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{{f5samples
{{f5samples
|DRA_sample_Accession=CAGE@DRS008667
|ancestors_in_anatomy_facet=
|ancestors_in_anatomy_facet=
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003
Line 40: Line 41:
|is_a=EFO:0002091;;FF:0000002;;FF:0000103
|is_a=EFO:0002091;;FF:0000002;;FF:0000103
|is_obsolete=
|is_obsolete=
|library_ids=CNhs12543
|name=MC1+Gr1+ myeloid-derived suppressor cells control, donor3 (0128 PBS)
|name=MC1+Gr1+ myeloid-derived suppressor cells control, donor3 (0128 PBS)
|namespace=FANTOM5
|namespace=FANTOM5
Line 82: Line 84:
|top_motifs=SPI1:4.18792226764;CEBPA,B_DDIT3:3.80737645001;SPIB:3.38222499846;HLF:3.15280538262;ETS1,2:3.09553022785;PAX2:3.07058081988;ELF1,2,4:2.87144494775;RUNX1..3:2.5067303263;SREBF1,2:2.45509307426;NFE2:2.33816579577;IRF7:2.15054308797;ELK1,4_GABP{A,B1}:1.89338050981;ATF5_CREB3:1.76642484966;FOXO1,3,4:1.6912979805;ATF4:1.68527175598;NKX2-2,8:1.63017691708;PPARG:1.55467170587;NANOG{mouse}:1.38477784554;ZNF148:1.38372950196;CREB1:1.35009810567;NR3C1:1.33809604423;FOXP3:1.32525244398;MYB:1.29095568294;HOX{A5,B5}:1.25575085505;BACH2:1.23067095735;NFE2L2:1.21078046964;IRF1,2:1.15388286119;STAT5{A,B}:0.996870391531;NFKB1_REL_RELA:0.943964930034;TLX2:0.870798055427;NFIX:0.810124136684;DMAP1_NCOR{1,2}_SMARC:0.682918846503;RXRA_VDR{dimer}:0.658339522772;ALX1:0.634773445921;PAX1,9:0.602205152275;AIRE:0.55223133587;POU2F1..3:0.54493873125;FOX{D1,D2}:0.533129956674;POU5F1:0.491322296962;ALX4:0.399710445345;EBF1:0.389073083776;TAL1_TCF{3,4,12}:0.378825778439;STAT2,4,6:0.312876835807;NR6A1:0.29585170834;FOX{I1,J2}:0.279097110252;FOS_FOS{B,L1}_JUN{B,D}:0.253002152624;ARID5B:0.250966150045;NFIL3:0.214568604304;E2F1..5:0.198562839512;GLI1..3:0.163808958552;EN1,2:0.154040957046;SPZ1:0.135495209538;TGIF1:0.125669691291;NFY{A,B,C}:0.114336244128;ZBTB16:0.0529152266808;SRF:0.0215609751197;NFATC1..3:-0.0496460410364;FOX{F1,F2,J1}:-0.0744206285836;RFX2..5_RFXANK_RFXAP:-0.0883234206331;PRDM1:-0.105051094307;LHX3,4:-0.116383434428;HBP1_HMGB_SSRP1_UBTF:-0.165502343088;MAFB:-0.212136294078;NR5A1,2:-0.229058296116;BPTF:-0.232576441353;GATA6:-0.233541868916;HOX{A4,D4}:-0.297557872581;JUN:-0.327613629736;EP300:-0.344484530517;NFE2L1:-0.353232317957;LMO2:-0.35434308948;FOSL2:-0.355654109138;FOXM1:-0.362086827768;YY1:-0.444290459679;FOXQ1:-0.507267881081;SOX2:-0.512540927452;FOXN1:-0.528597974318;