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{{Coexpression_clusters
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dehydrogenase (NADP+) activity!0.00856587778170257!4967$GO:0006101!citrate metabolic process!0.0102180544862346!50$GO:0015858!nucleoside transport!0.0102180544862346!2030$GO:0003994!aconitate hydratase activity!0.0102180544862346!50$GO:0004591!oxoglutarate dehydrogenase (succinyl-transferring) activity!0.0102180544862346!4967$GO:0044262!cellular carbohydrate metabolic process!0.0102180544862346!4967;50$GO:0005975!carbohydrate metabolic process!0.0176404857305316!4967;50$GO:0044248!cellular catabolic process!0.0176404857305316!4967;50$GO:0005337!nucleoside transmembrane transporter activity!0.0176404857305316!2030$GO:0016624!oxidoreductase activity, acting on the aldehyde or oxo group of donors, disulfide as acceptor!0.0176404857305316!4967$GO:0015932!nucleobase, nucleoside, nucleotide and nucleic acid transmembrane transporter activity!0.0176404857305316!2030$GO:0006091!generation of precursor metabolites and energy!0.0176404857305316!4967;50$GO:0009056!catabolic process!0.0176404857305316!4967;50$GO:0005739!mitochondrion!0.0176404857305316!4967;50$GO:0006100!tricarboxylic acid cycle intermediate metabolic process!0.0182572018144486!50$GO:0046356!acetyl-CoA catabolic process!0.0189659602939553!50$GO:0006099!tricarboxylic acid cycle!0.0189659602939553!50$GO:0051539!4 iron, 4 sulfur cluster binding!0.0189659602939553!50$GO:0006084!acetyl-CoA metabolic process!0.0189659602939553!50$GO:0009109!coenzyme catabolic process!0.0189659602939553!50$GO:0051187!cofactor catabolic process!0.0189659602939553!50$GO:0016620!oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor!0.0189659602939553!4967$GO:0009060!aerobic respiration!0.0189659602939553!50$GO:0045333!cellular respiration!0.020666156364307!50$GO:0016903!oxidoreductase activity, acting on the aldehyde or oxo group of donors!0.0246182032524606!4967$GO:0051536!iron-sulfur cluster binding!0.0274611072022562!50$GO:0016836!hydro-lyase activity!0.0274611072022562!50$GO:0051540!metal cluster binding!0.0274611072022562!50$GO:0016835!carbon-oxygen lyase activity!0.0296050977840218!50$GO:0015931!nucleobase, nucleoside, nucleotide and nucleic acid transport!0.0296050977840218!2030$GO:0015980!energy derivation by oxidation of organic compounds!0.0322190111754213!50$GO:0006096!glycolysis!0.0344012461821712!4967$GO:0006007!glucose catabolic process!0.0369496971186839!4967$GO:0019320!hexose catabolic process!0.0369496971186839!4967$GO:0046365!monosaccharide catabolic process!0.0369496971186839!4967$GO:0046164!alcohol catabolic process!0.0369496971186839!4967$GO:0031980!mitochondrial lumen!0.0398882641926015!4967$GO:0005759!mitochondrial matrix!0.0398882641926015!4967$GO:0044275!cellular carbohydrate catabolic process!0.0398882641926015!4967$GO:0016052!carbohydrate catabolic process!0.0398882641926015!4967$GO:0006006!glucose metabolic