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|fonse_treatment_closure=
|fonse_treatment_closure=
|top_motifs=FOXL1:1.66996773276;PAX1,9:1.65485229188;ZNF423:1.60185290511;NANOG{mouse}:1.52488342711;GATA6:1.50026370319;NKX2-3_NKX2-5:1.36608057585;RREB1:1.35300656011;SMAD1..7,9:1.34779740125;HOX{A4,D4}:1.31146004352;SOX{8,9,10}:1.19941720528;NFY{A,B,C}:1.1324969034;MZF1:1.12238824107;PATZ1:1.11298906094;OCT4_SOX2{dimer}:1.05690486617;GFI1:1.05579907472;EP300:1.0481726741;TBP:1.01784142529;PBX1:1.01218027003;TGIF1:0.983799150015;HSF1,2:0.983278962992;PRRX1,2:0.979432075494;CUX2:0.927072840691;HOXA9_MEIS1:0.926769294156;ONECUT1,2:0.913132529234;POU5F1:0.908829165674;MAZ:0.9021018025;PAX6:0.884414780452;E2F1..5:0.878718987457;SOX2:0.865955984368;LHX3,4:0.818484464789;FOX{F1,F2,J1}:0.812927896033;KLF4:0.769737823956;ZNF238:0.768457695275;BREu{core}:0.766689587849;ZNF148:0.746050738041;NKX3-2:0.735661183994;TFAP4:0.734309600077;NHLH1,2:0.734232622416;GTF2I:0.72627193007;TFCP2:0.711932704679;ADNP_IRX_SIX_ZHX:0.710910399337;SOX5:0.703002207447;TFDP1:0.702177264752;MYBL2:0.695508305205;VSX1,2:0.693575225665;LEF1_TCF7_TCF7L1,2:0.660545155321;SOX17:0.645826949592;TBX4,5:0.643883626793;NANOG:0.631279895999;MED-1{core}:0.621626529551;SRF:0.61821484043;ZNF143:0.611451782152;GZF1:0.609926541305;MYFfamily:0.598401272591;AHR_ARNT_ARNT2:0.574564709542;NRF1:0.546934289196;EN1,2:0.53544954341;ZNF384:0.518602731043;MEF2{A,B,C,D}:0.516000164394;HIC1:0.507151440625;MAFB:0.501450552858;RXR{A,B,G}_{NR1H2,PPAR}dimers:0.459063298952;EGR1..3:0.422648214866;T:0.415793127818;NKX2-1,4:0.414815937767;FOXA2:0.413277156079;TLX1..3_NFIC{dimer}:0.40996198913;MTF1:0.405513614766;EBF1:0.396043797416;ZFP161:0.394725596716;HBP1_HMGB_SSRP1_UBTF:0.393930813112;DBP:0.380645162577;POU2F1..3:0.37921925989;MYOD1:0.379029073246;PRDM1:0.372782782063;XCPE1{core}:0.369193264819;GFI1B:0.368315607657;TFAP2B:0.359379725129;ZIC1..3:0.350286610621;TOPORS:0.346824602432;TFAP2{A,C}:0.343961368135;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:0.342711863904;FOXM1:0.342533725057;POU6F1:0.33341370124;HOX{A5,B5}:0.321248042474;RFX1:0.30202202087;RBPJ:0.296587887015;HES1:0.29531206662;NFE2L1:0.286122525504;FOXD3:0.284888739862;TAL1_TCF{3,4,12}:0.281685290758;HNF1A:0.279201904878;NFIX:0.274