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Coexpression cluster:C565: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters|coexpression_dpi_cluster_scores_median=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.19806162489724,0,0,0,0,0,0,0,0.807299032547931,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0771709305212165,0,0,0,0,0,0,0,1.34454825353437,0.973480156564438,0.549848238547467,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.068591177124475,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.350779273814533,0.0833856393724342,0,0.368745804840252,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.357451879411068,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0171321976371551,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0135642422894877,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0135909688377214,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0|full_id=C565_CD34_CD133_acute_thymus_Hodgkin_Burkitt_testis|gostat_on_coexpression_clusters=GO:0045870!positive regulation of retroviral genome replication!0.00479806899799835!7153$GO:0019035!viral integration complex!0.00479806899799835!7153$GO:0009330!DNA topoisomerase complex (ATP-hydrolyzing)!0.00479806899799835!7153$GO:0030263!apoptotic chromosome condensation!0.010278852721011!7153$GO:0045091!regulation of retroviral genome replication!0.010278852721011!7153$GO:0045070!positive regulation of viral genome replication!0.010278852721011!7153$GO:0045090!retroviral genome replication!0.010278852721011!7153$GO:0048524!positive regulation of viral reproduction!0.010278852721011!7153$GO:0005814!centriole!0.010278852721011!7153$GO:0008508!bile acid:sodium symporter activity!0.010278852721011!347051$GO:0006266!DNA ligation!0.010278852721011!7153$GO:0015125!bile acid transmembrane transporter activity!0.010278852721011!347051$GO:0003918!DNA topoisomerase (ATP-hydrolyzing) activity!0.010278852721011!7153$GO:0005080!protein kinase C binding!0.010278852721011!7153$GO:0042826!histone deacetylase binding!0.0115116372212286!7153$GO:0045069!regulation of viral genome replication!0.0116469659001242!7153$GO:0043130!ubiquitin binding!0.0116469659001242!7153$GO:0032182!small conjugating protein binding!0.0116469659001242!7153$GO:0050792!regulation of viral reproduction!0.0116469659001242!7153$GO:0006265!DNA topological change!0.0116469659001242!7153$GO:0003916!DNA topoisomerase activity!0.0116469659001242!7153$GO:0008144!drug binding!0.0126590733377437!7153$GO:0030261!chromosome condensation!0.0126590733377437!7153$GO:0030262!apoptotic nuclear changes!0.0126590733377437!7153$GO:0008028!monocarboxylic acid transmembrane transporter activity!0.0126590733377437!347051$GO:0044450!microtubule organizing center part!0.0127250924038854!7153$GO:0019079!viral genome replication!0.0154477049253973!7153$GO:0006997!nuclear organization and biogenesis!0.0188408388029977!7153$GO:0005343!organic acid:sodium symporter activity!0.0188408388029977!347051$GO:0019058!viral infectious cycle!0.0239557574527735!7153$GO:0022415!viral reproductive process!0.0264231617084463!7153$GO:0007059!chromosome segregation!0.0264940328844091!7153$GO:0008022!protein C-terminus binding!0.0322086059666091!7153$GO:0019901!protein kinase binding!0.0340525037523818!7153$GO:0008094!DNA-dependent ATPase activity!0.0340525037523818!7153$GO:0015370!solute:sodium symporter activity!0.0345342885688741!347051$GO:0008632!apoptotic program!0.0345342885688741!7153$GO:0031402!sodium ion binding!0.0346565724290078!347051$GO:0046943!carboxylic acid transmembrane transporter activity!0.0346565724290078!347051$GO:0005342!organic acid transmembrane transporter activity!0.0346565724290078!347051$GO:0019900!kinase binding!0.0346565724290078!7153$GO:0046982!protein heterodimerization activity!0.03587546151678!7153$GO:0015294!solute:cation symporter