process!0.0398882641926015!4967|id=C4103|ontology_enrichment_celltype=|ontology_enrichment_disease=|ontology_enrichment_uberon=UBERON:0007023!5.39e-33!114;UBERON:0001049!1.24e-24!56;UBERON:0005068!1.24e-24!56;UBERON:0006241!1.24e-24!56;UBERON:0007135!1.24e-24!56;UBERON:0000073!3.05e-23!53;UBERON:0002616!3.05e-23!53;UBERON:0003075!1.44e-22!82;UBERON:0007284!1.44e-22!82;UBERON:0002346!1.08e-21!86;UBERON:0010371!2.78e-20!104;UBERON:0001017!8.45e-19!81;UBERON:0000955!3.32e-18!68;UBERON:0006238!3.32e-18!68;UBERON:0002780!1.18e-17!41;UBERON:0001890!1.18e-17!41;UBERON:0003080!1.18e-17!41;UBERON:0006240!1.18e-17!41;UBERON:0010314!1.92e-17!132;UBERON:0001893!1.35e-16!34;UBERON:0003056!1.89e-16!61;UBERON:0003528!2.06e-16!34;UBERON:0002020!2.06e-16!34;UBERON:0000481!2.48e-16!342;UBERON:0001869!6.91e-16!32;UBERON:0001016!7.52e-16!89;UBERON:0002791!1.79e-15!32;UBERON:0000477!1.44e-13!373;UBERON:0000025!2.21e-13!192;UBERON:0002619!2.96e-13!22;UBERON:0004121!6.82e-13!171;UBERON:0000924!6.82e-13!171;UBERON:0006601!6.82e-13!171;UBERON:0000483!7.78e-13!306;UBERON:0000119!9.64e-13!309;UBERON:0001950!2.90e-12!20;UBERON:0000956!7.68e-12!25;UBERON:0000203!7.68e-12!25;UBERON:0000064!9.68e-11!218;UBERON:0000468!1.45e-10!656;UBERON:0004111!2.16e-10!240;UBERON:0000922!3.49e-10!592;UBERON:0005423!7.46e-10!581;UBERON:0011216!1.92e-09!223;UBERON:0000479!2.51e-09!773;UBERON:0000923!1.73e-08!560;UBERON:0010316!1.73e-08!560;UBERON:0005291!1.73e-08!560;UBERON:0006598!1.73e-08!560;UBERON:0010317!1.73e-08!560;UBERON:0002532!1.73e-08!560;UBERON:0002050!2.73e-08!564;UBERON:0003076!3.37e-08!15;UBERON:0003057!3.37e-08!15;UBERON:0000467!4.78e-08!624;UBERON:0000480!7.96e-08!625;UBERON:0000062!1.69e-07!503;UBERON:0004732!3.77e-07!13;UBERON:0004733!6.80e-07!12;UBERON:0002028!6.80e-07!12;UBERON:0007277!6.80e-07!12|pathway_enrichment=3.20096624129033e-06;0.00121078598126186;2;30;Citrate cycle (TCA cycle) (KEGG):00020!3.88503833680646e-06;0.00121078598126186;2;33;TCA Cycle (Wikipathways):WP78!5.73832218607515e-06;0.00121078598126186;2;40;Pyruvate metabolism and Citric Acid (TCA) cycle 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|full_id=C4103_heart_left_diaphragm_tongue_medial_skeletal_brain
|gostat_on_coexpression_clusters=GO:0050164!oxoglutarate dehydrogenase (NADP+) activity!0.00856587778170257!4967$GO:0006101!citrate metabolic process!0.0102180544862346!50$GO:0015858!nucleoside transport!0.0102180544862346!2030$GO:0003994!aconitate hydratase activity!0.0102180544862346!50$GO:0004591!oxoglutarate dehydrogenase (succinyl-transferring) activity!0.0102180544862346!4967$GO:0044262!cellular carbohydrate metabolic process!0.0102180544862346!4967;50$GO:0005975!carbohydrate metabolic process!0.0176404857305316!4967;50$GO:0044248!cellular catabolic process!0.0176404857305316!4967;50$GO:0005337!nucleoside transmembrane transporter activity!0.0176404857305316!2030$GO:0016624!oxidoreductase activity, acting on the aldehyde or oxo group of donors, disulfide as acceptor!0.0176404857305316!4967$GO:0015932!nucleobase, nucleoside, nucleotide and nucleic acid transmembrane transporter activity!0.0176404857305316!2030$GO:0006091!generation of precursor metabolites and energy!0.0176404857305316!4967;50$GO:0009056!catabolic process!0.0176404857305316!4967;50$GO:0005739!mitochondrion!0.0176404857305316!4967;50$GO:0006100!tricarboxylic acid cycle intermediate metabolic process!0.0182572018144486!50$GO:0046356!acetyl-CoA catabolic process!0.0189659602939553!50$GO:0006099!tricarboxylic acid cycle!0.0189659602939553!50$GO:0051539!4 