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|fonse_treatment_closure=
|fonse_treatment_closure=
|top_motifs=TBP:1.96671128688;SMAD1..7,9:1.76988428479;NKX2-3_NKX2-5:1.73391663477;PAX1,9:1.69378057023;FOXL1:1.60761881605;HOX{A4,D4}:1.43105020246;TGIF1:1.35774760418;PBX1:1.2754846209;GTF2I:1.23014055721;RREB1:1.21526633698;FOX{F1,F2,J1}:1.20828988825;ZNF148:1.20775144364;PATZ1:1.2028981253;LEF1_TCF7_TCF7L1,2:1.19015792622;TBX4,5:1.18232673986;MAZ:1.16452988767;NANOG{mouse}:1.11053951922;NKX3-2:1.07213806221;TFCP2:1.06999470506;TLX2:1.0314921813;HSF1,2:1.0297700148;EP300:1.02963801814;T:1.02739361773;TFAP4:1.00470591123;TAL1_TCF{3,4,12}:0.964866036773;ZNF238:0.937596424991;ZNF423:0.933351641756;GATA6:0.927694677179;XCPE1{core}:0.922444253526;MEF2{A,B,C,D}:0.917260051765;MAFB:0.892511616057;SRF:0.888844732704;EBF1:0.877862525822;MYFfamily:0.861984283644;TFAP2{A,C}:0.840088078432;MZF1:0.822904276534;SOX{8,9,10}:0.81044944126;LHX3,4:0.787916875762;RBPJ:0.779667350522;HIC1:0.774102480604;GCM1,2:0.769234738181;POU5F1:0.763297842577;TFAP2B:0.758548227919;HOXA9_MEIS1:0.752002559671;CUX2:0.747238697475;FOXA2:0.745998802443;TLX1..3_NFIC{dimer}:0.71787069023;BREu{core}:0.689344094043;NHLH1,2:0.681488859579;RXR{A,B,G}_{NR1H2,PPAR}dimers:0.66396178578;MTF1:0.636212947147;EN1,2:0.635196363937;MED-1{core}:0.622486824031;GLI1..3:0.617620602987;NR3C1:0.616807924913;ZIC1..3:0.610259758621;FOSL2:0.606139788278;EGR1..3:0.592541928106;SP1:0.591506196017;KLF4:0.58626832416;GFI1:0.574201523528;PAX6:0.568166575355;SOX5:0.564884337004;PRRX1,2:0.550376224929;HNF1A:0.528676210548;TEAD1:0.51912939927;DBP:0.508140449164;ADNP_IRX_SIX_ZHX:0.506634636366;ZFP161:0.47984089827;LMO2:0.471095917276;TFDP1:0.465396202003;ONECUT1,2:0.459274372141;MYOD1:0.45732714203;TP53:0.455010859213;NR5A1,2:0.44492014946;SNAI1..3:0.427814000437;NKX2-1,4:0.421210932116;FOX{D1,D2}:0.408390965072;VSX1,2:0.403751839574;ZBTB6:0.400810508825;MTE{core}:0.400470320161;HES1:0.399775158231;FOS_FOS{B,L1}_JUN{B,D}:0.391400402821;HLF:0.383877267313;ATF2:0.376362012354;NANOG:0.374662793272;CEBPA,B_DDIT3:0.358292976294;OCT4_SOX2{dimer}:0.352314490236;POU2F1..3:0.340852923482;NFE2L2:0.337197373423;FOXM1:0.335064752615;RFX1:0.325384626458;HNF4A_NR2F1,2:0.315423578477;HIF1A:0.308514906698;