activity!0.0380345867309035!347051$GO:0003682!chromatin binding!0.0384698454457164!7153$GO:0048015!phosphoinositide-mediated 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839,0.0594415,0.805089,0.268189,0.234283,0.355038,0.0400361,0.309388,0.393521,0.851457,0.511522,0.0927064,0.171822,0.306606,0.907313,0.179594,0.251588,0.12232,0.18461,0.374311,0.89505,0.249905,0.127478,0.274385,0.622094,0.544857,0.0750467,0.15896,0.104423,0.266293,0.102549,0.258546,0.622505,0.0503272,1.67713,0.205653,0.097714,0.391064,0.0508002,0.173971,0.319738,0.226038,0.339857,0.12756,0.386472,0.329494,0.0752075,0.615394,0.758742,0.311792,0.130259,0.2852,0.113556,0.284391,0.582323,0.321692,0.0585016,0.48664,0.336598,1.15514,0.843028,1.20113,0.535417,1.04233,0.19602,0.836913,0.0158491,0.756844,0.0383048,0.135657,0.288432,0.471562,0.532468,0.18023,0.70768,0.48568,2.4286,0.82567,0.70821,0.0274989,0.0112665,0.263815,0.408949,1.29895,0.932961,0.68283,1.37726,0.270867,0.12599,0.60642,0.385004,0.599297,0.412954,0.020964,0.626127,0.555021,0.594155,0.514828,0.445845,0.230832,0.500571,0.306566,0.18443,0.115618,0.938911,0.591605,0.149112,0.241506,0.886618,0.333119,0.0111366,0.216858,0.453946,0.275094,0.748992,1.0486,0.71014,0.345739,0.993708,0.472239,0.313614,0.564749,0.78949,0.0864157,0.683478,0.219902,1.88336,0.342946,0.945426,0.249246,0.21329,0.250344,0.904406,1.74999,1.35069,0.868456,0.315034,0.596045,0.447394,0.76278,0.432737,1.59165,0.203207,0.266036,0.0134468,0.0298174,0.683836,0.201134,0.321292,1.07219,0.394947,0.116843,0.184652,0.493594,0.867287,0.66649,0.531753,0.166635,1.1672,0.335644,0.24839,0.317742,0.000284037|tfbs_overrepresentation_jaspar=MA0003.1;0.114205,MA0004.1;0.238283,MA0006.1;0.124371,MA0007.1;0.223897,MA0009.1;0.644692,MA0014.1;0.0018064,MA0017.1;0.45828,MA0019.1;0.359322,MA0024.1;0.547222,MA0025.1;0.771296,MA0027.1;2.23171,MA0028.1;0.134741,MA0029.1;0.565022,MA0030.1;0.554453,MA0031.1;0.495474,MA0038.1;0.321141,MA0040.1;0.570428,MA0041.1;2.00914,MA0042.1;0.646075,MA0043.1;0.644989,MA0046.1;0.634468,MA0048.1;0.201309,MA0050.1;0.228625,MA0051.1;0.317617,MA0052.1;0.574006,MA0055.1;1.26219,MA0056.1;0,MA0057.1;0.0733461,MA0058.1;0.167587,MA0059.1;0.166682,MA0060.1;0.212419,MA0061.1;0.0461955,MA0063.1;0,MA0066.1;0.321498,MA0067.1;0.948938,MA0068.1;0.0313753,MA0069.1;0.630852,MA0070.1;0.620368,MA0071.1;0.787225,MA0072.1;0.616162,MA0073.1;0.000946877,MA0074.1;0.316991,MA0076.1;0.528959,MA0077.1;0.608956,MA0078.1;0.402443,MA0081.1;0.499456,MA0083.1;0.651755,MA0084.1;1.13204,MA0087.1;0.613875,MA0088.1;0.0965118,MA0089.1;0,MA0090.1;1.0561,MA0091.1;0.240316,MA0092.1;0.211423,MA0093.1;0.12631,MA0095.1;0,MA0098.1;0,MA0100.1;0.332778,MA0101.1;0.128426,MA0103.1;0.377626,MA0105.1;0.0129929,MA0106.1;0.355999,MA0107.1;0.0842574,MA0108.2;1.23385,MA0109.1;0,MA0111.1;0.199239,MA0113.1;0.370073,MA0114.1;0.278245,MA0115.1;0.874839,MA0116.1;0.0861811,MA0117.1;0.680135,MA0119.1;0.155538,MA0122.1;0.70466,MA0124.1;0.834787,MA0125.1;0.75419,MA0130.1;0,MA0131.1;0.418384,MA0132.1;0,MA0133.1;0,MA0135.1;3.95289,MA0136.1;0.87256,MA0139.1;0.0410754,MA0140.1;0.7823,MA0141.1;0.496178,MA0142.1;0.4668,MA0143.1;0.370225,MA0144.1;0.25687,MA0145.1;0.23881,MA0146.1;0.00119685,MA0147.1;0.0881384,MA0148.1;1.31921,MA0149.1;2.14464,MA0062.2;0.382208,MA0035.2;1.42445,MA0039.2;0.0116984,MA0138.2;0.403517,MA0002.2;1.16356,MA0137.2;0.138998,MA0104.2;0.0580852,MA0047.2;0.914023,MA0112.2;0.0357356,MA0065.2;0.118053,MA0150.1;0.185024,MA0151.1;0,MA0152.1;0.292357,MA0153.1;0.738108,MA0154.1;0.542249,MA0155.1;0.0321475,MA0156.1;0.854962,MA0157.1;0.442323,MA0158.1;0,MA0159.1;0.0884959,MA0160.1;0.743405,MA0161.1;0,MA0162.1;0.00454805,MA0163.1;0.207536,MA0164.1;0.99163,MA0080.2;0.793571,MA0018.2;0.357181,MA0099.2;0.292649,MA0079.2;3.01277e-05,MA0102.2;1.16862,MA0258.1;0.242841,MA0259.1;0.309645,MA0442.1;0}}
|full_id=C565_CD34_CD133_acute_thymus_Hodgkin_Burkitt_testis
|id=C565
}}

