated phagocytosis (KEGG):04666
0.0001363586559315220.0215787573011634371Bacterial invasion of epithelial cells (KEGG):05100
0.0001252428076610580.0215787573011634369IL-5 Signaling Pathway (Wikipathways):WP127
3.00804519216102e-060.001904092606637935161B Cell Receptor Signaling Pathway (Wikipathways):WP23
9.08047147404293e-060.00287396922153459329MAPK Cascade (Wikipathways):WP422
0.0002569256141766280.0325267827547611217{HCLS1,17} (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

GO IDGO nameFDR corrected p-value
GO:0007154cell communication0.000219800609395661
GO:0009966regulation of signal transduction0.000585506406463515
GO:0007165signal transduction0.00112135234340188
GO:0030695GTPase regulator activity0.00139879786256928
GO:0005515protein binding0.00821279443007198
GO:0030048actin filament-based movement0.0113800714176354
GO:0030036actin cytoskeleton organization and biogenesis0.0113800714176354
GO:0065007biological regulation0.0113800714176354
GO:0030029actin filament-based process0.0113800714176354
GO:0007242intracellular signaling cascade0.0113800714176354
GO:0005737cytoplasm0.0113800714176354
GO:0006464protein modification process0.0239540251157988
GO:0043687post-translational protein modification0.0244979746616004
GO:0043412biopolymer modification0.0282238563994342
GO:0007010cytoskeleton organization and biogenesis0.0315329711302865
GO:0001726ruffle0.0315329711302865
GO:0001891phagocytic cup0.0315329711302865
GO:0050528acyloxyacyl hydrolase activity0.0315329711302865
GO:0002378immunoglobulin biosynthetic process0.0315329711302865
GO:0019975interleukin-17 binding0.0315329711302865
GO:0030368interleukin-17 receptor activity0.0315329711302865
GO:0006468protein amino acid phosphorylation0.0418521866255157
GO:0005083small GTPase regulator activity0.0434877302590047
GO:0051056regulation of small GTPase mediated signal transduction0.0434877302590047
GO:0008154actin polymerization and/or depolymerization0.0456442428978856
GO:0006793phosphorus metabolic process0.0456442428978856
GO:0006796phosphate metabolic process0.0456442428978856
GO:0043209myelin sheath0.0456442428978856
GO:0006710androgen catabolic process0.0456442428978856



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>

Cell Type
Ontology termp-valuen
hematopoietic stem cell9.67e-79168
angioblastic mesenchymal cell9.67e-79168
hematopoietic oligopotent progenitor cell1.50e-74161
hematopoietic multipotent progenitor cell1.50e-74161
hematopoietic cell7.68e-74177
leukocyte7.30e-72136
hematopoietic lineage restricted progenitor cell1.36e-60120
nongranular leukocyte6.87e-59115
myeloid cell3.44e-52108
common myeloid progenitor3.44e-52108
myeloid leukocyte8.13e-4772
granulocyte monocyte progenitor cell9.86e-4267
myeloid lineage restricted progenitor cell2.03e-4066
macrophage dendritic cell progenitor2.47e-3861
monopoietic cell1.09e-3759
monocyte1.09e-3759
monoblast1.09e-3759
promonocyte1.09e-3759
defensive cell2.21e-3448
phagocyte2.21e-3448
classical monocyte4.41e-3142
CD14-positive, CD16-negative classical monocyte4.41e-3142
nucleate cell7.20e-1955
lymphocyte1.32e-1853
common lymphoid progenitor1.32e-1853
lymphoid lineage restricted progenitor cell1.90e-1852
mesenchymal cell2.22e-11354
connective tissue cell2.21e-10361
T cell4.19e-1025
pro-T cell4.19e-1025
mature alpha-beta T cell1.26e-0918
alpha-beta T cell1.26e-0918
immature T cell1.26e-0918
mature T cell1.26e-0918
immature alpha-beta T cell1.26e-0918
stuff accumulating cell2.98e-0987
lymphocyte of B lineage3.47e-0824
pro-B cell3.47e-0824
intermediate monocyte5.15e-089
CD14-positive, CD16-positive monocyte5.15e-089
granulocyte1.46e-078
B cell3.68e-0714
CD8-positive, alpha-beta T cell7.96e-0711
Uber Anatomy
Ontology termp-valuen
hematopoietic system5.75e-4898
blood island5.75e-4898
hemolymphoid system2.11e-43108
bone marrow1.47e-3576
immune system2.58e-3493
bone element9.46e-3182
skeletal element1.06e-2590
adult organism3.89e-24114
skeletal system1.17e-20100
lateral plate mesoderm6.62e-13203
blood8.68e-1015
haemolymphatic fluid8.68e-1015
organism substance8.68e-1015
connective tissue3.44e-09371
Disease
Ontology termp-valuen
hematologic cancer1.18e-0851
immune system cancer1.18e-0851
leukemia3.46e-0839
myeloid leukemia6.86e-0731