MEF2{A,B,C,D}:-0.556089723527;PAX4:-0.557148068462;OCT4_SOX2{dimer}:-0.580762836274;NKX6-1,2:-0.595368995799;TEF:-0.597550595404;FOXL1:-0.606208221461;IKZF2:-0.614492028612;GFI1:-0.634079183785;HNF4A_NR2F1,2:-0.634616579427;MYOD1:-0.660270977294;POU6F1:-0.667481742077;PITX1..3:-0.718219697772;ZNF423:-0.724385924435;SOX17:-0.736561628319;TFDP1:-0.738798194532;PRRX1,2:-0.748935776195;POU1F1:-0.757692545279;RFX1:-0.765352977043;FOXP1:-0.774283013992;ZEB1:-0.799142046963;AR:-0.824146541914;NKX2-1,4:-0.841653137932;HNF1A:-0.847122958176;POU3F1..4:-0.847363999179;ESRRA:-0.851736669314;RORA:-0.867011288693;NKX3-1:-0.869972987221;MYFfamily:-0.883056903391;NKX2-3_NKX2-5:-0.887398777421;NR1H4:-0.892113920308;TFAP4:-0.900159918867;IKZF1:-0.917128399388;TBX4,5:-0.932906667491;PAX5:-0.939173342257;TFCP2:-0.94904753957;ATF2:-0.95285781636;TBP:-0.963139126742;PBX1:-0.98812334032;SP1:-1.01279374524;FOXA2:-1.02256010302;ZNF384:-1.06704760943;HES1:-1.07791961696;MZF1:-1.08785424785;VSX1,2:-1.09143069227;EVI1:-1.11377116489;NRF1:-1.12673047929;ATF6:-1.13453279083;CUX2:-1.1406186047;ZBTB6:-1.14141219977;SNAI1..3:-1.16067892377;T:-1.17324260602;ZFP161:-1.18714938037;REST:-1.18737764177;NANOG:-1.19745461527;SMAD1..7,9:-1.21650062972;PAX8:-1.22539467212;MTF1:-1.24420793121;CDC5L:-1.27817887278;ZNF143:-1.34830840469;FOXD3:-1.36157032042;EGR1..3:-1.36789844525;XCPE1{core}:-1.36992011758;ZIC1..3:-1.37392069117;ONECUT1,2:-1.3814919186;GATA4:-1.38759034516;TP53:-1.38905292824;SOX{8,9,10}:-1.4077350489;GFI1B:-1.41940669164;NHLH1,2:-1.43160455433;MTE{core}:-1.44004776717;CRX:-1.46032353187;MED-1{core}:-1.4688423431;BREu{core}:-1.50648340489;LEF1_TCF7_TCF7L1,2:-1.50967230126;ADNP_IRX_SIX_ZHX:-1.51029685695;CDX1,2,4:-1.51705872601;HSF1,2:-1.53705367446;TFAP2B:-1.55726507881;SOX5:-1.57276332658;HIF1A:-1.57905035686;ZNF238:-1.63595863268;HOXA9_MEIS1:-1.65686196207;GTF2I:-1.65814364154;RXR{A,B,G}:-1.65864381136;RREB1:-1.68258162739;PAX6:-1.68886910232;PATZ1:-1.76704613538;STAT1,3:-1.77134230795;HMGA1,2:-1.7719788236;MAZ:-1.78469117007;MYBL2:-1.80552344285;UFEwm:-1.81869651898;RBPJ:-1.81893993488;ESR1:-1.8578847206;AHR_ARNT_ARNT2:-1.8647351869;DBP:-1.87445836556;HAND1,2:-1.90281215744;TFAP2{A,C}:-1.9337691816;GTF2A1,2:-1.98753211468;PDX1:-2.00132594219;TLX1..3_NFIC{dimer}:-2.02776602508;NKX3-2:-2.08322790547;KLF4:-2.11329506456;TEAD1:-2.14647684581;GZF1:-2.30213476041;bHLH_family:-2.3784310811;HMX1:-2.49538876683;HIC1:-2.53624581581;TOPORS:-2.54597498301;RXR{A,B,G}_{NR1H2,PPAR}dimers:-2.76325679485;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:-2.92790343152;GCM1,2:-3.25348348357