Latest revision as of 11:25, 17 September 2013


Full id: C565_CD34_CD133_acute_thymus_Hodgkin_Burkitt_testis



Phase1 CAGE Peaks

Hg19::chr12:58329819..58329867,-p1@ENST00000547492
p1@ENST00000551421
p1@ENST00000553102
p1@uc001sqo.2
Hg19::chr15:50367664..50367673,-p@chr15:50367664..50367673
-
Hg19::chr15:51295063..51295067,-p@chr15:51295063..51295067
-
Hg19::chr17:38545799..38545823,-p4@TOP2A
Hg19::chr18:36894194..36894210,+p@chr18:36894194..36894210
+
Hg19::chr19:3479160..3479176,-p7@C19orf77
Hg19::chr21:16816472..16816488,-p@chr21:16816472..16816488
-
Hg19::chr22:43660399..43660404,+p@chr22:43660399..43660404
+
Hg19::chr2:16659873..16659891,-p@chr2:16659873..16659891
-
Hg19::chr2:207565092..207565103,-p@chr2:207565092..207565103
-
Hg19::chr3:87841949..87841976,+p@chr3:87841949..87841976
+
Hg19::chr4:75196177..75196198,-p1@ENST00000513776
p1@uc003hhv.1
Hg19::chr5:146864161..146864177,+p@chr5:146864161..146864177
+
Hg19::chr6:130834916..130834919,-p@chr6:130834916..130834919
-
Hg19::chr6:46847996..46847997,-p12@GPR116
Hg19::chr8:82607407..82607417,-p2@SLC10A5


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

No results for this coexpression

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:0045870positive regulation of retroviral genome replication0.00479806899799835
GO:0019035viral integration complex0.00479806899799835
GO:0009330DNA topoisomerase complex (ATP-hydrolyzing)0.00479806899799835
GO:0030263apoptotic chromosome condensation0.010278852721011
GO:0045091regulation of retroviral genome replication0.010278852721011
GO:0045070positive regulation of viral genome replication0.010278852721011
GO:0045090retroviral genome replication0.010278852721011
GO:0048524positive regulation of viral reproduction0.010278852721011
GO:0005814centriole0.010278852721011
GO:0008508bile acid:sodium symporter activity0.010278852721011
GO:0006266DNA ligation0.010278852721011
GO:0015125bile acid transmembrane transporter activity0.010278852721011
GO:0003918DNA topoisomerase (ATP-hydrolyzing) activity0.010278852721011
GO:0005080protein kinase C binding0.010278852721011
GO:0042826histone deacetylase binding0.0115116372212286
GO:0045069regulation of viral genome replication0.0116469659001242
GO:0043130ubiquitin binding0.0116469659001242
GO:0032182small conjugating protein binding0.0116469659001242
GO:0050792regulation of viral reproduction0.0116469659001242
GO:0006265DNA topological change0.0116469659001242
GO:0003916DNA topoisomerase activity0.0116469659001242
GO:0008144drug binding0.0126590733377437
GO:0030261chromosome condensation0.0126590733377437
GO:0030262apoptotic nuclear changes0.0126590733377437
GO:0008028monocarboxylic acid transmembrane transporter activity0.0126590733377437
GO:0044450microtubule organizing center part0.0127250924038854
GO:0019079viral genome replication0.0154477049253973
GO:0006997nuclear organization and biogenesis0.0188408388029977
GO:0005343organic acid:sodium symporter activity0.0188408388029977
GO:0019058viral infectious cycle0.0239557574527735
GO:0022415viral reproductive process0.0264231617084463
GO:0007059chromosome segregation0.0264940328844091
GO:0008022protein C-terminus binding0.0322086059666091
GO:0019901protein kinase binding0.0340525037523818
GO:0008094DNA-dependent ATPase activity0.0340525037523818
GO:0015370solute:sodium symporter activity0.0345342885688741
GO:0008632apoptotic program0.0345342885688741
GO:0031402sodium ion binding0.0346565724290078
GO:0046943carboxylic acid transmembrane transporter activity0.0346565724290078
GO:0005342organic acid transmembrane transporter activity0.0346565724290078
GO:0019900kinase binding0.0346565724290078
GO:0046982protein heterodimerization activity0.03587546151678
GO:0015294solute:cation symporter activity0.0380345867309035
GO:0003682chromatin binding0.0384698454457164
GO:0048015phosphoinositide-mediated signaling0.0402144554204852
GO:0005813centrosome0.0402144554204852
GO:0005815microtubule organizing center0.0448269676400632
GO:0042803protein homodimerization activity0.0471622913629572
GO:0007218neuropeptide signaling pathway0.0491093518050705
GO:0006814sodium ion transport0.0495522148119735



