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|sample_strain=
|sample_strain=
|sample_tissue=
|sample_tissue=
|timecourse=T-cell_differentiation
|top_motifs=PDX1:3.66799164922;HBP1_HMGB_SSRP1_UBTF:2.29008974836;NR3C1:2.17840188091;ZNF238:1.92940380416;GLI1..3:1.72453369614;SOX5:1.69031209229;FOXP3:1.68989416498;TLX1..3_NFIC{dimer}:1.52406828387;RXR{A,B,G}:1.48619434614;ESR1:1.41592525514;TEAD1:1.32580915875;NFE2L2:1.31987037689;CDC5L:1.27321454965;CDX1,2,4:1.25873108886;RORA:1.13501641463;HIC1:1.12346258312;PAX8:1.11409351816;SOX17:1.07175972186;GFI1B:1.06330050067;BACH2:1.06297339749;TLX2:1.02726032402;NKX2-2,8:1.02234981835;HOX{A4,D4}:0.979654554729;HOXA9_MEIS1:0.979316355071;TFDP1:0.958125541531;NKX3-1:0.955175630468;MTE{core}:0.944975078312;EBF1:0.869284471318;NR1H4:0.815563639581;SREBF1,2:0.810098236983;GTF2I:0.79330447841;SPZ1:0.778246839767;HSF1,2:0.775728479252;FOXO1,3,4:0.758325728411;SMAD1..7,9:0.755894217828;HLF:0.747611490969;MYBL2:0.731346498435;MZF1:0.696834371067;FOS_FOS{B,L1}_JUN{B,D}:0.690156012669;GCM1,2:0.672165286521;PPARG:0.671778993939;HIF1A:0.659169669533;SRF:0.638790269538;ALX4:0.634031201455;NKX2-3_NKX2-5:0.62416504466;STAT2,4,6:0.602778722308;POU3F1..4:0.561592088547;PITX1..3:0.55034895561;NFIL3:0.542196054555;NR6A1:0.538136407235;MAFB:0.518564513149;NFATC1..3:0.516647999639;FOXM1:0.510517913448;PAX4:0.508448532527;RUNX1..3:0.48283081247;ADNP_IRX_SIX_ZHX:0.451943581835;HMGA1,2:0.448509741489;TAL1_TCF{3,4,12}:0.441062987452;AR:0.423597919551;PAX6:0.423301979612;DMAP1_NCOR{1,2}_SMARC:0.400646357509;EGR1..3:0.389137178693;POU5F1:0.377273062651;RXR{A,B,G}_{NR1H2,PPAR}dimers:0.342779340682;ONECUT1,2:0.34160860859;MTF1:0.333718789701;TFAP2B:0.325268205334;RFX2..5_RFXANK_RFXAP:0.293924762171;IKZF1:0.290895343978;HES1:0.288524051598;TEF:0.275912392753;PRRX1,2:0.270113113926;NFKB1_REL_RELA:0.269644825508;CRX:0.268803304475;AHR_ARNT_ARNT2:0.263802879202;NFE2:0.25684639986;FOX{F1,F2,J1}:0.242380693174;FOXD3:0.239790310666;NANOG{mouse}:0.232080456782;ZFP161:0.214360310355;MAZ:0.193305156092;MYB:0.193230927008;RREB1:0.181008832651;NKX2-1,4:0.17539709809;FOSL2:0.168079604881;IKZF2:0.164094845645;ZBTB16:0.159962823838;TP53:0.13130301491;FOX{D1,D2}:0.124192831493;TFAP2{A,C}:0.0950874700976;SPIB:0.0877927533776;GATA4:0.0739720650559;IRF1,2:0.0651212057328;MED-1{core}:0.0633756240895;PATZ1:0.0617054203783;IRF7:0.0325925069;FOXP1:0.0259490532103;STAT5{A,B}:0.00412324123499;PRDM1:-0.00061469214757;ATF4:-0.0152624019858;NKX6-1,2:-0.0289797009207;JUN:-0.032228110502;MYFfamily:-0.0392478444818;FOXQ1:-0.0514306191494;bHLH_family:-0.054116048687;RFX1:-0.0567776873164;ZNF384:-0.061168021893;FOXN1:-0.0980633415292;HMX1:-0.107865337628;FOXL1:-0.128169788368;TFAP4:-0.12871946313;PAX5:-0.135730617583;GTF2A1,2:-0.157896040866;SPI1:-0.165677921444;NHLH1,2:-0.215735896662;VSX1,2:-0.216898912238;KLF4:-0.247424029276;AIRE:-0.262040638419;ATF5_CREB3:-0.284521592497;PAX2:-0.288955099725;POU2F1..3:-0.296791214328;BREu{core}:-0.308059806162;ATF6:-0.313755679427;