AHR_ARNT_ARNT2:0.303461253028;HMX1:0.300563343529;JUN:0.295179031288;TOPORS:0.294716737831;RFX2..5_RFXANK_RFXAP:0.292779115017;NFIX:0.291687902455;SOX17:0.284926658817;PAX5:0.276127757621;RORA:0.269887392212;GFI1B:0.264936936173;MYBL2:0.253030431794;GTF2A1,2:0.251438974137;BACH2:0.251215511407;ESR1:0.247940712721;REST:0.241800509803;NFY{A,B,C}:0.238886533983;E2F1..5:0.23109398713;AR:0.229441375609;IKZF1:0.224271513273;POU6F1:0.212278037053;SOX2:0.199281371231;PDX1:0.181656635742;NFATC1..3:0.173784420847;ZNF384:0.171852904576;GZF1:0.154416524999;POU3F1..4:0.151301728898;HMGA1,2:0.128636424131;PPARG:0.105557032915;PRDM1:0.100320000466;HBP1_HMGB_SSRP1_UBTF:0.0859588195944;ZNF143:0.0559093557882;PAX2:0.0539423696358;NRF1:0.0453138561069;CDC5L:0.0349898980597;ATF6:0.00678144682143;ESRRA:-0.00811664131358;HAND1,2:-0.0191375266332;STAT2,4,6:-0.0325528468074;NFE2L1:-0.0598648917527;HOX{A5,B5}:-0.0738477935416;IKZF2:-0.0768545206658;RUNX1..3:-0.0798665576821;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:-0.0923325061022;ZEB1:-0.111408985425;MYB:-0.132614402795;FOXP3:-0.155657346505;NFIL3:-0.219259618004;DMAP1_NCOR{1,2}_SMARC:-0.245430037488;EVI1:-0.255084453683;FOXD3:-0.268479362199;RXRA_VDR{dimer}:-0.27455699241;NFE2:-0.307894470506;NKX3-1:-0.320769463202;SPZ1:-0.327883000172;STAT5{A,B}:-0.336340129609;FOXQ1:-0.351619682532;GATA4:-0.359397405174;bHLH_family:-0.363287022338;NR1H4:-0.393201925992;ATF4:-0.404461790732;UFEwm:-0.419068978504;CRX:-0.425382791937;NFKB1_REL_RELA:-0.4372504249;SPI1:-0.453683107907;ETS1,2:-0.459710798825;ALX1:-0.48000571991;YY1:-0.498488766935;IRF7:-0.514679031043;ALX4:-0.520539608202;RXR{A,B,G}:-0.531088155866;FOXN1:-0.53302646129;ATF5_CREB3:-0.535071707649;SPIB:-0.553958958855;CREB1:-0.561295966237;FOXO1,3,4:-0.566193554735;NKX6-1,2:-0.659280915249;STAT1,3:-0.661144164904;NR6A1:-0.688571942695;NKX2-2,8:-0.728587034644;ELF1,2,4:-0.744593777501;AIRE:-0.772776420697;IRF1,2:-0.777079286541;PAX8:-0.823223583619;PAX4:-0.862844999684;ELK1,4_GABP{A,B1}:-0.905983622401;CDX1,2,4:-0.963453060455;SREBF1,2:-0.978528066091;POU1F1:-1.10181533809;PITX1..3:-1.1096394455;TEF:-1.20649464416;ARID5B:-1.20792921818;FOX{I1,J2}:-1.26796479539;FOXP1:-1.7238107356;ZBTB16:-1.78824290334;BPTF:-1.93738542221