iron, 4 sulfur cluster binding!0.0189659602939553!50$GO:0006084!acetyl-CoA metabolic process!0.0189659602939553!50$GO:0009109!coenzyme catabolic process!0.0189659602939553!50$GO:0051187!cofactor catabolic process!0.0189659602939553!50$GO:0016620!oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor!0.0189659602939553!4967$GO:0009060!aerobic respiration!0.0189659602939553!50$GO:0045333!cellular respiration!0.020666156364307!50$GO:0016903!oxidoreductase activity, acting on the aldehyde or oxo group of donors!0.0246182032524606!4967$GO:0051536!iron-sulfur cluster binding!0.0274611072022562!50$GO:0016836!hydro-lyase activity!0.0274611072022562!50$GO:0051540!metal cluster binding!0.0274611072022562!50$GO:0016835!carbon-oxygen lyase activity!0.0296050977840218!50$GO:0015931!nucleobase, nucleoside, nucleotide and nucleic acid transport!0.0296050977840218!2030$GO:0015980!energy derivation by oxidation of organic compounds!0.0322190111754213!50$GO:0006096!glycolysis!0.0344012461821712!4967$GO:0006007!glucose catabolic process!0.0369496971186839!4967$GO:0019320!hexose catabolic process!0.0369496971186839!4967$GO:0046365!monosaccharide catabolic process!0.0369496971186839!4967$GO:0046164!alcohol catabolic process!0.0369496971186839!4967$GO:0031980!mitochondrial lumen!0.0398882641926015!4967$GO:0005759!mitochondrial matrix!0.0398882641926015!4967$GO:0044275!cellular carbohydrate catabolic process!0.0398882641926015!4967$GO:0016052!carbohydrate catabolic process!0.0398882641926015!4967$GO:0006006!glucose metabolic process!0.0398882641926015!4967
|id=C4103
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!4.14e-36!115;UBERON:0001049!3.02e-27!57;UBERON:0005068!3.02e-27!57;UBERON:0006241!3.02e-27!57;UBERON:0007135!3.02e-27!57;UBERON:0002616!5.62e-25!59;UBERON:0003075!7.90e-25!86;UBERON:0007284!7.90e-25!86;UBERON:0002346!6.95e-24!90;UBERON:0005743!4.39e-23!86;UBERON:0001017!2.75e-22!82;UBERON:0000955!6.50e-21!69;UBERON:0006238!6.50e-21!69;UBERON:0003080!2.78e-20!42;UBERON:0002780!6.93e-20!41;UBERON:0001890!6.93e-20!41;UBERON:0006240!6.93e-20!41;UBERON:0003056!2.81e-19!61;UBERON:0000073!6.82e-19!94;UBERON:0001016!6.82e-19!94;UBERON:0001893!4.71e-17!34;UBERON:0002020!6.39e-17!34;UBERON:0003528!6.39e-17!34;UBERON:0002791!1.77e-16!33;UBERON:0001869!3.36e-16!32;UBERON:0000033!1.47e-14!123;UBERON:0000153!3.26e-14!129;UBERON:0007811!3.26e-14!129;UBERON:0000481!6.20e-14!347;UBERON:0004121!1.12e-13!169;UBERON:0000924!1.90e-13!173;UBERON:0006601!1.90e-13!173;UBERON:0000025!3.10e-13!194;UBERON:0002619!3.58e-13!22;UBERON:0000119!3.92e-13!312;UBERON:0000483!6.60e-13!309;UBERON:0000956!3.19e-12!25;UBERON:0000203!3.19e-12!25;UBERON:0000064!3.96e-12!219;UBERON:0001950!4.19e-12!20;UBERON:0000477!1.26e-11!286;UBERON:0000475!3.25e-11!365;UBERON:0004111!1.46e-10!241;UBERON:0000468!8.26e-09!659;UBERON:0000922!2.03e-08!612;UBERON:0003076!4.11e-08!15;UBERON:0003057!4.11e-08!15;UBERON:0002050!1.47e-07!605;UBERON:0005423!1.47e-07!605;UBERON:0000923!2.16e-07!604;UBERON:0005291!2.16e-07!604;UBERON:0006598!2.16e-07!604;UBERON:0002532!2.16e-07!604;UBERON:0004732!2.80e-07!13;UBERON:0000062!4.51e-07!511;UBERON:0004733!5.91e-07!12;UBERON:0002028!5.91e-07!12;UBERON:0007277!5.91e-07!12;UBERON:0000467!8.40e-07!625
}}