ZNF423:-0.319534176779;POU6F1:-0.327613702923;TFCP2:-0.349899375439;TGIF1:-0.358299151461;ZBTB6:-0.378157378555;HNF4A_NR2F1,2:-0.378901371625;NFE2L1:-0.383505628002;CREB1:-0.400087224106;DBP:-0.406031264175;OCT4_SOX2{dimer}:-0.41000645687;HNF1A:-0.448635529463;FOXA2:-0.454539326002;ETS1,2:-0.46951230624;MEF2{A,B,C,D}:-0.477200604132;EVI1:-0.47916201349;UFEwm:-0.504524260506;REST:-0.519797498637;HOX{A5,B5}:-0.520532142833;LHX3,4:-0.526841493888;HAND1,2:-0.531064929894;RXRA_VDR{dimer}:-0.553431935223;NR5A1,2:-0.553788342669;CEBPA,B_DDIT3:-0.565119983805;ELK1,4_GABP{A,B1}:-0.576586164418;SOX{8,9,10}:-0.577542989122;CUX2:-0.591019313523;RBPJ:-0.600004437888;PBX1:-0.628591176306;SOX2:-0.650944335018;E2F1..5:-0.660732133774;ESRRA:-0.664006842318;ATF2:-0.67511046304;YY1:-0.687626752664;EN1,2:-0.735352701219;SP1:-0.853329040678;TBP:-0.854596239802;BPTF:-0.867560080703;EP300:-0.872295719855;TOPORS:-0.910158862395;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:-0.919271638623;ELF1,2,4:-0.943738319198;GATA6:-0.945300065817;T:-0.964398147153;NANOG:-0.993225519251;TBX4,5:-1.02745002232;ZNF148:-1.0702763437;LEF1_TCF7_TCF7L1,2:-1.08117570624;XCPE1{core}:-1.15361732559;ZIC1..3:-1.17158906364;ZNF143:-1.19966208859;POU1F1:-1.24415842386;NRF1:-1.25482773024;NFIX:-1.3147988059;NKX3-2:-1.32036850847;GFI1:-1.36830898183;ALX1:-1.57326561256;NFY{A,B,C}:-1.75310461886;PAX1,9:-1.81430984137;ARID5B:-2.01338632638;SNAI1..3:-2.01406896833;ZEB1:-2.02987173972;GZF1:-2.08201600063;FOX{I1,J2}:-2.42309892568;LMO2:-2.52575825501;STAT1,3:-2.53369861825;MYOD1:-2.95323531331
|top_motifs=PDX1:3.66799164922;HBP1_HMGB_SSRP1_UBTF:2.29008974836;NR3C1:2.17840188091;ZNF238:1.92940380416;GLI1..3:1.72453369614;SOX5:1.69031209229;FOXP3:1.68989416498;TLX1..3_NFIC{dimer}:1.52406828387;RXR{A,B,G}:1.48619434614;ESR1:1.41592525514;TEAD1:1.32580915875;NFE2L2:1.31987037689;CDC5L:1.27321454965;CDX1,2,4:1.25873108886;RORA:1.13501641463;HIC1:1.12346258312;PAX8:1.11409351816;SOX17:1.07175972186;GFI1B:1.06330050067;BACH2:1.06297339749;TLX2:1.02726032402;NKX2-2,8:1.02234981835;HOX{A4,D4}:0.979654554729;HOXA9_MEIS1:0.979316355071;TFDP1:0.958125541531;NKX3-1:0.955175630468;MTE{core}:0.944975078312;EBF1:0.869284471318;NR1H4:0.815563639581;SREBF1,2:0.810098236983;GTF2I:0.79330447841;SPZ1:0.778246839767;HSF1,2:0.775728479252;FOXO1,3,4:0.758325728411;SMAD1..7,9:0.755894217828;HLF:0.747611490969;MYBL2:0.731346498435;MZF1:0.696834371067;FOS_FOS{B,L1}_JUN{B,D}:0.690156012669;GCM1,2:0.672165286521;PPARG:0.671778993939;HIF1A:0.659169669533;SRF:0.638790269538;ALX4:0.634031201455;NKX2-3_NKX2-5:0.62416504466;STAT2,4,6:0.602778722308;POU3F1..4:0.561592088547;PITX1..3:0.55034895561;NFIL3:0.542196054555;NR6A1:0.538136407235;MAFB:0.518564513149;NFATC1..3:0.516647999639;FOXM1:0.510517913448;PAX4:0.508448532527;RUNX1..3:0.48283081247;ADNP_IRX_SIX_ZHX:0.451943581835;HMGA1,2:0.448509741489;TAL1_TCF{3,4,12}:0.441062987452;AR:0.423597919551;PAX6:0.423301979612;DMAP1_NCOR{1,2}_SMARC:0.400646357509;EGR1..3:0.389137178693;POU5F1:0.377273