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Coexpression cluster:C1501: Difference between revisions

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|gostat_on_coexpression_clusters=GO:0051087!chaperone binding!6.17474325659817e-05!3329;3336$GO:0006986!response to unfolded protein!0.000293224101723009!3329;3336$GO:0051789!response to protein stimulus!0.000293224101723009!3329;3336$GO:0031980!mitochondrial lumen!0.00170046604163955!3329;3336$GO:0005759!mitochondrial matrix!0.00170046604163955!3329;3336$GO:0051082!unfolded protein binding!0.00170046604163955!3329;3336$GO:0009607!response to biotic stimulus!0.00304274984538471!3329;3336$GO:0030150!protein import into mitochondrial matrix!0.00327824217005075!3329$GO:0006457!protein folding!0.00337076692797348!3329;3336$GO:0019907!cyclin-dependent protein kinase activating kinase holoenzyme complex!0.00524472426633574!3329$GO:0042981!regulation of apoptosis!0.0062930254510129!3329;3336$GO:0043067!regulation of programmed cell death!0.0062930254510129!3329;3336$GO:0044429!mitochondrial part!0.0062930254510129!3329;3336$GO:0042221!response to chemical stimulus!0.0062930254510129!3329;3336$GO:0043681!protein import into mitochondrion!0.00757415180743216!3329$GO:0006915!apoptosis!0.0104087539166046!3329;3336$GO:0012501!programmed cell death!0.0104087539166046!3329;3336$GO:0006626!protein targeting to mitochondrion!0.0104087539166046!3329$GO:0016265!death!0.0104087539166046!3329;3336$GO:0008219!cell death!0.0104087539166046!3329;3336$GO:0031974!membrane-enclosed lumen!0.0108082869144582!3329;3336$GO:0043233!organelle lumen!0.0108082869144582!3329;3336$GO:0005739!mitochondrion!0.0109590825739654!3329;3336$GO:0006950!response to stress!0.0150515336650597!3329;3336$GO:0048468!cell development!0.0150515336650597!3329;3336$GO:0006919!caspase activation!0.0150515336650597!3336$GO:0006839!mitochondrial transport!0.0150515336650597!3329$GO:0043280!positive regulation of caspase activity!0.0150515336650597!3336$GO:0007219!Notch signaling pathway!0.0150515336650597!55759$GO:0043281!regulation of caspase activity!0.0174546374220374!3336$GO:0051345!positive regulation of hydrolase activity!0.0213859255099137!3336$GO:0008632!apoptotic program!0.0232212881218106!3336$GO:0007005!mitochondrion organization and biogenesis!0.0232212881218106!3329$GO:0048869!cellular developmental process!0.0232212881218106!3329;3336$GO:0030154!cell differentiation!0.0232212881218106!3329;3336$GO:0017038!protein import!0.0295219359384132!3329$GO:0043231!intracellular membrane-bound organelle!0.0456897064861589!3329;3336;55759$GO:0043227!membrane-bound organelle!0.0456897064861589!3329;3336;55759$GO:0005515!protein binding!0.0458582552281764!3329;3336;55759$GO:0006605!protein targeting!0.0458582552281764!3329$GO:0005524!ATP binding!0.0458582552281764!3329;3336$GO:0032559!adenyl ribonucleotide binding!0.0458582552281764!3329;3336$GO:0030554!adenyl nucleotide binding!0.0485713528048677!3329;3336
|gostat_on_coexpression_clusters=GO:0051087!chaperone binding!6.17474325659817e-05!3329;3336$GO:0006986!response to unfolded protein!0.000293224101723009!3329;3336$GO:0051789!response to protein stimulus!0.000293224101723009!3329;3336$GO:0031980!mitochondrial lumen!0.00170046604163955!3329;3336$GO:0005759!mitochondrial matrix!0.00170046604163955!3329;3336$GO:0051082!unfolded protein binding!0.00170046604163955!3329;3336$GO:0009607!response to biotic stimulus!0.00304274984538471!3329;3336$GO:0030150!protein import into mitochondrial matrix!0.00327824217005075!3329$GO:0006457!protein folding!0.00337076692797348!3329;3336$GO:0019907!cyclin-dependent protein