|top_motifs=SPI1:4.18792226764;CEBPA,B_DDIT3:3.80737645001;SPIB:3.38222499846;HLF:3.15280538262;ETS1,2:3.09553022785;PAX2:3.07058081988;ELF1,2,4:2.87144494775;RUNX1..3:2.5067303263;SREBF1,2:2.45509307426;NFE2:2.33816579577;IRF7:2.15054308797;ELK1,4_GABP{A,B1}:1.89338050981;ATF5_CREB3:1.76642484966;FOXO1,3,4:1.6912979805;ATF4:1.68527175598;NKX2-2,8:1.63017691708;PPARG:1.55467170587;NANOG{mouse}:1.38477784554;ZNF148:1.38372950196;CREB1:1.35009810567;NR3C1:1.33809604423;FOXP3:1.32525244398;MYB:1.29095568294;HOX{A5,B5}:1.25575085505;BACH2:1.23067095735;NFE2L2:1.21078046964;IRF1,2:1.15388286119;STAT5{A,B}:0.996870391531;NFKB1_REL_RELA:0.943964930034;TLX2:0.870798055427;NFIX:0.810124136684;DMAP1_NCOR{1,2}_SMARC:0.682918846503;RXRA_VDR{dimer}:0.658339522772;ALX1:0.634773445921;PAX1,9:0.602205152275;AIRE:0.55223133587;POU2F1..3:0.54493873125;FOX{D1,D2}:0.533129956674;POU5F1:0.491322296962;ALX4:0.399710445345;EBF1:0.389073083776;TAL1_TCF{3,4,12}:0.378825778439;STAT2,4,6:0.312876835807;NR6A1:0.29585170834;FOX{I1,J2}:0.279097110252;FOS_FOS{B,L1}_JUN{B,D}:0.253002152624;ARID5B:0.250966150045;NFIL3:0.214568604304;E2F1..5:0.198562839512;GLI1..3:0.163808958552;EN1,2:0.154040957046;SPZ1:0.135495209538;TGIF1:0.125669691291;NFY{A,B,C}:0.114336244128;ZBTB16:0.0529152266808;SRF:0.0215609751197;NFATC1..3:-0.0496460410364;FOX{F1,F2,J1}:-0.0744206285836;RFX2..5_RFXANK_RFXAP:-0.0883234206331;PRDM1:-0.105051094307;LHX3,4:-0.116383434428;HBP1_HMGB_SSRP1_UBTF:-0.165502343088;MAFB:-0.212136294078;NR5A1,2:-0.229058296116;BPTF:-0.232576441353;GATA6:-0.233541868916;HOX{A4,D4}:-0.297557872581;JUN:-0.327613629736;EP300:-0.344484530517;NFE2L1:-0.353232317957;LMO2:-0.35434308948;FOSL2:-0.355654109138;FOXM1:-0.362086827768;YY1:-0.444290459679;FOXQ1:-0.507267881081;SOX2:-0.512540927452;FOXN1:-0.528597974318;MEF2{A,B,C,D}:-0.556089723527;PAX4:-0.557148068462;OCT4_SOX2{dimer}:-0.580762836274;NKX6-1,2:-0.595368995799;TEF:-0.597550595404;FOXL1:-0.606208221461;IKZF2:-0.614492028612;GFI1:-0.634079183785;HNF4A_NR2F1,2:-0.634616579427;MYOD1:-0.660270977294;POU6F1:-0.667481742077;PITX1..3:-0.718219697772;ZNF423:-0.724385924435;SOX17:-0.736561628319;TFDP1:-0.738798194532;PRRX1,2:-0.748935