062651;RXR{A,B,G}_{NR1H2,PPAR}dimers:0.342779340682;ONECUT1,2:0.34160860859;MTF1:0.333718789701;TFAP2B:0.325268205334;RFX2..5_RFXANK_RFXAP:0.293924762171;IKZF1:0.290895343978;HES1:0.288524051598;TEF:0.275912392753;PRRX1,2:0.270113113926;NFKB1_REL_RELA:0.269644825508;CRX:0.268803304475;AHR_ARNT_ARNT2:0.263802879202;NFE2:0.25684639986;FOX{F1,F2,J1}:0.242380693174;FOXD3:0.239790310666;NANOG{mouse}:0.232080456782;ZFP161:0.214360310355;MAZ:0.193305156092;MYB:0.193230927008;RREB1:0.181008832651;NKX2-1,4:0.17539709809;FOSL2:0.168079604881;IKZF2:0.164094845645;ZBTB16:0.159962823838;TP53:0.13130301491;FOX{D1,D2}:0.124192831493;TFAP2{A,C}:0.0950874700976;SPIB:0.0877927533776;GATA4:0.0739720650559;IRF1,2:0.0651212057328;MED-1{core}:0.0633756240895;PATZ1:0.0617054203783;IRF7:0.0325925069;FOXP1:0.0259490532103;STAT5{A,B}:0.00412324123499;PRDM1:-0.00061469214757;ATF4:-0.0152624019858;NKX6-1,2:-0.0289797009207;JUN:-0.032228110502;MYFfamily:-0.0392478444818;FOXQ1:-0.0514306191494;bHLH_family:-0.054116048687;RFX1:-0.0567776873164;ZNF384:-0.061168021893;FOXN1:-0.0980633415292;HMX1:-0.107865337628;FOXL1:-0.128169788368;TFAP4:-0.12871946313;PAX5:-0.135730617583;GTF2A1,2:-0.157896040866;SPI1:-0.165677921444;NHLH1,2:-0.215735896662;VSX1,2:-0.216898912238;KLF4:-0.247424029276;AIRE:-0.262040638419;ATF5_CREB3:-0.284521592497;PAX2:-0.288955099725;POU2F1..3:-0.296791214328;BREu{core}:-0.308059806162;ATF6:-0.313755679427;ZNF423:-0.319534176779;POU6F1:-0.327613702923;TFCP2:-0.349899375439;TGIF1:-0.358299151461;ZBTB6:-0.378157378555;HNF4A_NR2F1,2:-0.378901371625;NFE2L1:-0.383505628002;CREB1:-0.400087224106;DBP:-0.406031264175;OCT4_SOX2{dimer}:-0.41000645687;HNF1A:-0.448635529463;FOXA2:-0.454539326002;ETS1,2:-0.46951230624;MEF2{A,B,C,D}:-0.477200604132;EVI1:-0.47916201349;UFEwm:-0.504524260506;REST:-0.519797498637;HOX{A5,B5}:-0.520532142833;LHX3,4:-0.526841493888;HAND1,2:-0.531064929894;RXRA_VDR{dimer}:-0.553431935223;NR5A1,2:-0.553788342669;CEBPA,B_DDIT3:-0.565119983805;ELK1,4_GABP{A,B1}:-0.576586164418;SOX{8,9,10}:-0.577542989122;CUX2:-0.591019313523;RBPJ:-0.600004437888;PBX1:-0.628591176306;SOX2:-0.650944335018;E2F1..5:-0.660732133774;ESRRA:-0.664006842318;ATF2:-0.67511046304;YY1:-0.687626752664;EN1,2:-0.735352701219;SP1:-0.853329040678;TBP:-0.854596239802;BPTF:-0.867560080703;EP300:-0.872295719855;TOPORS:-0.910158862395;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:-0.919271638623;ELF1,2,4:-0.943738319198;GATA6:-0.945300065817;T:-0.964398147153;NANOG:-0.993225519251;TBX4,5:-1.02745002232;ZNF148:-1.0702763437;LEF1_TCF7_TCF7L1,2:-1.08117570624;XCPE1{core}:-1.15361732559;ZIC1..3:-1.17158906364;ZNF143:-1.19966208859;POU1F1:-1.24415842386;NRF1:-1.25482773024;NFIX:-1.3147988059;NKX3-2:-1.32036850847;GFI1:-1.36830898183;ALX1:-1.57326561256;NFY{A,B,C}:-1.75310461886;PAX1,9:-1.81430984137;ARID5B:-2.01338632638;SNAI1..3:-2.01406896833;ZEB1:-2.02987173972;GZF1:-2.08201600063;FOX{I1,J2}:-2.42309892568;LMO2:-2.52575825501;STAT1,3:-2.53369861825;MYOD1:-2.95323531331
|xref=
|xref=
}}
}}