930243235;GLI1..3:0.269908311203;RORA:0.257946213456;TEAD1:0.223559989429;ATF2:0.206861321555;JUN:0.188947546109;TLX2:0.182367824591;PDX1:0.167725966257;UFEwm:0.16535466018;MTE{core}:0.143713186584;GCM1,2:0.136407227356;IKZF2:0.126917508932;NFE2L2:0.126257665643;REST:0.122692270856;POU3F1..4:0.120889033378;RFX2..5_RFXANK_RFXAP:0.116168467169;MYB:0.107488390675;LMO2:0.105244701393;HMX1:0.0984049906459;HIF1A:0.084537283167;PAX2:0.0658704240611;ZBTB6:0.057127620108;STAT5{A,B}:0.0560391958389;EVI1:0.0515348360605;IKZF1:0.042327304269;NKX3-1:0.0388397495307;NFATC1..3:0.0290970151438;HNF4A_NR2F1,2:0.0234613496625;CDC5L:0.000326751293077;HMGA1,2:0.000194585955411;RUNX1..3:-0.00845139077689;SP1:-0.0143352325665;ALX1:-0.0200178313814;SNAI1..3:-0.0265229642188;STAT1,3:-0.0331533341811;CEBPA,B_DDIT3:-0.0352114244261;GTF2A1,2:-0.0362929115039;YY1:-0.0399490236469;ATF4:-0.0642177238157;NFE2:-0.0724339618789;PAX5:-0.0857685959583;NR3C1:-0.102695441594;ATF6:-0.111455505624;ATF5_CREB3:-0.135947237182;GATA4:-0.140093292392;BACH2:-0.149129643672;HAND1,2:-0.184444199731;HLF:-0.213282722917;PPARG:-0.214808539446;bHLH_family:-0.221049540241;PITX1..3:-0.237736410669;AIRE:-0.26614828625;CREB1:-0.271934960979;CDX1,2,4:-0.277041163453;FOSL2:-0.281278421758;ELK1,4_GABP{A,B1}:-0.283111770443;TP53:-0.293282455761;ARID5B:-0.294804598768;FOS_FOS{B,L1}_JUN{B,D}:-0.295008906252;PAX8:-0.323071074042;TEF:-0.347569272657;NR5A1,2:-0.365866419487;PAX4:-0.370874581804;DMAP1_NCOR{1,2}_SMARC:-0.384727013846;ESRRA:-0.406041762285;FOX{D1,D2}:-0.421822190205;RXRA_VDR{dimer}:-0.436777637454;SPI1:-0.448188090463;CRX:-0.462893349795;AR:-0.468431614673;FOXP3:-0.487211401125;IRF7:-0.488035566772;SPIB:-0.488256839221;NFKB1_REL_RELA:-0.492658216114;ESR1:-0.507492912587;RXR{A,B,G}:-0.51081141906;ELF1,2,4:-0.513317247468;NFIL3:-0.535484126512;ZEB1:-0.544303601139;NKX6-1,2:-0.564633766684;STAT2,4,6:-0.577213678973;FOXN1:-0.604671275774;ETS1,2:-0.60500228992;ALX4:-0.655377457604;NR6A1:-0.665675805437;FOXQ1:-0.671055131466;SPZ1:-0.680474676038;FOX{I1,J2}:-0.850963543807;IRF1,2:-0.907315967897;ZBTB16:-0.958178137645;POU1F1:-0.967723502707;NKX2-2,8:-0.979559998467;FOXO1,3,4:-0.990598428091;SREBF1,2:-1.04458628017;NR1H4:-1.05046405578;FOXP1:-1.18678322172;BPTF:-1.50615994155