776195;POU1F1:-0.757692545279;RFX1:-0.765352977043;FOXP1:-0.774283013992;ZEB1:-0.799142046963;AR:-0.824146541914;NKX2-1,4:-0.841653137932;HNF1A:-0.847122958176;POU3F1..4:-0.847363999179;ESRRA:-0.851736669314;RORA:-0.867011288693;NKX3-1:-0.869972987221;MYFfamily:-0.883056903391;NKX2-3_NKX2-5:-0.887398777421;NR1H4:-0.892113920308;TFAP4:-0.900159918867;IKZF1:-0.917128399388;TBX4,5:-0.932906667491;PAX5:-0.939173342257;TFCP2:-0.94904753957;ATF2:-0.95285781636;TBP:-0.963139126742;PBX1:-0.98812334032;SP1:-1.01279374524;FOXA2:-1.02256010302;ZNF384:-1.06704760943;HES1:-1.07791961696;MZF1:-1.08785424785;VSX1,2:-1.09143069227;EVI1:-1.11377116489;NRF1:-1.12673047929;ATF6:-1.13453279083;CUX2:-1.1406186047;ZBTB6:-1.14141219977;SNAI1..3:-1.16067892377;T:-1.17324260602;ZFP161:-1.18714938037;REST:-1.18737764177;NANOG:-1.19745461527;SMAD1..7,9:-1.21650062972;PAX8:-1.22539467212;MTF1:-1.24420793121;CDC5L:-1.27817887278;ZNF143:-1.34830840469;FOXD3:-1.36157032042;EGR1..3:-1.36789844525;XCPE1{core}:-1.36992011758;ZIC1..3:-1.37392069117;ONECUT1,2:-1.3814919186;GATA4:-1.38759034516;TP53:-1.38905292824;SOX{8,9,10}:-1.4077350489;GFI1B:-1.41940669164;NHLH1,2:-1.43160455433;MTE{core}:-1.44004776717;CRX:-1.46032353187;MED-1{core}:-1.4688423431;BREu{core}:-1.50648340489;LEF1_TCF7_TCF7L1,2:-1.50967230126;ADNP_IRX_SIX_ZHX:-1.51029685695;CDX1,2,4:-1.51705872601;HSF1,2:-1.53705367446;TFAP2B:-1.55726507881;SOX5:-1.57276332658;HIF1A:-1.57905035686;ZNF238:-1.63595863268;HOXA9_MEIS1:-1.65686196207;GTF2I:-1.65814364154;RXR{A,B,G}:-1.65864381136;RREB1:-1.68258162739;PAX6:-1.68886910232;PATZ1:-1.76704613538;STAT1,3:-1.77134230795;HMGA1,2:-1.7719788236;MAZ:-1.78469117007;MYBL2:-1.80552344285;UFEwm:-1.81869651898;RBPJ:-1.81893993488;ESR1:-1.8578847206;AHR_ARNT_ARNT2:-1.8647351869;DBP:-1.87445836556;HAND1,2:-1.90281215744;TFAP2{A,C}:-1.9337691816;GTF2A1,2:-1.98753211468;PDX1:-2.00132594219;TLX1..3_NFIC{dimer}:-2.02776602508;NKX3-2:-2.08322790547;KLF4:-2.11329506456;TEAD1:-2.14647684581;GZF1:-2.30213476041;bHLH_family:-2.3784310811;HMX1:-2.49538876683;HIC1:-2.53624581581;TOPORS:-2.54597498301;RXR{A,B,G}_{NR1H2,PPAR}dimers:-2.76325679485;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:-2.92790343152;GCM1,2:-3.25348348357
|xref=
|xref=
}} {{DRAAccessionNumbers
|DRA_sample_Accession=CAGE@DRS008667
|accession_numbers=DRX008777;DRR009649;DRZ001074;DRZ002459;CAGE
|library_id=CNhs12543
}}
}}