|top_motifs=TBP:1.96671128688;SMAD1..7,9:1.76988428479;NKX2-3_NKX2-5:1.73391663477;PAX1,9:1.69378057023;FOXL1:1.60761881605;HOX{A4,D4}:1.43105020246;TGIF1:1.35774760418;PBX1:1.2754846209;GTF2I:1.23014055721;RREB1:1.21526633698;FOX{F1,F2,J1}:1.20828988825;ZNF148:1.20775144364;PATZ1:1.2028981253;LEF1_TCF7_TCF7L1,2:1.19015792622;TBX4,5:1.18232673986;MAZ:1.16452988767;NANOG{mouse}:1.11053951922;NKX3-2:1.07213806221;TFCP2:1.06999470506;TLX2:1.0314921813;HSF1,2:1.0297700148;EP300:1.02963801814;T:1.02739361773;TFAP4:1.00470591123;TAL1_TCF{3,4,12}:0.964866036773;ZNF238:0.937596424991;ZNF423:0.933351641756;GATA6:0.927694677179;XCPE1{core}:0.922444253526;MEF2{A,B,C,D}:0.917260051765;MAFB:0.892511616057;SRF:0.888844732704;EBF1:0.877862525822;MYFfamily:0.861984283644;TFAP2{A,C}:0.840088078432;MZF1:0.822904276534;SOX{8,9,10}:0.81044944126;LHX3,4:0.787916875762;RBPJ:0.779667350522;HIC1:0.774102480604;GCM1,2:0.769234738181;POU5F1:0.763297842577;TFAP2B:0.758548227919;HOXA9_MEIS1:0.752002559671;CUX2:0.747238697475;FOXA2:0.745998802443;TLX1..3_NFIC{dimer}:0.71787069023;BREu{core}:0.689344094043;NHLH1,2:0.681488859579;RXR{A,B,G}_{NR1H2,PPAR}dimers:0.66396178578;MTF1:0.636212947147;EN1,2:0.635196363937;MED-1{core}:0.622486824031;GLI1..3:0.617620602987;NR3C1:0.616807924913;ZIC1..3:0.610259758621;FOSL2:0.606139788278;EGR1..3:0.592541928106;SP1:0.591506196017;KLF4:0.58626832416;GFI1:0.574201523528;PAX6:0.568166575355;SOX5:0.564884337004;PRRX1,2:0.550376224929;HNF1A:0.528676210548;TEAD1:0.51912939927;DBP:0.508140449164;ADNP_IRX_SIX_ZHX:0.506634636366;ZFP161:0.47984089827;LMO2:0.471095917276;TFDP1:0.465396202003;ONECUT1,2:0.459274372141;MYOD1:0.45732714203;TP53:0.455010859213;NR5A1,2:0.44492014946;SNAI1..3:0.427814000437;NKX2-1,4:0.421210932116;FOX{D1,D2}:0.408390965072;VSX1,2:0.403751839574;ZBTB6:0.400810508825;MTE{core}:0.400470320161;HES1:0.399775158231;FOS_FOS{B,L1}_JUN{B,D}:0.391400402821;HLF:0.383877267313;ATF2:0.376362012354;NANOG:0.374662793272;CEBPA,B_DDIT3:0.358292976294;OCT4_SOX2{dimer}:0.352314490236;POU2F1..3:0.340852923482;NFE2L2:0.337197373423;FOXM1:0.335064752615;RFX1:0.325384626458;HNF4A_NR2F1,2:0.315423578477;HIF1A:0.308514906698;AHR_ARNT_ARNT2:0.303461253028;HMX1:0.300563343529;JUN:0.295179031288;TOPORS:0.294716737831;RFX2..5_RFXANK_RFXAP:0.292779115017;NFIX:0.291687902455;SOX17:0.284926658817;PAX5:0.276127757621;RORA:0.269887392212;GFI1B:0.264936936173;MYBL2:0.253030431794;GTF2A1,2:0.251438974137;BACH2:0.251215511407;ESR1:0.247940712721;REST:0.241800509803;NFY{A,B,C}:0.238886533983;E2F1..5:0.23109398713;AR:0.229441375609;IKZF1:0.224271513273;POU6F1:0.212278037053;SOX2:0.199281371231;PDX1:0.181656635742;NFATC1..3:0.173784420847;ZNF384:0.171852904576;GZF1:0.154416524999;POU3F1..4:0.151301728898;HMGA1,2:0.128636424131;PPARG:0.105557032915;PRDM1:0.100320000466;HBP1_HMGB_SSRP1_UBTF:0.0859588195944;ZNF143:0.0559093557882;PAX2:0.0539423696358;NRF1:0.0453138561069;CDC5L:0.0349898980597;ATF6:0.00678144682143;ESRRA:-0.00811664131358;HAND1,2:-0.0191375266332;STAT2,4,6:-0.0325528468074;NFE2L1:-0.0598648917527;HOX{A5,B5}:-0.0738477935416;IKZF2:-0.0768545206658;RUNX1..3:-0.0798665576821;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:-0.0923325061022;ZEB1:-0.111408985425;MYB:-0.132614402795;FOXP3:-0.155657346505;NFIL3:-0.219259618004;DMAP1_NCOR{1,2}_SMARC:-0.245430037488;EVI1:-0.255084453683;FOXD3:-0.268479362199;RXRA_VDR{dimer}:-0.27455699241;NFE2:-0.307894470506;NKX3-1:-0.320769463202;SPZ1:-0.327883000172;STAT5{A,B}:-0.336340129609;FOXQ1:-0.351619682532;GATA4:-0.359397405174;bHLH_family:-0.363287022338;NR1H4:-0.393201925992;ATF4:-0.404461790732;UFEwm:-0.419068978504;CRX:-0.425382791937;NFKB1_REL_RELA:-0.4372504249;SPI1:-0.453683107907;ETS1,2:-0.459710798825;ALX1:-0.48000571991;YY1:-0.498488766935;IRF7:-0.514679031043;ALX4:-0.520539608202;RXR{A,B,G}:-0.531088155866;FOXN1:-0.53302646129;ATF5_CREB3:-0.535071707649;SPIB:-0.553958958855;CREB1:-0.561295966237;FOXO1,3,4:-0.566193554735;NKX6-1,2:-0.659280915249;STAT1,3:-0.661144164904;NR6A1:-0.688571942695;NKX2-2,8:-0.728587034644;ELF1,2,4:-0.744593777501;AIRE:-0.772776420697;IRF1,2:-0.777079286541;PAX8:-0.823223583619;PAX4:-0.862844999684;ELK1,4_GABP{A,B1}:-0.905983622401;CDX1,2,4:-0.963453060455;SREBF1,2:-0.978528066091;POU1F1:-1.10181533809;PITX1..3:-1.1096394455;TEF:-1.20649464416;ARID5B:-1.20792921818;FOX{I1,J2}:-1.26796479539;FOXP1:-1.7238107356;ZBTB16:-1.78824290334;BPTF:-1.93738542221
|comment=
|created_by=
|creation_date=
|def=
|has_quality=
|is_a=EFO:0002091;;FF:0000004;;FF:0000103;;FF:0011354
|namespace=FANTOM5
|part_of=
}}
}}