|top_motifs=FOXL1:1.66996773276;PAX1,9:1.65485229188;ZNF423:1.60185290511;NANOG{mouse}:1.52488342711;GATA6:1.50026370319;NKX2-3_NKX2-5:1.36608057585;RREB1:1.35300656011;SMAD1..7,9:1.34779740125;HOX{A4,D4}:1.31146004352;SOX{8,9,10}:1.19941720528;NFY{A,B,C}:1.1324969034;MZF1:1.12238824107;PATZ1:1.11298906094;OCT4_SOX2{dimer}:1.05690486617;GFI1:1.05579907472;EP300:1.0481726741;TBP:1.01784142529;PBX1:1.01218027003;TGIF1:0.983799150015;HSF1,2:0.983278962992;PRRX1,2:0.979432075494;CUX2:0.927072840691;HOXA9_MEIS1:0.926769294156;ONECUT1,2:0.913132529234;POU5F1:0.908829165674;MAZ:0.9021018025;PAX6:0.884414780452;E2F1..5:0.878718987457;SOX2:0.865955984368;LHX3,4:0.818484464789;FOX{F1,F2,J1}:0.812927896033;KLF4:0.769737823956;ZNF238:0.768457695275;BREu{core}:0.766689587849;ZNF148:0.746050738041;NKX3-2:0.735661183994;TFAP4:0.734309600077;NHLH1,2:0.734232622416;GTF2I:0.72627193007;TFCP2:0.711932704679;ADNP_IRX_SIX_ZHX:0.710910399337;SOX5:0.703002207447;TFDP1:0.702177264752;MYBL2:0.695508305205;VSX1,2:0.693575225665;LEF1_TCF7_TCF7L1,2:0.660545155321;SOX17:0.645826949592;TBX4,5:0.643883626793;NANOG:0.631279895999;MED-1{core}:0.621626529551;SRF:0.61821484043;ZNF143:0.611451782152;GZF1:0.609926541305;MYFfamily:0.598401272591;AHR_ARNT_ARNT2:0.574564709542;NRF1:0.546934289196;EN1,2:0.53544954341;ZNF384:0.518602731043;MEF2{A,B,C,D}:0.516000164394;HIC1:0.507151440625;MAFB:0.501450552858;RXR{A,B,G}_{NR1H2,PPAR}dimers:0.459063298952;EGR1..3:0.422648214866;T:0.415793127818;NKX2-1,4:0.414815937767;FOXA2:0.413277156079;TLX1..3_NFIC{dimer}:0.40996198913;MTF1:0.405513614766;EBF1:0.396043797416;ZFP161:0.394725596716;HBP1_HMGB_SSRP1_UBTF:0.393930813112;DBP:0.380645162577;POU2F1..3:0.37921925989;MYOD1:0.379029073246;PRDM1:0.372782782063;XCPE1{core}:0.369193264819;GFI1B:0.368315607657;TFAP2B:0.359379725129;ZIC1..3:0.350286610621;TOPORS:0.346824602432;TFAP2{A,C}:0.343961368135;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:0.342711863904;FOXM1:0.342533725057;POU6F1:0.33341370124;HOX{A5,B5}:0.321248042474;RFX1:0.30202202087;RBPJ:0.296587887015;HES1:0.29531206662;NFE2L1:0.286122525504;FOXD3:0.284888739862;TAL1_TCF{3,4,12}:0.281685290758;HNF1A:0.279201904878;NFIX:0.274930243235;GLI1..3:0.269908311203;RORA:0.257946213456;TEAD1:0.223559989429;ATF2:0.206861321555;JUN:0.188947546109;TLX2:0.182367