Revision as of 18:46, 16 October 2013


Name:MC1+Gr1+ myeloid-derived suppressor cells control, donor3 (0128 PBS)
Species:Mouse (Mus musculus)
Library ID:{{{library_id}}}
Sample type:primary cells
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuebone marrow
dev stageNA
sexNA
ageNA
cell typestem cell
cell lineNA
companyNA
collaborationHozumi Motohashi (Tohoku University Graduate School of Medicine)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberNA
sample typetotal RNA
extraction protocol (Details)NA

CAGE Accession numbers
MethodSample accession id
CAGE  DRS008667
Library accession numbers

Library idMethodExp. accession idRun accession id
{{{library_id}}} {{{accession_numbers}}}
Accession ID Mm9

Library idBAMCTSS
{{{library_id}}}
Download raw sequence, BAM & CTSS
Mm9
BAMCTSS
[{{{mm9bam}}} download][{{{mm9ctss}}} donwload]
Mm10
BAMCTSS
[{{{mm10bam}}} download][{{{mm10ctss}}} donwload]


Relative expression to median (log10)

Transcription factors with enriched expression in this sampleRanked list of transcription factor promoter expression in this sample relative to the median expression in the FANTOM5 collection is shown. Value is log10 transformed.



Co-expression clusters with enriched expression in this sampleRanked list of co-expression cluster expression in this sample relative to the median expression in the FANTOM5 collection is shown. Value is log10 transformed. <br>Analyst:NA <br><br>link to dataset.<br>data

CNhs12543

00
10
100
1000
1000-0.0355
1001-0.0749
1002-0.116
1003-0.175
10040
10051.149
1006-0.143
1007-0.0702
10080
1009-0.2
101-0.32
10100
1011-0.0992
10120
1013-0.101
1014-0.0874
1015-0.303
1016-0.594
10170
10180
10190
1020
10200
1021-0.0487
1022-0.315
10230.535
1024-0.14
1025-0.0611
10260
1027-0.048
10280
1029-0.115
103-0.0861
10300
1031-0.911
1032-0.831
10330.105
10340
10350
10360.0567
10370
1038-0.545
1039-0.549
1040
1040-0.436
10410



Repeat families with enriched expression in this sample<b>Summary:</b>Ranked list of repeat family expression in this sample relative tothe median expression in the FANTOM5 collection is shown. Value is log10transformed.<br><b>Analyst:</b>NA<br><br>link to dataset.<br>data



TFBS(DNA)motifs over-represented in proximal region of promoters active in this sample

JASPAR motifs<b>Summary:</b>Association of JASPAR motif to the promoter expression in thissample. Pearson's correlation between the number of TFBSs estimated byusing the position-weight matrix for each promoter and its expression isexpressed as Z-score by taking the ones based on random position-weightmatrix, and the tail probability of the normal distribution correspondingto the Z-score is taken as the resulting P-value. Lower P-value indicatesmore (non-random) association of the motif to promoter expression<br><b>Analyst:</b> Michiel de Hoon <br><br><br>link to dataset.<br>data

library id: CNhs12543

Jaspar motifP-value
MA0002.21.40588e-12
MA0003.10.993
MA0004.10.559
MA0006.10.208
MA0007.10.6
MA0009.10.69
MA0014.10.176
MA0017.10.413
MA0018.20.196
MA0019.10.978
MA0024.10.244
MA0025.10.0922
MA0027.10.799
MA0028.11.44214e-5
MA0029.10.794
MA0030.10.913
MA0031.10.0594
MA0035.20.631
MA0038.10.112
MA0039.20.0281
MA0040.10.119
MA0041.10.497
MA0042.10.702
MA0043.13.4197e-4
MA0046.11.50869e-9
MA0047.20.0993
MA0048.10.152
MA0050.18.18985e-6
MA0051.11.7031e-4
MA0052.10.0052
MA0055.10.207
MA0057.10.931
MA0058.10.796
MA0059.10.391
MA0060.10.101
MA0061.10.0134
MA0062.22.68204e-20
MA0065.20.23
MA0066.10.135
MA0067.10.0176
MA0068.10.801
MA0069.10.567
MA0070.10.413
MA0071.10.245
MA0072.10.119
MA0073.10.728
MA0074.10.576
MA0076.12.01371e-6
MA0077.10.102
MA0078.10.835
MA0079.20.554
MA0080.21.12155e-15
MA0081.11.84152e-4
MA0083.10.781
MA0084.10.793
MA0087.10.382
MA0088.10.866
MA0090.10.0295
MA0091.10.806
MA0092.10.476
MA0093.10.564
MA0099.20.00344
MA0100.10.0451
MA0101.10.0228
MA0102.24.9213e-10
MA0103.10.689
MA0104.20.0861
MA0105.13.49701e-4
MA0106.10.853
MA0107.10.0195
MA0108.20.00768
MA0111.10.725
MA0112.20.00114
MA0113.10.567
MA0114.10.961
MA0115.10.315
MA0116.10.00131
MA0117.10.171
MA0119.10.498
MA0122.10.603
MA0124.10.855
MA0125.10.0241
MA0131.10.631
MA0135.10.775
MA0136.11.29359e-30
MA0137.20.101
MA0138.20.197
MA0139.10.493
MA0140.10.87
MA0141.10.272
MA0142.10.218
MA0143.10.109
MA0144.10.0969
MA0145.10.202
MA0146.10.0354
MA0147.10.0635
MA0148.10.262
MA0149.10.33
MA0150.11.67541e-5
MA0152.10.615
MA0153.10.00803
MA0154.10.0373
MA0155.10.856
MA0156.14.48485e-28
MA0157.10.221
MA0159.10.017
MA0160.10.198
MA0162.10.482
MA0163.10.0262
MA0164.10.539
MA0258.10.00756
MA0259.10.474