Revision as of 15:47, 20 June 2014


Name:TSt-4/DLL1 feeder cells, biol_rep2
Species:Mouse (Mus musculus)
Library ID:CNhs13408
Sample type:time courses
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueNA
dev stageNA
sexNA
ageNA
cell typeunclassifiable
cell lineNA
companyNA
collaborationTomokatsu Ikawa (RCAI)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberNA
sample typeNA
extraction protocol (Details)NA

CAGE Accession numbers
MethodSample accession id
CAGE  DRS008772
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs13408 CAGE DRX008909 DRR009783
Accession ID Mm9

Library idBAMCTSS
CNhs13408 DRZ001208 DRZ002591
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

CNhs13408

00
10
100
1000
10000
1001-0.0749
10020
1003-0.175
10040
1005-0.154
1006-0.183
10070.742
10080
10090.938
101-0.108
10100
1011-0.337
10120
1013-0.0976
1014-0.0874
10150.0647
10160.854
10170
10180
10190
1020
10200
1021-0.0487
1022-0.124
10230
1024-0.307
10250
10260
1027-0.048
10280
1029-0.176
1030
10300
10310.255
1032-0.353
1033-0.0752
10340
10350
1036-0.38
10370
10381.081
1039-0.026
1040
10401.017
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: CNhs13408

Jaspar motifP-value
MA0002.20.00278
MA0003.10.927
MA0004.10.357
MA0006.10.269
MA0007.10.93
MA0009.10.578
MA0014.10.85
MA0017.10.124
MA0018.20.0615
MA0019.10.946
MA0024.10.00322
MA0025.10.693
MA0027.10.351
MA0028.11.02974e-6
MA0029.10.983
MA0030.10.665
MA0031.10.72
MA0035.20.131
MA0038.10.00596
MA0039.24.21121e-4
MA0040.10.964
MA0041.10.646
MA0042.10.564
MA0043.10.374
MA0046.13.13162e-5
MA0047.20.985
MA0048.10.0309
MA0050.10.661
MA0051.10.229
MA0052.10.426
MA0055.10.882
MA0057.10.909
MA0058.10.463
MA0059.10.556
MA0060.11.64422e-11
MA0061.10.0658
MA0062.21.96907e-6
MA0065.20.243
MA0066.10.0895
MA0067.10.975
MA0068.10.757
MA0069.10.992
MA0070.10.708
MA0071.10.05
MA0072.10.00447
MA0073.10.526
MA0074.10.284
MA0076.16.13196e-5
MA0077.10.242
MA0078.19.37614e-4
MA0079.20.413
MA0080.20.135
MA0081.10.116
MA0083.13.61076e-4
MA0084.10.778
MA0087.10.804
MA0088.10.655
MA0090.18.76044e-5
MA0091.10.336
MA0092.10.141
MA0093.10.545
MA0099.20.0074
MA0100.10.11
MA0101.10.499
MA0102.20.264
MA0103.11.51952e-4
MA0104.20.103
MA0105.10.658
MA0106.10.00506
MA0107.10.178
MA0108.29.98286e-6
MA0111.10.983
MA0112.20.773
MA0113.10.944
MA0114.10.0287
MA0115.10.449
MA0116.10.308
MA0117.10.115
MA0119.10.0496
MA0122.10.547
MA0124.10.867
MA0125.10.00627
MA0131.10.0391
MA0135.10.273
MA0136.10.0851
MA0137.20.322
MA0138.20.0118
MA0139.10.207
MA0140.10.205
MA0141.10.141
MA0142.10.322
MA0143.10.00637
MA0144.10.405
MA0145.10.425
MA0146.10.263
MA0147.10.0494
MA0148.10.718
MA0149.10.488
MA0150.10.00485
MA0152.10.613
MA0153.19.93577e-5
MA0154.10.204
MA0155.10.688
MA0156.10.0234
MA0157.10.256
MA0159.10.369
MA0160.10.0521
MA0162.10.904
MA0163.10.344
MA0164.10.779
MA0258.10.0809
MA0259.10.59