kinase activating kinase holoenzyme complex!0.00524472426633574!3329$GO:0042981!regulation of apoptosis!0.0062930254510129!3329;3336$GO:0043067!regulation of programmed cell death!0.0062930254510129!3329;3336$GO:0044429!mitochondrial part!0.0062930254510129!3329;3336$GO:0042221!response to chemical stimulus!0.0062930254510129!3329;3336$GO:0043681!protein import into mitochondrion!0.00757415180743216!3329$GO:0006915!apoptosis!0.0104087539166046!3329;3336$GO:0012501!programmed cell death!0.0104087539166046!3329;3336$GO:0006626!protein targeting to mitochondrion!0.0104087539166046!3329$GO:0016265!death!0.0104087539166046!3329;3336$GO:0008219!cell death!0.0104087539166046!3329;3336$GO:0031974!membrane-enclosed lumen!0.0108082869144582!3329;3336$GO:0043233!organelle lumen!0.0108082869144582!3329;3336$GO:0005739!mitochondrion!0.0109590825739654!3329;3336$GO:0006950!response to stress!0.0150515336650597!3329;3336$GO:0048468!cell development!0.0150515336650597!3329;3336$GO:0006919!caspase activation!0.0150515336650597!3336$GO:0006839!mitochondrial transport!0.0150515336650597!3329$GO:0043280!positive regulation of caspase activity!0.0150515336650597!3336$GO:0007219!Notch signaling pathway!0.0150515336650597!55759$GO:0043281!regulation of caspase activity!0.0174546374220374!3336$GO:0051345!positive regulation of hydrolase activity!0.0213859255099137!3336$GO:0008632!apoptotic program!0.0232212881218106!3336$GO:0007005!mitochondrion organization and biogenesis!0.0232212881218106!3329$GO:0048869!cellular developmental process!0.0232212881218106!3329;3336$GO:0030154!cell differentiation!0.0232212881218106!3329;3336$GO:0017038!protein import!0.0295219359384132!3329$GO:0043231!intracellular membrane-bound organelle!0.0456897064861589!3329;3336;55759$GO:0043227!membrane-bound organelle!0.0456897064861589!3329;3336;55759$GO:0005515!protein binding!0.0458582552281764!3329;3336;55759$GO:0006605!protein targeting!0.0458582552281764!3329$GO:0005524!ATP binding!0.0458582552281764!3329;3336$GO:0032559!adenyl ribonucleotide binding!0.0458582552281764!3329;3336$GO:0030554!adenyl nucleotide binding!0.0485713528048677!3329;3336
|id=C1501
|id=C1501
|ontology_enrichment_celltype=CL:0000066!1.04e-11!254
|ontology_enrichment_celltype=CL:0000066!1.46e-11!253
|ontology_enrichment_disease=DOID:14566!6.11e-61!239;DOID:162!1.29e-59!235;DOID:0050687!4.08e-32!143;DOID:0050686!9.12e-30!137;DOID:305!9.38e-27!106;DOID:2531!6.61e-18!51;DOID:0060083!6.61e-18!51;DOID:1240!1.16e-14!39;DOID:8692!3.97e-12!31;DOID:3095!4.31e-07!22;DOID:2994!4.31e-07!22
|ontology_enrichment_disease=DOID:14566!4.67e-59!239;DOID:162!1.15e-57!235;DOID:0050687!1.11e-30!143;DOID:0050686!2.95e-28!137;DOID:305!1.26e-25!106;DOID:2531!1.14e-17!51;DOID:0060083!1.14e-17!51;DOID:1240!1.57e-14!39;DOID:8692!5.50e-12!31;DOID:3095!5.08e-07!22;DOID:2994!5.08e-07!22
|ontology_enrichment_uberon=
|ontology_enrichment_uberon=UBERON:0001737!9.78e-07!9
|tf_chipseq_enrich=ATF3#467;4:14.9754496840058:5.47577390976406e-05:0.000927480297375688!BCLAF1#9774;5:18.0438730084349:1.21080990322265e-06:4.89948762040568e-05!BRCA1#672;5:16.8201922026865:1.71529178571936e-06:6.4766217935193e-05!CHD2#1106;5:8.62001902843071:4.6560374997265e-05:0.000815071908203044!E2F1#1869;5:4.08949101239944:0.00174981759776199:0.0107594465759591!E2F4#1874;5:10.5567169294037:1.71705502564041e-05:0.000392659316450315!E2F6#1876;6:5.01715573169739:6.26776799983417e-05:0.00102505390249715!ELF1#1997;5:3.54841496567295:0.00344683777572169:0.0175319870675789!ELK4#2005;6:16.235681658468:5.45305335722442e-08:3.4432372404786e-06!EP300#2033;5:5.64495143851933:0.000368813893181486:0.00367