824591;PDX1:0.167725966257;UFEwm:0.16535466018;MTE{core}:0.143713186584;GCM1,2:0.136407227356;IKZF2:0.126917508932;NFE2L2:0.126257665643;REST:0.122692270856;POU3F1..4:0.120889033378;RFX2..5_RFXANK_RFXAP:0.116168467169;MYB:0.107488390675;LMO2:0.105244701393;HMX1:0.0984049906459;HIF1A:0.084537283167;PAX2:0.0658704240611;ZBTB6:0.057127620108;STAT5{A,B}:0.0560391958389;EVI1:0.0515348360605;IKZF1:0.042327304269;NKX3-1:0.0388397495307;NFATC1..3:0.0290970151438;HNF4A_NR2F1,2:0.0234613496625;CDC5L:0.000326751293077;HMGA1,2:0.000194585955411;RUNX1..3:-0.00845139077689;SP1:-0.0143352325665;ALX1:-0.0200178313814;SNAI1..3:-0.0265229642188;STAT1,3:-0.0331533341811;CEBPA,B_DDIT3:-0.0352114244261;GTF2A1,2:-0.0362929115039;YY1:-0.0399490236469;ATF4:-0.0642177238157;NFE2:-0.0724339618789;PAX5:-0.0857685959583;NR3C1:-0.102695441594;ATF6:-0.111455505624;ATF5_CREB3:-0.135947237182;GATA4:-0.140093292392;BACH2:-0.149129643672;HAND1,2:-0.184444199731;HLF:-0.213282722917;PPARG:-0.214808539446;bHLH_family:-0.221049540241;PITX1..3:-0.237736410669;AIRE:-0.26614828625;CREB1:-0.271934960979;CDX1,2,4:-0.277041163453;FOSL2:-0.281278421758;ELK1,4_GABP{A,B1}:-0.283111770443;TP53:-0.293282455761;ARID5B:-0.294804598768;FOS_FOS{B,L1}_JUN{B,D}:-0.295008906252;PAX8:-0.323071074042;TEF:-0.347569272657;NR5A1,2:-0.365866419487;PAX4:-0.370874581804;DMAP1_NCOR{1,2}_SMARC:-0.384727013846;ESRRA:-0.406041762285;FOX{D1,D2}:-0.421822190205;RXRA_VDR{dimer}:-0.436777637454;SPI1:-0.448188090463;CRX:-0.462893349795;AR:-0.468431614673;FOXP3:-0.487211401125;IRF7:-0.488035566772;SPIB:-0.488256839221;NFKB1_REL_RELA:-0.492658216114;ESR1:-0.507492912587;RXR{A,B,G}:-0.51081141906;ELF1,2,4:-0.513317247468;NFIL3:-0.535484126512;ZEB1:-0.544303601139;NKX6-1,2:-0.564633766684;STAT2,4,6:-0.577213678973;FOXN1:-0.604671275774;ETS1,2:-0.60500228992;ALX4:-0.655377457604;NR6A1:-0.665675805437;FOXQ1:-0.671055131466;SPZ1:-0.680474676038;FOX{I1,J2}:-0.850963543807;IRF1,2:-0.907315967897;ZBTB16:-0.958178137645;POU1F1:-0.967723502707;NKX2-2,8:-0.979559998467;FOXO1,3,4:-0.990598428091;SREBF1,2:-1.04458628017;NR1H4:-1.05046405578;FOXP1:-1.18678322172;BPTF:-1.50615994155
|comment=
|created_by=
|creation_date=
|def=
|has_quality=
|is_a=EFO:0002091;;FF:0000004;;FF:0000103;;FF:0011333
|namespace=FANTOM5
|part_of=
}}
}}