Latest revision as of 12:39, 17 September 2013


Full id: C4103_heart_left_diaphragm_tongue_medial_skeletal_brain



Phase1 CAGE Peaks

Hg19::chr22:41865109..41865152,+p1@ACO2
Hg19::chr6:44194733..44194752,+p6@SLC29A1
Hg19::chr7:44646162..44646176,+p3@OGDH


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
3.20096624129033e-060.00121078598126186230Citrate cycle (TCA cycle) (KEGG):00020
3.88503833680646e-060.00121078598126186233TCA Cycle (Wikipathways):WP78
5.73832218607515e-060.00121078598126186240Pyruvate metabolism and Citric Acid (TCA) cycle (Reactome):REACT_1046



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:0050164oxoglutarate dehydrogenase (NADP+) activity0.00856587778170257
GO:0006101citrate metabolic process0.0102180544862346
GO:0015858nucleoside transport0.0102180544862346
GO:0003994aconitate hydratase activity0.0102180544862346
GO:0004591oxoglutarate dehydrogenase (succinyl-transferring) activity0.0102180544862346
GO:0044262cellular carbohydrate metabolic process0.0102180544862346
GO:0005975carbohydrate metabolic process0.0176404857305316
GO:0044248cellular catabolic process0.0176404857305316
GO:0005337nucleoside transmembrane transporter activity0.0176404857305316
GO:0016624oxidoreductase activity, acting on the aldehyde or oxo group of donors, disulfide as acceptor0.0176404857305316
GO:0015932nucleobase, nucleoside, nucleotide and nucleic acid transmembrane transporter activity0.0176404857305316
GO:0006091generation of precursor metabolites and energy0.0176404857305316
GO:0009056catabolic process0.0176404857305316
GO:0005739mitochondrion0.0176404857305316
GO:0006100tricarboxylic acid cycle intermediate metabolic process0.0182572018144486
GO:0046356acetyl-CoA catabolic process0.0189659602939553
GO:0006099tricarboxylic acid cycle0.0189659602939553
GO:00515394 iron, 4 sulfur cluster binding0.0189659602939553
GO:0006084acetyl-CoA metabolic process0.0189659602939553
GO:0009109coenzyme catabolic process0.0189659602939553
GO:0051187cofactor catabolic process0.0189659602939553
GO:0016620oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor0.0189659602939553
GO:0009060aerobic respiration0.0189659602939553
GO:0045333cellular respiration0.020666156364307
GO:0016903oxidoreductase activity, acting on the aldehyde or oxo group of donors0.0246182032524606
GO:0051536iron-sulfur cluster binding0.0274611072022562
GO:0016836hydro-lyase activity0.0274611072022562
GO:0051540metal cluster binding0.0274611072022562
GO:0016835carbon-oxygen lyase activity0.0296050977840218
GO:0015931nucleobase, nucleoside, nucleotide and nucleic acid transport0.0296050977840218
GO:0015980energy derivation by oxidation of organic compounds0.0322190111754213
GO:0006096glycolysis0.0344012461821712
GO:0006007glucose catabolic process0.0369496971186839
GO:0019320hexose catabolic process0.0369496971186839
GO:0046365monosaccharide catabolic process0.0369496971186839
GO:0046164alcohol catabolic process0.0369496971186839
GO:0031980mitochondrial lumen0.0398882641926015
GO:0005759mitochondrial matrix0.0398882641926015
GO:0044275cellular carbohydrate catabolic process0.0398882641926015
GO:0016052carbohydrate catabolic process0.0398882641926015
GO:0006006glucose metabolic process0.0398882641926015