123086065394!ETS1#2113;6:9.72876092220234:1.17854759771003e-06:4.80618245049739e-05!FOS#2353;5:7.49829609074534:9.22669120642035e-05:0.00134340778322506!FOSL2#2355;5:14.1085005038014:4.09784291596229e-06:0.000130162596198353!FOXA1#3169;6:11.0814197493855:5.39600313513231e-07:2.50690912557866e-05!GABPB1#2553;5:5.88973653015181:0.000300017597367021:0.00309895538041879!GATA1#2623;6:13.5603081438004:1.60671883176178e-07:8.90679979142081e-06!GATA3#2625;5:22.6970969643383:3.87517465667206e-07:1.8868035709472e-05!GTF2B#2959;2:10.6479433114414:0.0135134586576011:0.0477252843480727!HDAC2#3066;5:11.1796835305219:1.29408913564529e-05:0.000317112565081319!HEY1#23462;6:4.04011104310571:0.000229896855580751:0.00253352302416356!HNF4A#3172;6:23.1322903629537:6.51490260560877e-09:5.13516915643151e-07!HNF4G#3174;6:28.7534225264468:1.76556713337063e-09:1.54046838631659e-07!HSF1#3297;5:136.908888888889:4.94363085166209e-11:5.56966410481917e-09!IRF4#3662;4:14.6096751244961:6.03404227507469e-05:0.000991487320903911!JUN#3725;5:10.4273576602803:1.82465747415735e-05:0.000415446701424721!JUND#3727;5:5.82888661822586:0.000315568248503075:0.00323462874721883!MAX#4149;6:6.45255550900712:1.3848964723355e-05:0.000334575995082692!MEF2A#4205;5:15.61935909137:2.47611227471544e-06:8.74248444418545e-05!MEF2C#4208;5:34.4261287438534:4.87546598482441e-08:3.1450820999943e-06!MXI1#4601;6:9.9615716287593:1.02262624227062e-06:4.30306454941583e-05!MYC#4609;6:5.2222818716094:4.92821127172503e-05:0.000854553307334702!NFKB1#4790;6:5.48806342419384:3.65870229532191e-05:0.000707744413819457!NR2C2#7182;6:32.6146109052409:8.2872822148748e-10:7.78341247517364e-08!NR3C1#2908;5:12.4775194426442:7.52342219908436e-06:0.000214976386060238!NRF1#4899;5:10.1752328730924:2.0585884796849e-05:0.000455501953876718!PAX5#5079;5:5.55797127598152:0.000397717619661286:0.00388707004302873!POLR2A#5430;6:2.14745317655807:0.0101957067681878:0.0380568055454884!POU2F2#5452;5:7.58843671478544:8.70203885493171e-05:0.00129095488063951!PPARGC1A#10891;5:291.70928030303:1.11748890111184e-12:1.56237514515688e-10!REST#5978;4:6.43335247741868:0.00145495422303207:0.00932633426006546!RFX5#5993;5:10.0399256893292:2.19894173045095e-05:0.00048267186924457!RXRA#6256;5:16.7288476159444:1.76223204684013e-06:6.62750279942156e-05!SETDB1#9869;5:33.6000218150087:5.50253359077372e-08:3.45567712379324e-06!SIN3A#25942;6:5.40888472681514:3.99207083571449e-05:0.000743319461599546!SIX5#147912;6:17.086715355459:4.01311308210759e-08:2.65269314672301e-06!SP1#6667;5:4.74865114845075:0.000852370402732661:0.00641822007865872!SRF#6722;6:13.7971782621678:1.44812893459755e-07:8.17519663786129e-06!STAT1#6772;5:17.2554895809993:1.51117799335256e-06:5.8195397657724e-05!STAT3#6774;5:8.76622083096187:4.28672496720299e-05:0.000766480515065421!TAF1#6872;6:3.34304628574529:0.000716247428463562:0.00573519628776401!TAF7#6879;6:11.4330694049239:4.47357982339933e-07:2.12757833868854e-05!TBP#6908;6:3.70677068709639:0.00038541647290796:0.00378028841228723!TCF7L2#6934;5:8.97514713594779:3.818060286338e-05:0.000720033221821695!TFAP2C#7022;5:9.00769050821686:3.75071472654799e-05:0.000723934384265285!TRIM28#10155;6:18.5905250452625:2.41896703530258e-08:1.69553354496622e-06!USF1#7391;6:6.36149927720796:1.50818327938273e-05:0.000357010774060411!USF2#7392;5:10.8268311542247:1.51592052313491e-05:0.000358598467759201!YY1#7528;6:4.91117074985386:7.12445972864136e-05:0.00112414480978936!ZBTB33#10009;5:26.3872708583176:1.83222607625143e-07:1.00081516306288e-05!ZNF143#7702;6:13.5008765522279:1.64963374888971e-07:9.12532304556633e-06
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}}
}}