Revision as of 16:01, 7 March 2012


Name:whole body, embryo E14
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 stage14 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

CNhs10519

00
10.0826
100
1000.0826
10000.00421
1001-0.0749
10020.0663
10030.0441
10040.0413
10050
10060.0826
1007-0.012
10080
1009-0.117
1010.0734
10100
10110.0136
10120
1013-0.3
10140.264
10150.139
10160.0255
10170
10180.0826
10190
1020
10200
10210
1022-0.124
10230
1024-0.0427
10250.191
10260.0272
10270.0627
10280
1029-0.115
1030.00443
10300
10310.128
1032-0.109
1033-0.0665
10340.0826
10350.033
1036-0.0152
10370
1038-0.119
1039-0.00323
1040
1040-0.00376
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: CNhs10519

Jaspar motifP-value
MA0002.20.00987
MA0003.10.834
MA0004.10.344
MA0006.10.213
MA0007.10.00723
MA0009.10.446
MA0014.10.0914
MA0017.10.00956
MA0018.20.437
MA0019.10.619
MA0024.18.72663e-6
MA0025.10.276
MA0027.10.567
MA0028.10.0161
MA0029.10.276
MA0030.10.505
MA0031.10.24
MA0035.26.23234e-4
MA0038.10.00913
MA0039.20.526
MA0040.10.88
MA0041.10.302
MA0042.10.732
MA0043.10.659
MA0046.14.38127e-7
MA0047.20.898
MA0048.10.0806
MA0050.11.78165e-7
MA0051.12.79483e-6
MA0052.12.45646e-5
MA0055.10.0276
MA0057.10.305
MA0058.10.473
MA0059.10.182
MA0060.12.14359e-16
MA0061.10.117
MA0062.21.17664e-5
MA0065.20.00976
MA0066.10.106
MA0067.10.024
MA0068.10.547
MA0069.10.926
MA0070.10.502
MA0071.10.0293
MA0072.10.148
MA0073.10.962
MA0074.10.0636
MA0076.10.0324
MA0077.10.208
MA0078.10.689
MA0079.20.281
MA0080.24.26206e-10
MA0081.10.137
MA0083.13.75769e-4
MA0084.10.599
MA0087.10.336
MA0088.10.402
MA0090.10.669
MA0091.10.772
MA0092.10.535
MA0093.10.396
MA0099.20.00806
MA0100.10.36
MA0101.10.0413
MA0102.20.727
MA0103.10.00207
MA0104.20.778
MA0105.10.441
MA0106.10.0435
MA0107.10.0456
MA0108.22.46842e-24
MA0111.10.258
MA0112.21.37628e-5
MA0113.10.088
MA0114.10.0543
MA0115.10.444
MA0116.10.134
MA0117.10.791
MA0119.10.679
MA0122.10.763
MA0124.10.253
MA0125.10.0122
MA0131.10.831
MA0135.10.00431
MA0136.13.63734e-10
MA0137.20.00188
MA0138.20.337
MA0139.10.0581
MA0140.11.65826e-6
MA0141.11.56043e-4
MA0142.10.229
MA0143.10.0231
MA0144.10.0261
MA0145.10.165
MA0146.10.0881
MA0147.10.817
MA0148.10.885
MA0149.10.00399
MA0150.10.0656
MA0152.10.996
MA0153.18.96608e-4
MA0154.10.0245
MA0155.10.931
MA0156.15.26285e-8
MA0157.10.105
MA0159.10.0217
MA0160.10.0353
MA0162.10.763
MA0163.10.0065
MA0164.10.707
MA0258.14.00149e-4
MA0259.10.791



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: CNhs10519

Novel motifP-value
10.0472
100.0265
1000.788
1010.878
1020.271
1030.019
1040.815
1050.586
1060.0235
1070.395
1080.579
1090.0103
110.0655
1100.0532
1110.00119
1120.0155
1130.584
1140.0144
1150.719
1160.895
1170.021
1180.397
1190.0208
120.834
1200.899
1210.903
1220.735
1230.701
1240.624
1250.0912
1260.0973
1270.134
1280.26
1290.344
130.00126
1300.419
1310.0245
1320.365
1330.0196
1340.451
1350.787
1360.028
1370.576
1380.654
1390.00261
140.696
1400.291
1410.173
1420.477
1430.515
1440.802
1450.0369
1460.995
1470.627
1480.0292
1490.703
150.0443
1500.156
1510.23
1520.0847
1530.146
1540.206
1550.233
1560.418
1570.774
1580.0299
1590.0114
1600.934
1610.199
1620.427
1630.746
1640.0133
1650.445
1660.62
1670.417
1680.214
1690.00828
170.0779
180.783
190.283
20.556
200.022
210.676
220.316
230.821
240.207
250.685
260.00492
270.612
280.311
290.046
30.0743
300.288
310.749
320.065
330.355
340.643
350.351
360.496
370.0129
380.172
390.201
40.703
400.556
410.73
420.487
430.091
440.244
450.99
460.145
470.199
480.0492
490.0404
50.327
500.533
510.711
520.811
530.444
540.959
550.893
560.657
570.492
580.312
590.254
60.53
600.063
610.12
620.251
630.0996
640.786
650.29
660.235
670.704
680.248
690.379
70.16
700.00363
710.0463
720.51
730.0081
740.67
750.0352
760.0177
770.305
780.312
790.657
80.173
800.468
810.872
820.085
830.825
840.479
850.0273
860.138
870.578
880.204
890.828
90.893
900.0203
910.958
920.244
930.23
940.955
950.00351
960.863
970.649
980.704
990.916



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: CNhs10519


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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