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
CD34-positive, CD38-negative hematopoietic stem cell7.46e-161
Uber Anatomy
Ontology termp-valuen
hemopoietic organ7.11e-097
immune organ7.11e-097
Disease
Ontology termp-valuen
myeloid leukemia1.36e-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)
MA0003.10.114205
MA0004.10.238283
MA0006.10.124371
MA0007.10.223897
MA0009.10.644692
MA0014.10.0018064
MA0017.10.45828
MA0019.10.359322
MA0024.10.547222
MA0025.10.771296
MA0027.12.23171
MA0028.10.134741
MA0029.10.565022
MA0030.10.554453
MA0031.10.495474
MA0038.10.321141
MA0040.10.570428
MA0041.12.00914
MA0042.10.646075
MA0043.10.644989
MA0046.10.634468
MA0048.10.201309
MA0050.10.228625
MA0051.10.317617
MA0052.10.574006
MA0055.11.26219
MA0056.10
MA0057.10.0733461
MA0058.10.167587
MA0059.10.166682
MA0060.10.212419
MA0061.10.0461955
MA0063.10
MA0066.10.321498
MA0067.10.948938
MA0068.10.0313753
MA0069.10.630852
MA0070.10.620368
MA0071.10.787225
MA0072.10.616162
MA0073.10.000946877
MA0074.10.316991
MA0076.10.528959
MA0077.10.608956
MA0078.10.402443
MA0081.10.499456
MA0083.10.651755
MA0084.11.13204
MA0087.10.613875
MA0088.10.0965118
MA0089.10
MA0090.11.0561
MA0091.10.240316
MA0092.10.211423
MA0093.10.12631
MA0095.10
MA0098.10
MA0100.10.332778
MA0101.10.128426
MA0103.10.377626
MA0105.10.0129929
MA0106.10.355999
MA0107.10.0842574
MA0108.21.23385
MA0109.10
MA0111.10.199239
MA0113.10.370073
MA0114.10.278245
MA0115.10.874839
MA0116.10.0861811
MA0117.10.680135
MA0119.10.155538
MA0122.10.70466
MA0124.10.834787
MA0125.10.75419
MA0130.10
MA0131.10.418384
MA0132.10
MA0133.10
MA0135.13.95289
MA0136.10.87256
MA0139.10.0410754
MA0140.10.7823
MA0141.10.496178
MA0142.10.4668
MA0143.10.370225
MA0144.10.25687
MA0145.10.23881
MA0146.10.00119685
MA0147.10.0881384
MA0148.11.31921
MA0149.12.14464
MA0062.20.382208
MA0035.21.42445
MA0039.20.0116984
MA0138.20.403517
MA0002.21.16356
MA0137.20.138998
MA0104.20.0580852
MA0047.20.914023
MA0112.20.0357356
MA0065.20.118053
MA0150.10.185024
MA0151.10
MA0152.10.292357
MA0153.10.738108
MA0154.10.542249
MA0155.10.0321475
MA0156.10.854962
MA0157.10.442323
MA0158.10
MA0159.10.0884959
MA0160.10.743405
MA0161.10
MA0162.10.00454805
MA0163.10.207536
MA0164.10.99163
MA0080.20.793571
MA0018.20.357181
MA0099.20.292649
MA0079.23.01277e-05
MA0102.21.16862
MA0258.10.242841
MA0259.10.309645
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

No analysis results for this cluster

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

This analysis result is provided for C0 - C305 clusters.

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