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|fonse_treatment_closure=
|fonse_treatment_closure=
|top_motifs=NFY{A,B,C}:2.37057364123;ZNF143:1.8072188306;LEF1_TCF7_TCF7L1,2:1.73831279723;ZNF384:1.6533180509;NANOG{mouse}:1.63857803123;PAX8:1.59804168032;SOX2:1.58047584289;E2F1..5:1.5192183303;TFDP1:1.42511551784;PDX1:1.42428358263;STAT5{A,B}:1.32739106131;GFI1:1.31155766895;SOX17:1.22933597421;YY1:1.22472446691;VSX1,2:1.17516164283;NRF1:1.15872301309;CDC5L:1.10854491723;FOXP3:1.07236251156;ELK1,4_GABP{A,B1}:1.05469737661;EN1,2:1.03312397962;ZNF238:0.987303819232;TOPORS:0.976704110758;RXR{A,B,G}:0.955558356819;BREu{core}:0.894270320281;SOX{8,9,10}:0.887711436615;SOX5:0.881373533875;CDX1,2,4:0.849802362545;HMX1:0.835308092679;ZBTB16:0.769568621552;POU1F1:0.737891069938;PAX6:0.734233623751;HES1:0.714783186434;LHX3,4:0.713292468687;RREB1:0.712883618678;MZF1:0.707608378721;POU2F1..3:0.652756091354;NANOG:0.649735865034;TEF:0.624264479541;HSF1,2:0.60512123326;PATZ1:0.599737839421;PAX5:0.587984259342;MED-1{core}:0.576438413672;TFAP2{A,C}:0.566418366744;FOXQ1:0.556163127241;UFEwm:0.540423004919;MYB:0.521842541924;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:0.511770284322;CUX2:0.506138894232;MAZ:0.490051959978;PAX1,9:0.451246798318;GATA4:0.446980834021;ALX1:0.446597930056;ONECUT1,2:0.437115489373;RXR{A,B,G}_{NR1H2,PPAR}dimers:0.40521222367;GTF2A1,2:0.39857973837;PRRX1,2:0.396885361411;IKZF2:0.395302506608;STAT1,3:0.390421634049;HIC1:0.343769826706;EP300:0.306298955054;ALX4:0.296516839845;PITX1..3:0.280382082516;MTE{core}:0.272293862892;KLF4:0.266272185467;NKX2-3_NKX2-5:0.266256111539;NKX3-1:0.248763266553;HMGA1,2:0.248114668127;MYBL2:0.234055464011;RFX1:0.230505358242;HIF1A:0.22043898189;PBX1:0.192775602427;GTF2I:0.159132666345;RORA:0.146041121237;FOX{I1,J2}:0.145086244608;SPZ1:0.138296337938;ZFP161:0.137455340245;ATF2:0.136973954791;RBPJ:0.136047054294;AHR_ARNT_ARNT2:0.13502952177;RFX2..5_RFXANK_RFXAP:0.0927598110427;FOXD3:0.0866386671969;NKX6-1,2:0.066585569186;AIRE:0.0542975742653;ELF1,2,4:0.0484659858;ESR1:0.0342172926112;HAND1,2:0.0310947673304;ADNP_IRX_SIX_ZHX:0.0238411536581;EGR1..3:0.0211044490872;XCPE1{core}:0.0206760729447;NR6A1:0.0200385990015;TEAD1:0.0121000856565;GCM1,2:0.0114421440666;HOXA9_MEIS1:-0.000389289383433;GFI1B:-0.00288666291827;ATF4:-0.00737807459224;IKZF1:-0.0200575167799;TFAP2B:-0.0500804592461;NKX2-1,4:-0.0579875653192;HOX{A4,D4}:-0.0697160517125;ZIC1..3:-0.0703687983801;OCT4_SOX2{dimer}:-0.0923937427078;NFE2L1:-0.0975257068483;DBP:-0.100119355008;POU5F1:-0.110248958453;T:-0.128723150844;CRX:-0.12978599004;CREB1:-0.13180714187;SREBF1,2:-0.132269202932;TP53:-0.144113939204;GZF1:-0.144297993864;TBX4,5:-0.183326330292;SPIB:-0.186292454523;POU3F1..4:-0.188652149094;NHLH1,2:-0.189912823906;DMAP1_NCOR{1,2}_SMARC:-0.21481624735;PAX4:-0.226078742046;BPTF:-0.233345327908;RUNX1..3:-0.247195059012;bHLH_family:-0.256285781093;ATF6:-0.259859063499;FOXO1,3,4:-0.269298366417;HBP1_HMGB_SSRP1_UBTF:-0.293903753432;NFKB1_REL_RELA:-0.309921622635;FOXP1:-0.31919091967;ZNF423:-0.327201204