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: CNhs13408

Novel motifP-value
10.399
100.857
1000.28
1010.79
1020.359
1030.636
1040.754
1050.129
1060.00402
1070.00199
1080.675
1090.563
110.34
1100.211
1110.228
1120.299
1130.77
1140.0175
1150.107
1160.978
1170.872
1180.734
1190.855
120.764
1200.823
1210.617
1220.79
1230.877
1240.282
1250.0194
1260.407
1270.208
1280.0279
1290.0817
130.431
1300.735
1310.355
1320.426
1330.766
1340.908
1350.306
1360.121
1370.653
1380.427
1390.594
140.979
1400.688
1410.469
1420.523
1430.0695
1440.0843
1450.11
1460.885
1470.339
1480.493
1490.288
150.36
1500.0407
1510.432
1520.63
1530.286
1540.369
1550.726
1560.821
1570.637
1580.112
1590.915
1600.909
1610.193
1620.528
1630.654
1640.0924
1650.405
1660.833
1670.576
1680.548
1690.191
170.131
180.072
190.0751
20.663
200.357
210.104
220.103
230.0148
240.915
250.633
260.0041
270.918
280.753
290.87
30.634
300.689
310.962
320.856
330.593
340.505
350.476
360.204
370.786
380.23
390.49
40.414
400.139
410.0375
420.492
430.0912
440.988
450.411
460.0462
470.707
480.908
490.0891
50.197
500.879
510.381
520.271
530.654
540.404
550.275
560.587
570.236
580.462
590.073
60.815
600.0361
610.836
620.206
630.507
640.837
650.389
660.129
670.579
680.156
690.368
70.186
700.0483
710.176
720.888
730.805
740.982
750.474
760.53
770.338
780.144
790.839
80.694
800.759
810.541
820.16
830.215
840.0614
850.405
860.6
870.293
880.813
890.705
90.36
900.121
910.272
920.00628
936.79852e-5
940.171
950.00355
960.165
970.0721
980.953
990.7



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: CNhs13408


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)
0000548 (animal cell)
0000066 (epithelial cell)
0002371 (somatic cell)
0000255 (eukaryotic cell)
0002076 (endo-epithelial cell)
0002293 (epithelial cell of thymus)

UBERON: Anatomy
0000468 (multi-cellular organism)
0002370 (thymus)
0004119 (endoderm-derived structure)
0000062 (organ)
0000475 (organism subdivision)
0004120 (mesoderm-derived structure)
0000077 (mixed endoderm/mesoderm-derived structure)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0002368 (endocrine gland)
0004177 (hemopoietic organ)
0005057 (immune organ)
0002530 (gland)
0005058 (hemolymphoid system gland)
0010317 (germ layer / neural crest derived structure)
0000153 (anterior region of body)
0002390 (hematopoietic system)
0000949 (endocrine system)
0002193 (hemolymphoid system)
0002405 (immune system)
0009113 (thymic region)

FF: FANTOM5
0000102 (sample by type)
0000003 (cell line sample)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000343 (control treatment sample)
0000350 (experimentally modified sample)
0011508 (mouse TSt-4/DLL1 feeder cells 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
CL:0000223 (endodermal cell)

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