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)
MA0003.14.40458
MA0004.11.12451
MA0006.10.711509
MA0007.10.433958
MA0009.10.236621
MA0014.13.41919
MA0017.10.62193
MA0019.10.512722
MA0024.10.50805
MA0025.10.332246
MA0027.11.70646
MA0028.12.20328
MA0029.10.181853
MA0030.10.998443
MA0031.10.428362
MA0038.10.426428
MA0040.10.185414
MA0041.12.124
MA0042.12.39906
MA0043.10.236833
MA0046.10.229332
MA0048.11.50961
MA0050.10.236451
MA0051.11.12988
MA0052.10.550571
MA0055.11.21376
MA0056.10
MA0057.11.18916
MA0058.11.3728
MA0059.10.463899
MA0060.11.27527
MA0061.10.0532868
MA0063.10
MA0066.10.192218
MA0067.10.479528
MA0068.11.13471
MA0069.10.643319
MA0070.10.625977
MA0071.10.357341
MA0072.10.216466
MA0073.18.88524
MA0074.11.58736
MA0076.11.10363
MA0077.10.211468
MA0078.10.0875216
MA0081.11.36575
MA0083.10.241697
MA0084.10.642191
MA0087.10.214876
MA0088.10.544796
MA0089.10
MA0090.10.0628294
MA0091.10.258639
MA0092.10.396383
MA0093.11.32367
MA0095.10
MA0098.10
MA0100.10.452318
MA0101.10.503042
MA0103.10.148295
MA0105.10.385157
MA0106.10.065918
MA0107.10.0780368
MA0108.20.13665
MA0109.10
MA0111.10.898762
MA0113.10.252164
MA0114.10.827858
MA0115.10.41656
MA0116.10.643334
MA0117.10.262426
MA0119.10.65163
MA0122.10.280745
MA0124.10.38339
MA0125.10.318799
MA0130.10
MA0131.11.60341
MA0132.10
MA0133.10
MA0135.10.257383
MA0136.12.1802
MA0139.10.249231
MA0140.10.352775
MA0141.10.0461584
MA0142.10.121662
MA0143.10.0722469
MA0144.10.225073
MA0145.10.402364
MA0146.13.40008
MA0147.10.660855
MA0148.10.0298305
MA0149.10.0364861
MA0062.23.66572
MA0035.20.351568
MA0039.24.04445
MA0138.20.0880528
MA0002.20.915965
MA0137.20.196936
MA0104.20.767436
MA0047.20.221346
MA0112.20.594057
MA0065.21.45423
MA0150.10.0123642
MA0151.10
MA0152.10.04095
MA0153.10.306295
MA0154.12.20435
MA0155.12.10385
MA0156.12.74571
MA0157.10.350409
MA0158.10
MA0159.10.295707
MA0160.10.135178
MA0161.10
MA0162.12.12783
MA0163.14.43749
MA0164.10.0771206
MA0080.24.5299
MA0018.20.0664342
MA0099.20.0410516
MA0079.212.3567
MA0102.22.73044
MA0258.10.327986
MA0259.10.0942416
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
E2F1#1869211.908429139119740.001386579613364560.0090243028753151
EBF1#1879203.298691424655197.07426279704601e-073.16957928897764e-05
EGR1#1958252.309342173523211.24908008657656e-050.000308398759248156
ELF1#1997453.548414965672952.42527982603946e-206.28520594917456e-18
ETS1#2113152.702433589500650.0002603822885367630.00279113885173878
GABPB1#2553222.879426748074221.5732290254349e-065.99221247948196e-05
GATA1#2623123.013401809733430.000472657304680220.00433853544063082
HEY1#23462292.16968926389014.86121192221296e-060.000150474247760521
IRF1#3659162.26286333438930.001124619232987250.00771151651723164
MAX#4149161.911868298965070.006374622351216720.0277538429105687
MYC#4609252.417723088708065.37755905274527e-060.000164314479201189
NFKB1#4790333.353816537007343.46966644243456e-124.59858494392668e-10
NRF1#4899112.487279146755930.003890623381118560.0189671295010335
PBX3#509083.246594472110240.002982231886885480.0158754939616919
POLR2A#5430481.908847268051627.80036710520287e-118.55737962290213e-09
POU2F2#5452193.204006612909412.34324371142833e-068.32401462509739e-05
PRDM1#63937.323941987636710.008103318624247130.0320047836401976
RFX5#5993112.454204057391590.004307415328088520.0204510683025066
SIN3A#25942282.804606895385633.40948872317986e-082.27966448630078e-06
SP2#666873.39027247142430.004365421577038960.0206935486603292
SPI1#6688284.254093671085861.84045789291855e-122.51591075757226e-10
SREBF1#672054.352393466711880.005794213120965760.0260488926064544
TAF1#6872392.414422317482711.78566113836129e-101.86866396422159e-08
TBP#6908342.333892654838473.37944588907238e-082.26247403338994e-06
YY1#7528211.909899736054280.001372491889427190.00902939719306368
ZBTB7A#51341172.314489967294260.0005721445091567530.0048313551416415
ZEB1#6935144.378482374918782.19157431595235e-067.8573920351441e-05
ZNF263#10127131.979332245947010.01126973450254020.0413664570242432



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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