139;REST:-0.331678941044;SPI1:-0.341515632028;HNF4A_NR2F1,2:-0.344794272739;TFCP2:-0.351678245389;SRF:-0.362584500433;PRDM1:-0.378826018144;GATA6:-0.401886643996;ATF5_CREB3:-0.407951482959;MEF2{A,B,C,D}:-0.407980814056;ETS1,2:-0.408290633298;ZBTB6:-0.427277085033;HLF:-0.441473858733;NR3C1:-0.443165106904;NR1H4:-0.453703311451;EVI1:-0.487199614771;JUN:-0.507460343156;HNF1A:-0.513504852617;TLX2:-0.547726224146;SP1:-0.55645470879;SNAI1..3:-0.573209217169;TBP:-0.574542328684;FOXL1:-0.58054564818;TFAP4:-0.587055125149;TAL1_TCF{3,4,12}:-0.588583304976;ZEB1:-0.590029005842;MTF1:-0.595654099503;NFATC1..3:-0.609496564935;NFIL3:-0.63221561504;BACH2:-0.648495953534;FOX{D1,D2}:-0.663372188166;GLI1..3:-0.67202261956;NKX2-2,8:-0.69793454484;TGIF1:-0.705675756185;FOS_FOS{B,L1}_JUN{B,D}:-0.709290943483;NR5A1,2:-0.744255704636;PPARG:-0.752401393374;FOSL2:-0.77279825109;ESRRA:-0.783566372896;FOXM1:-0.807468183154;MYOD1:-0.815267589656;MYFfamily:-0.820057434102;POU6F1:-0.827974905081;FOXA2:-0.831247442056;TLX1..3_NFIC{dimer}:-0.832791383434;PAX2:-0.842651525081;SMAD1..7,9:-0.855552277364;RXRA_VDR{dimer}:-0.873447904129;ARID5B:-0.876842508221;NFIX:-0.891957784214;HOX{A5,B5}:-0.899001998859;FOX{F1,F2,J1}:-0.9044551636;NFE2:-0.913377779652;AR:-0.913840403693;ZNF148:-0.941100022352;FOXN1:-0.947108127035;MAFB:-0.952636868991;NFE2L2:-1.05525290526;IRF1,2:-1.06124285994;IRF7:-1.09002168467;NKX3-2:-1.13355456949;CEBPA,B_DDIT3:-1.25882771535;EBF1:-1.32561039424;LMO2:-1.59440815601;STAT2,4,6:-1.60253731176
|top_motifs=NFY{A,B,C}:2.37057364123;ZNF143:1.8072188306;LEF1_TCF7_TCF7L1,2:1.73831279723;ZNF384:1.6533180509;NANOG{mouse}:1.63857803123;PAX8:1.59804168032;SOX2:1.58047584289;E2F1..5:1.5192183303;TFDP1:1.42511551784;PDX1:1.42428358263;STAT5{A,B}:1.32739106131;GFI1:1.31155766895;SOX17:1.22933597421;YY1:1.22472446691;VSX1,2:1.17516164283;NRF1:1.15872301309;CDC5L:1.10854491723;FOXP3:1.07236251156;ELK1,4_GABP{A,B1}:1.05469737661;EN1,2:1.03312397962;ZNF238:0.987303819232;TOPORS:0.976704110758;RXR{A,B,G}:0.955558356819;BREu{core}:0.894270320281;SOX{8,9,10}:0.887711436615;SOX5:0.881373533875;CDX1,2,4:0.849802362545;HMX1:0.835308092679;ZBTB16:0.769568621552;POU1F1:0.737891069938;PAX6:0.734233623751;HES1:0.714783186434;LHX3,4:0.713292468687;RREB1:0.712883618678;MZF1:0.707608378721;POU2F1..3:0.652756091354;NANOG:0.649735865034;TEF:0.624264479541;HSF1,2:0.60512123326;PATZ1:0.599737839421;PAX5:0.587984259342;MED-1{core}:0.576438413672;TFAP2{A,C}:0.566418366744;FOXQ1:0.556163127241;UFEwm:0.540423004919;MYB:0.521842541924;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:0.511770284322;CUX2:0.506138894232;MAZ:0.490051959978;PAX1,9:0.451246798318;GATA4:0.446980834021;ALX1:0.446597930056;ONECUT1,2:0.437115489373;RXR{A,B,G}_{NR1H2,PPAR}dimers:0.40521222367;GTF2A1,2:0.39857973837;PRRX1,2:0.396885361411;IKZF2:0.395302506608;STAT1,3:0.390421634049;HIC1:0.343769826706;EP300:0.306298955054;ALX4:0.296516839845;PITX1..3:0.280382082516;MTE{core}:0.272293862892;KLF4:0.266272185467;NKX2-3_NKX2-5:0.266256111539;NKX3-1:0.248763266553;HMGA1,2:0.248114