FANTOM5 phase1 novel unique motifs<b>Summary:</b>Association of the 169 novel and unique motifs discovered in FANTOM5 phase1 in this sample. Among the de-novo motifs discovered by DMF, HOMER,ChIPMunk, and ScanAll, only novel motifs are selected after comparison with known motif sets, and their clustering based on MACRO-APE resulted in169 novel and unique motifs. Their association to the promoter expression is evaluated in the same way to the JASPAR motif above<br><b>Analyst:</b> Michiel de Hoon <br><br><br>link to dataset.<br>data

library id: CNhs12543

Novel motifP-value
10.188
100.0603
1000.612
1010.716
1020.319
1030.2
1040.713
1050.489
1060.0611
1070.579
1080.923
1090.0518
110.0741
1100.228
1110.579
1120.0345
1130.87
1140.0864
1150.894
1160.977
1172.76422e-4
1180.475
1190.447
120.437
1200.0431
1210.575
1220.388
1230.367
1240.845
1250.16
1260.497
1270.221
1280.0989
1290.451
130.0852
1300.474
1310.701
1320.852
1330.0897
1340.947
1350.287
1360.409
1370.0688
1380.283
1390.0331
140.318
1400.762
1410.697
1420.0537
1430.00117
1440.771
1450.129
1460.909
1470.649
1480.184
1490.964
150.0377
1500.394
1510.179
1520.245
1530.215
1540.778
1550.435
1560.00609
1570.798
1580.027
1590.623
1600.851
1610.109
1620.631
1630.271
1640.0259
1650.138
1660.656
1670.722
1680.214
1690.0118
170.175
180.165
190.476
20.335
200.0539
210.458
220.348
230.257
240.186
250.264
260.199
270.731
280.0835
290.0201
30.0587
300.521
310.68
320.709
330.241
340.868
350.587
360.178
370.0745
380.354
390.898
40.779
400.254
410.0123
420.277
430.131
440.797
450.768
460.354
470.326
480.215
490.102
50.0935
500.791
510.864
520.883
530.555
540.684
550.489
560.209
570.861
580.189
590.445
60.708
600.187
610.19
620.101
630.6
640.657
650.312
660.592
670.18
680.992
690.625
70.136
700.0394
710.0692
720.171
730.0446
740.121
750.00371
760.156
770.984
780.113
790.829
80.373
800.0366
810.511
820.4
830.788
840.925
850.165
860.089
870.197
880.468
890.77
90.483
900.106
910.45
920.478
930.389
940.0652
950.0115
960.845
970.914
980.348
990.221



de novo motifs identified by HOMER in promoters active in this sample<b>Summary:</b>The result of HOMER in this sample is shown.<br><b>Analyst:</b>NA <br> library id: CNhs12543


FANTOM5 (FF) ontology

Direct parent terms


Ancestor terms (non development)<b>Summary:</b>Connected ontology terms with is_a, part_of or located_in relationship <br><b>Analyst:</b> Hideya Kawaji<br><br>link to source data<br>data

CL: Cell type
0000000 (cell), 0000000 (cell)
0000003 (native cell)

FF: FANTOM5
0000102 (sample by type)
0000002 (in vivo cell sample)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)

Ancestor terms (development)<b>Summary:</b>Connected ontology terms with develops_from, derives_from or preceded_by relationship <br><b>Analyst:</b> Hideya Kawaji <br><br>link to source data<br>data
NA

{{{1}}} Accession numbers
MethodSample accession id
{{{2}}} 
Library accession numbers

Library idMethodExp. accession idRun accession id
{{{4}}} {{{3}}}
Accession ID

Library idBAMCTSS
{{{4}}}
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