Revision as of 11:22, 19 October 2012


Full id: C1501_hepatocellular_acute_oral_signet_testicular_iPS_teratocarcinoma



Phase1 CAGE Peaks

Hg19::chr2:198364552..198364576,-p1@HSPD1
Hg19::chr2:198364581..198364596,-p2@HSPD1
Hg19::chr2:198365063..198365091,+p2@HSPE1
Hg19::chr2:198365095..198365116,+p1@HSPE1
Hg19::chr2:198365122..198365133,+p3@HSPE1
Hg19::chr2:203776344..203776423,-p1@WDR12


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:0051087chaperone binding6.17474325659817e-05
GO:0006986response to unfolded protein0.000293224101723009
GO:0051789response to protein stimulus0.000293224101723009
GO:0031980mitochondrial lumen0.00170046604163955
GO:0005759mitochondrial matrix0.00170046604163955
GO:0051082unfolded protein binding0.00170046604163955
GO:0009607response to biotic stimulus0.00304274984538471
GO:0030150protein import into mitochondrial matrix0.00327824217005075
GO:0006457protein folding0.00337076692797348
GO:0019907cyclin-dependent protein kinase activating kinase holoenzyme complex0.00524472426633574
GO:0042981regulation of apoptosis0.0062930254510129
GO:0043067regulation of programmed cell death0.0062930254510129
GO:0044429mitochondrial part0.0062930254510129
GO:0042221response to chemical stimulus0.0062930254510129
GO:0043681protein import into mitochondrion0.00757415180743216
GO:0006915apoptosis0.0104087539166046
GO:0012501programmed cell death0.0104087539166046
GO:0006626protein targeting to mitochondrion0.0104087539166046
GO:0016265death0.0104087539166046
GO:0008219cell death0.0104087539166046
GO:0031974membrane-enclosed lumen0.0108082869144582
GO:0043233organelle lumen0.0108082869144582
GO:0005739mitochondrion0.0109590825739654
GO:0006950response to stress0.0150515336650597
GO:0048468cell development0.0150515336650597
GO:0006919caspase activation0.0150515336650597
GO:0006839mitochondrial transport0.0150515336650597
GO:0043280positive regulation of caspase activity0.0150515336650597
GO:0007219Notch signaling pathway0.0150515336650597
GO:0043281regulation of caspase activity0.0174546374220374
GO:0051345positive regulation of hydrolase activity0.0213859255099137
GO:0008632apoptotic program0.0232212881218106
GO:0007005mitochondrion organization and biogenesis0.0232212881218106
GO:0048869cellular developmental process0.0232212881218106
GO:0030154cell differentiation0.0232212881218106
GO:0017038protein import0.0295219359384132
GO:0043231intracellular membrane-bound organelle0.0456897064861589
GO:0043227membrane-bound organelle0.0456897064861589
GO:0005515protein binding0.0458582552281764
GO:0006605protein targeting0.0458582552281764
GO:0005524ATP binding0.0458582552281764
GO:0032559adenyl ribonucleotide binding0.0458582552281764
GO:0030554adenyl nucleotide binding0.0485713528048677



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
epithelial cell1.46e-11253
Uber Anatomy
Ontology termp-valuen
larynx9.78e-079
Disease
Ontology termp-valuen
disease of cellular proliferation4.67e-59239
cancer1.15e-57235
cell type cancer1.11e-30143
organ system cancer2.95e-28137
carcinoma1.26e-25106
hematologic cancer1.14e-1751
immune system cancer1.14e-1751
leukemia1.57e-1439
myeloid leukemia5.50e-1231
germ cell and embryonal cancer5.08e-0722
germ cell cancer5.08e-0722


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)