668127;MYBL2:0.234055464011;RFX1:0.230505358242;HIF1A:0.22043898189;PBX1:0.192775602427;GTF2I:0.159132666345;RORA:0.146041121237;FOX{I1,J2}:0.145086244608;SPZ1:0.138296337938;ZFP161:0.137455340245;ATF2:0.136973954791;RBPJ:0.136047054294;AHR_ARNT_ARNT2:0.13502952177;RFX2..5_RFXANK_RFXAP:0.0927598110427;FOXD3:0.0866386671969;NKX6-1,2:0.066585569186;AIRE:0.0542975742653;ELF1,2,4:0.0484659858;ESR1:0.0342172926112;HAND1,2:0.0310947673304;ADNP_IRX_SIX_ZHX:0.0238411536581;EGR1..3:0.0211044490872;XCPE1{core}:0.0206760729447;NR6A1:0.0200385990015;TEAD1:0.0121000856565;GCM1,2:0.0114421440666;HOXA9_MEIS1:-0.000389289383433;GFI1B:-0.00288666291827;ATF4:-0.00737807459224;IKZF1:-0.0200575167799;TFAP2B:-0.0500804592461;NKX2-1,4:-0.0579875653192;HOX{A4,D4}:-0.0697160517125;ZIC1..3:-0.0703687983801;OCT4_SOX2{dimer}:-0.0923937427078;NFE2L1:-0.0975257068483;DBP:-0.100119355008;POU5F1:-0.110248958453;T:-0.128723150844;CRX:-0.12978599004;CREB1:-0.13180714187;SREBF1,2:-0.132269202932;TP53:-0.144113939204;GZF1:-0.144297993864;TBX4,5:-0.183326330292;SPIB:-0.186292454523;POU3F1..4:-0.188652149094;NHLH1,2:-0.189912823906;DMAP1_NCOR{1,2}_SMARC:-0.21481624735;PAX4:-0.226078742046;BPTF:-0.233345327908;RUNX1..3:-0.247195059012;bHLH_family:-0.256285781093;ATF6:-0.259859063499;FOXO1,3,4:-0.269298366417;HBP1_HMGB_SSRP1_UBTF:-0.293903753432;NFKB1_REL_RELA:-0.309921622635;FOXP1:-0.31919091967;ZNF423:-0.327201204139;REST:-0.331678941044;SPI1:-0.341515632028;HNF4A_NR2F1,2:-0.344794272739;TFCP2:-0.351678245389;SRF:-0.362584500433;PRDM1:-0.378826018144;GATA6:-0.401886643996;ATF5_CREB3:-0.407951482959;MEF2{A,B,C,D}:-0.407980814056;ETS1,2:-0.408290633298;ZBTB6:-0.427277085033;HLF:-0.441473858733;NR3C1:-0.443165106904;NR1H4:-0.453703311451;EVI1:-0.487199614771;JUN:-0.507460343156;HNF1A:-0.513504852617;TLX2:-0.547726224146;SP1:-0.55645470879;SNAI1..3:-0.573209217169;TBP:-0.574542328684;FOXL1:-0.58054564818;TFAP4:-0.587055125149;TAL1_TCF{3,4,12}:-0.588583304976;ZEB1:-0.590029005842;MTF1:-0.595654099503;NFATC1..3:-0.609496564935;NFIL3:-0.63221561504;BACH2:-0.648495953534;FOX{D1,D2}:-0.663372188166;GLI1..3:-0.67202261956;NKX2-2,8:-0.69793454484;TGIF1:-0.705675756185;FOS_FOS{B,L1}_JUN{B,D}:-0.709290943483;NR5A1,2:-0.744255704636;PPARG:-0.752401393374;FOSL2:-0.77279825109;ESRRA:-0.783566372896;FOXM1:-0.807468183154;MYOD1:-0.815267589656;MYFfamily:-0.820057434102;POU6F1:-0.827974905081;FOXA2:-0.831247442056;TLX1..3_NFIC{dimer}:-0.832791383434;PAX2:-0.842651525081;SMAD1..7,9:-0.855552277364;RXRA_VDR{dimer}:-0.873447904129;ARID5B:-0.876842508221;NFIX:-0.891957784214;HOX{A5,B5}:-0.899001998859;FOX{F1,F2,J1}:-0.9044551636;NFE2:-0.913377779652;AR:-0.913840403693;ZNF148:-0.941100022352;FOXN1:-0.947108127035;MAFB:-0.952636868991;NFE2L2:-1.05525290526;IRF1,2:-1.06124285994;IRF7:-1.09002168467;NKX3-2:-1.13355456949;CEBPA,B_DDIT3:-1.25882771535;EBF1:-1.32561039424;LMO2:-1.59440815601;STAT2,4,6:-1.60253731176
|comment=
|created_by=
|creation_date=
|def=
|has_quality=
|is_a=EFO:0002091;;FF:0000004;;FF:0000103;;FF:0011314
|namespace=FANTOM5
|part_of=
}}
}}