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><br>

Uber Anatomy
Ontology termp-valuen
adult organism5.39e-33114
neural tube1.24e-2456
neural rod1.24e-2456
future spinal cord1.24e-2456
neural keel1.24e-2456
regional part of nervous system3.05e-2353
regional part of brain3.05e-2353
neural plate1.44e-2282
presumptive neural plate1.44e-2282
neurectoderm1.08e-2186
ecto-epithelium2.78e-20104
central nervous system8.45e-1981
brain3.32e-1868
future brain3.32e-1868
regional part of forebrain1.18e-1741
forebrain1.18e-1741
anterior neural tube1.18e-1741
future forebrain1.18e-1741
structure with developmental contribution from neural crest1.92e-17132
telencephalon1.35e-1634
pre-chordal neural plate1.89e-1661
brain grey matter2.06e-1634
gray matter2.06e-1634
multi-tissue structure2.48e-16342
cerebral hemisphere6.91e-1632
nervous system7.52e-1689
regional part of telencephalon1.79e-1532
anatomical cluster1.44e-13373
tube2.21e-13192
regional part of cerebral cortex2.96e-1322
ectoderm-derived structure6.82e-13171
ectoderm6.82e-13171
presumptive ectoderm6.82e-13171
epithelium7.78e-13306
cell layer9.64e-13309
neocortex2.90e-1220
cerebral cortex7.68e-1225
pallium7.68e-1225
organ part9.68e-11218
multi-cellular organism1.45e-10656
anatomical conduit2.16e-10240
embryo3.49e-10592
developing anatomical structure7.46e-10581
organ system subdivision1.92e-09223
tissue2.51e-09773
germ layer1.73e-08560
germ layer / neural crest1.73e-08560
embryonic tissue1.73e-08560
presumptive structure1.73e-08560
germ layer / neural crest derived structure1.73e-08560
epiblast (generic)1.73e-08560
embryonic structure2.73e-08564
posterior neural tube3.37e-0815
chordal neural plate3.37e-0815
anatomical system4.78e-08624
anatomical group7.96e-08625
organ1.69e-07503
segmental subdivision of nervous system3.77e-0713
segmental subdivision of hindbrain6.80e-0712
hindbrain6.80e-0712
presumptive hindbrain6.80e-0712


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)
MA0003.10.178364
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.10.377374
MA0017.10.686276
MA0019.10.990656
MA0024.11.21731
MA0025.11.46617
MA0027.12.95767
MA0028.10.658629
MA0029.11.23771
MA0030.11.22561
MA0031.11.15713
MA0038.10.94098
MA0040.11.24388
MA0041.10.847069
MA0042.10.810843
MA0043.11.32783
MA0046.11.31611
MA0048.10.904546
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.11.06172
MA0056.10
MA0057.10.333427
MA0058.10.716037
MA0059.10.714521
MA0060.10.492218
MA0061.10.456531
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.10.405474
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.10.0834661
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.10.257905
MA0089.10
MA0090.10.751469
MA0091.10.829044
MA0092.10.785956
MA0093.10.642957
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.10.646932
MA0103.10.628063
MA0105.10.31555
MA0106.12.25834
MA0107.10.556367
MA0108.21.15387
MA0109.10
MA0111.10.767139
MA0113.11.00436
MA0114.10.549955
MA0115.11.57693
MA0116.10.560723
MA0117.11.36676
MA0119.10.695578
MA0122.11.39371
MA0124.11.53432
MA0125.11.44766
MA0130.10
MA0131.11.06461
MA0132.10
MA0133.10
MA0135.11.35921
MA0136.10.948776
MA0139.10.440097
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.10.273764
MA0146.10.348055
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.20.757898
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.20.264678
MA0065.20.277623
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.838867
MA0155.10.711948
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.10.149099
MA0163.10.122425
MA0164.11.01792
MA0080.20.643061
MA0018.22.26143
MA0099.20.902716
MA0079.20.181755
MA0102.21.88331
MA0258.10.519674
MA0259.10.575594
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
ATF3#467214.97544968400580.005768294540793880.0259603082627756
BRCA1#672213.45615376214920.007119807716084560.0296296460814534
THAP1#55145220.91276306856750.002983447413736940.0158714478628399



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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