{{{tfbs_overrepresentation_jaspar}}}



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#467414.97544968400585.47577390976406e-050.000927480297375688
BCLAF1#9774518.04387300843491.21080990322265e-064.89948762040568e-05
BRCA1#672516.82019220268651.71529178571936e-066.4766217935193e-05
CHD2#110658.620019028430714.6560374997265e-050.000815071908203044
E2F1#186954.089491012399440.001749817597761990.0107594465759591
E2F4#1874510.55671692940371.71705502564041e-050.000392659316450315
E2F6#187665.017155731697396.26776799983417e-050.00102505390249715
ELF1#199753.548414965672950.003446837775721690.0175319870675789
ELK4#2005616.2356816584685.45305335722442e-083.4432372404786e-06
EP300#203355.644951438519330.0003688138931814860.00367123086065394
ETS1#211369.728760922202341.17854759771003e-064.80618245049739e-05
FOS#235357.498296090745349.22669120642035e-050.00134340778322506
FOSL2#2355514.10850050380144.09784291596229e-060.000130162596198353
FOXA1#3169611.08141974938555.39600313513231e-072.50690912557866e-05
GABPB1#255355.889736530151810.0003000175973670210.00309895538041879
GATA1#2623613.56030814380041.60671883176178e-078.90679979142081e-06
GATA3#2625522.69709696433833.87517465667206e-071.8868035709472e-05
GTF2B#2959210.64794331144140.01351345865760110.0477252843480727
HDAC2#3066511.17968353052191.29408913564529e-050.000317112565081319
HEY1#2346264.040111043105710.0002298968555807510.00253352302416356
HNF4A#3172623.13229036295376.51490260560877e-095.13516915643151e-07
HNF4G#3174628.75342252644681.76556713337063e-091.54046838631659e-07
HSF1#32975136.9088888888894.94363085166209e-115.56966410481917e-09
IRF4#3662414.60967512449616.03404227507469e-050.000991487320903911
JUN#3725510.42735766028031.82465747415735e-050.000415446701424721
JUND#372755.828886618225860.0003155682485030750.00323462874721883
MAX#414966.452555509007121.3848964723355e-050.000334575995082692
MEF2A#4205515.619359091372.47611227471544e-068.74248444418545e-05
MEF2C#4208534.42612874385344.87546598482441e-083.1450820999943e-06
MXI1#460169.96157162875931.02262624227062e-064.30306454941583e-05
MYC#460965.22228187160944.92821127172503e-050.000854553307334702
NFKB1#479065.488063424193843.65870229532191e-050.000707744413819457
NR2C2#7182632.61461090524098.2872822148748e-107.78341247517364e-08
NR3C1#2908512.47751944264427.52342219908436e-060.000214976386060238
NRF1#4899510.17523287309242.0585884796849e-050.000455501953876718
PAX5#507955.557971275981520.0003977176196612860.00388707004302873
POLR2A#543062.147453176558070.01019570676818780.0380568055454884
POU2F2#545257.588436714785448.70203885493171e-050.00129095488063951
PPARGC1A#108915291.709280303031.11748890111184e-121.56237514515688e-10
REST#597846.433352477418680.001454954223032070.00932633426006546
RFX5#5993510.03992568932922.19894173045095e-050.00048267186924457
RXRA#6256516.72884761594441.76223204684013e-066.62750279942156e-05
SETDB1#9869533.60002181500875.50253359077372e-083.45567712379324e-06
SIN3A#2594265.408884726815143.99207083571449e-050.000743319461599546
SIX5#147912617.0867153554594.01311308210759e-082.65269314672301e-06
SP1#666754.748651148450750.0008523704027326610.00641822007865872
SRF#6722613.79717826216781.44812893459755e-078.17519663786129e-06
STAT1#6772517.25548958099931.51117799335256e-065.8195397657724e-05
STAT3#677458.766220830961874.28672496720299e-050.000766480515065421
TAF1#687263.343046285745290.0007162474284635620.00573519628776401
TAF7#6879611.43306940492394.47357982339933e-072.12757833868854e-05
TBP#690863.706770687096390.000385416472907960.00378028841228723
TCF7L2#693458.975147135947793.818060286338e-050.000720033221821695
TFAP2C#702259.007690508216863.75071472654799e-050.000723934384265285
TRIM28#10155618.59052504526252.41896703530258e-081.69553354496622e-06
USF1#739166.361499277207961.50818327938273e-050.000357010774060411
USF2#7392510.82683115422471.51592052313491e-050.000358598467759201
YY1#752864.911170749853867.12445972864136e-050.00112414480978936
ZBTB33#10009526.38727085831761.83222607625143e-071.00081516306288e-05
ZNF143#7702613.50087655222791.64963374888971e-079.12532304556633e-06



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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