Revision as of 16:01, 7 March 2012


Name:forelimb, embryo E11
Species:Mouse (Mus musculus)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissueforelimb
dev stage11 days embryo
sexmixture
ageNA
cell typeCELL MIXTURE - tissue sample
cell lineNA
companyNA
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberNA
sample typeNA
extraction protocol (Details)NA
Download raw sequence, BAM & CTSS
Mm9
BAMCTSS
[{{{mm9bam}}} download][{{{mm9ctss}}} donwload]
Mm10
BAMCTSS
[{{{mm10bam}}} download][{{{mm10ctss}}} donwload]





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

CNhs10596

00
10
100
1000
10000
1001-0.0496
1002-0.0517
1003-0.102
10040
1005-0.0641
1006-0.119
10070.118
10080
1009-0.0572
1010.149
10100
10110
10120
1013-0.217
10140
10150.374
10160.493
10170
10180.0848
10190
1020
10200
10210.0361
1022-0.0855
10230
1024-0.0905
10250
10260
10270
10280
1029-0.0921
103-0.0446
10300
1031-0.0342
1032-0.177
10330.053
10340
10350
10360.00662
10370
1038-0.065
1039-0.198
1040
10400.00172
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 no result for this sample


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: CNhs10596

Jaspar motifP-value
MA0002.20.0062
MA0003.10.0697
MA0004.10.422
MA0006.10.426
MA0007.10.568
MA0009.10.338
MA0014.10.103
MA0017.10.00201
MA0018.20.517
MA0019.10.745
MA0024.19.06651e-7
MA0025.10.305
MA0027.10.128
MA0028.10.0145
MA0029.10.878
MA0030.10.302
MA0031.10.077
MA0035.20.0867
MA0038.10.078
MA0039.20.00705
MA0040.10.485
MA0041.10.176
MA0042.10.992
MA0043.10.00836
MA0046.12.36024e-14
MA0047.20.0705
MA0048.10.0136
MA0050.16.50529e-8
MA0051.16.37755e-5
MA0052.10.00109
MA0055.10.0116
MA0057.10.169
MA0058.10.274
MA0059.10.236
MA0060.17.9107e-22
MA0061.10.199
MA0062.20.0288
MA0065.20.0124
MA0066.10.268
MA0067.10.293
MA0068.10.86
MA0069.10.724
MA0070.10.786
MA0071.10.232
MA0072.10.397
MA0073.10.953
MA0074.10.893
MA0076.10.00922
MA0077.10.00417
MA0078.10.0975
MA0079.20.736
MA0080.23.61812e-7
MA0081.10.552
MA0083.10.258
MA0084.10.617
MA0087.10.851
MA0088.10.704
MA0090.10.334
MA0091.10.971
MA0092.10.572
MA0093.10.397
MA0099.20.00188
MA0100.10.18
MA0101.10.835
MA0102.20.185
MA0103.10.0126
MA0104.20.0576
MA0105.10.107
MA0106.10.463
MA0107.10.639
MA0108.20.0712
MA0111.10.382
MA0112.26.67661e-4
MA0113.10.552
MA0114.10.0132
MA0115.10.802
MA0116.10.0153
MA0117.10.252
MA0119.10.00812
MA0122.10.872
MA0124.10.463
MA0125.10.0369
MA0131.10.128
MA0135.10.956
MA0136.10.212
MA0137.20.69
MA0138.23.43764e-5
MA0139.10.0372
MA0140.10.219
MA0141.10.0303
MA0142.10.678
MA0143.10.00104
MA0144.10.216
MA0145.10.0209
MA0146.10.968
MA0147.10.101
MA0148.15.97186e-4
MA0149.10.318
MA0150.10.00763
MA0152.10.974