Revision as of 16:02, 7 March 2012


Name:whole body, embryo E16
Species:Mouse (Mus musculus)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissuewhole body
dev stage16 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

CNhs10514

00
10.0954
100
1000.0733
10000.0733
1001-0.0625
10020
10030.0728
10040
1005-0.0389
10060.0548
10070.00792
10080
10090.0161
101-0.0295
10100
10110.0557
10120
1013-0.175
10140.272
10150.121
10160.122
10170.0733
10180.191
10190
1020
10200
10210
10220.0996
10230
1024-0.0663
10250.393
10260.0733
10270.075
10280
1029-0.148
1030.136
10300
10310.164
1032-0.177
10330
10340
10350
1036-0.0395
10370
1038-0.0126
10390.062
1040
10400.0494
10410.136



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: CNhs10514

Jaspar motifP-value
MA0002.20.395
MA0003.10.139
MA0004.10.0977
MA0006.10.651
MA0007.10.08
MA0009.10.836
MA0014.10.185
MA0017.10.308
MA0018.20.934
MA0019.10.874
MA0024.10.276
MA0025.10.934
MA0027.10.954
MA0028.15.62343e-6
MA0029.10.413
MA0030.10.197
MA0031.10.707
MA0035.20.0232
MA0038.10.0143
MA0039.20.43
MA0040.10.674
MA0041.10.293
MA0042.10.626
MA0043.10.82
MA0046.11.06254e-14
MA0047.20.21
MA0048.10.0156
MA0050.11.5814e-5
MA0051.11.61826e-4
MA0052.13.22171e-13
MA0055.10.00197
MA0057.10.875
MA0058.10.0466
MA0059.10.00815
MA0060.17.28869e-6
MA0061.10.0625
MA0062.21.8552e-11
MA0065.20.469
MA0066.10.25
MA0067.10.102
MA0068.10.493
MA0069.10.927
MA0070.10.272
MA0071.10.121
MA0072.10.864
MA0073.10.939
MA0074.10.312
MA0076.14.99031e-7
MA0077.10.228
MA0078.10.898
MA0079.20.0437
MA0080.21.58306e-7
MA0081.10.071
MA0083.17.58113e-8
MA0084.10.8
MA0087.10.417
MA0088.10.198
MA0090.10.247
MA0091.10.646
MA0092.10.922
MA0093.10.08
MA0099.20.636
MA0100.10.061
MA0101.10.0165
MA0102.20.185
MA0103.10.26
MA0104.20.442
MA0105.10.0448
MA0106.10.057
MA0107.10.0752
MA0108.27.99607e-47
MA0111.10.747
MA0112.20.00475
MA0113.10.176
MA0114.10.892
MA0115.10.479
MA0116.10.121
MA0117.10.684
MA0119.10.97
MA0122.10.829
MA0124.10.702
MA0125.10.105
MA0131.10.547
MA0135.10.00669
MA0136.11.39792e-10
MA0137.20.0161
MA0138.25.10351e-4
MA0139.10.0962
MA0140.10.0314
MA0141.10.118
MA0142.10.69
MA0143.10.0889
MA0144.10.139
MA0145.10.988
MA0146.10.277
MA0147.10.473
MA0148.10.271
MA0149.10.0214
MA0150.10.664
MA0152.10.943
MA0153.11.75853e-8
MA0154.10.48
MA0155.10.387
MA0156.11.39357e-11
MA0157.10.968
MA0159.10.0323
MA0160.10.565
MA0162.10.959
MA0163.10.00958
MA0164.10.286
MA0258.10.0939
MA0259.10.666



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: CNhs10514

Novel motifP-value
10.19
100.0148
1000.441
1010.73
1020.346
1030.0171
1040.889
1050.73
1060.428
1070.512
1080.483
1090.034
110.163
1100.053
1110.00375
1120.0109
1130.59
1140.127
1150.342
1160.398
1170.00344
1180.371
1190.15
120.751
1200.816
1210.828
1220.455
1230.232
1240.683
1250.146
1260.11
1270.208
1280.627
1290.628
132.81069e-4
1300.603
1310.0319
1320.917
1330.00874
1340.342
1350.8
1360.239
1370.368
1380.616
1390.0214
140.719
1400.0656
1410.49
1420.622
1430.601
1440.914
1450.014
1460.302
1470.656
1480.0263
1490.946
150.0448
1500.247
1510.505
1520.926
1530.31
1540.134
1550.137
1560.0706
1570.48
1580.0115
1590.00683
1600.499
1610.305
1620.381
1630.833
1640.00514
1650.76
1660.463
1670.0346
1680.0189
1690.0708
170.568
180.703
190.625
20.0969
200.00206
210.739
220.829
230.301
240.424
250.974
260.0341
270.274
280.365
290.00655
30.111
300.134
310.954
320.272
330.471
340.274
350.366
360.423
370.0381
380.511
390.366
40.973
400.806
410.961
420.398
430.288
440.446
450.399
460.295
470.376
480.164
490.0679
50.495
500.996
510.809
520.421
530.173
540.524
550.984
560.975
570.368
580.555
590.737
60.76
600.532
610.166
620.532
630.488
640.729
650.926
660.403
670.428
680.277
690.898
70.312
700.0256
710.0396
720.446
730.0293
740.983
750.0162
760.00204
770.521
780.173
790.702
80.231
800.272
810.994
820.251
830.55
840.331
850.23
860.347
870.119
880.119
890.925
90.691
900.038
910.866
920.798
930.113
940.35
950.0213
960.884
970.959
980.642
990.699



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: CNhs10514


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
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000468 (multi-cellular organism)
0000479 (tissue)
0000922 (embryo)
0001062 (anatomical entity)

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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