MA0153.12.38509e-10
MA0154.10.00158
MA0155.10.873
MA0156.10.609
MA0157.10.211
MA0159.10.0167
MA0160.10.184
MA0162.10.534
MA0163.10.183
MA0164.10.53
MA0258.10.0131
MA0259.10.376



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: CNhs10596

Novel motifP-value
10.0994
100.818
1000.534
1010.517
1020.691
1030.0145
1040.746
1050.227
1060.00707
1070.0371
1080.658
1090.314
110.321
1100.616
1110.0612
1120.0826
1130.515
1140.0782
1150.245
1160.868
1170.45
1180.771
1190.0308
120.865
1200.828
1210.327
1220.572
1230.0383
1240.248
1250.695
1260.793
1270.0509
1280.0592
1290.206
130.887
1300.735
1310.189
1320.311
1330.778
1340.862
1350.219
1360.479
1370.363
1380.739
1390.0134
140.297
1400.00542
1410.164
1420.238
1430.986
1440.98
1450.391
1460.664
1470.383
1480.547
1490.186
150.146
1500.729
1510.144
1520.151
1530.0572
1540.91
1550.283
1560.00253
1570.52
1580.868
1590.15
1600.739
1610.656
1620.72
1630.0431
1640.516
1650.476
1660.978
1670.811
1680.164
1690.0799
170.076
180.586
190.0878
20.486
200.271
210.773
220.342
230.0211
240.815
250.572
260.626
270.374
280.403
290.776
30.298
300.661
310.423
320.214
330.8
340.676
350.367
360.53
370.193
380.33
390.791
40.638
400.592
410.883
420.742
430.179
440.151
450.445
460.463
470.138
480.241
490.165
50.139
500.943
510.446
520.19
530.347
540.279
550.61
560.366
570.716
580.225
590.0928
60.535
600.104
610.473
620.0841
630.2
640.488
650.155
660.281
670.542
680.401
690.248
70.369
700.00254
710.467
720.537
730.353
740.247
750.659
760.488
770.152
780.448
790.32
80.463
800.151
810.297
820.0285
830.49
840.894
850.0241
860.802
870.889
880.457
890.0652
90.407
900.0923
910.532
920.0256
930.512
940.77
950.563
960.262
970.875
980.379
990.644



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: CNhs10596


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

UBERON: Anatomy
0000026 (appendage)
0000061 (anatomical structure)
0000153 (anterior region of body)
0000465 (material anatomical entity)
0000468 (multi-cellular organism)
0000475 (organism subdivision)
0000479 (tissue)
0000922 (embryo)
0000923 (germ layer)
0000926 (mesoderm)
0001048 (primordium)
0001062 (anatomical entity)
0002050 (embryonic structure)
0002101 (limb)
0002102 (forelimb)
0002532 (epiblast (generic))
0003081 (lateral plate mesoderm)
0003102 (surface structure)
0004120 (mesoderm-derived structure)
0004347 (limb bud)
0004357 (paired limb/fin bud)
0004708 (paired limb/fin)
0004710 (pectoral appendage)
0005423 (developing anatomical structure)
0005732 (limb/fin field)
0005733 (limb field)

FF: FANTOM5
NA

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

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