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|fonse_treatment_closure=
|fonse_treatment_closure=
|top_motifs=ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:2.24929551089;HNF4A_NR2F1,2:2.20894038856;HNF1A:1.84647819067;SREBF1,2:1.8148844119;ESRRA:1.66598223455;ATF6:1.46132461389;SNAI1..3:1.3497811091;PDX1:1.23690850305;NFIX:1.23423230935;XCPE1{core}:1.22593454566;RXRA_VDR{dimer}:1.16386361392;GZF1:1.00930639657;SRF:0.980608767431;DMAP1_NCOR{1,2}_SMARC:0.967879282627;TBX4,5:0.932374311277;FOXM1:0.922272366375;ZNF423:0.905647432433;CDX1,2,4:0.891820318996;TLX1..3_NFIC{dimer}:0.886810574232;ZEB1:0.831831182253;SP1:0.815509481732;MYBL2:0.772464388476;TBP:0.756433752184;FOXA2:0.74318237869;TOPORS:0.741325718045;RXR{A,B,G}_{NR1H2,PPAR}dimers:0.738040193835;ZNF148:0.716319459464;NR1H4:0.689505666645;NFY{A,B,C}:0.651976263042;GATA6:0.647199612735;GFI1:0.627275257855;HMX1:0.53650721762;FOX{D1,D2}:0.53605413393;TP53:0.53230293371;ZNF238:0.515773581359;ADNP_IRX_SIX_ZHX:0.496881539206;FOSL2:0.492591167178;TLX2:0.482380419061;TFCP2:0.480365371623;TFAP4:0.436553882558;GCM1,2:0.4230804688;ONECUT1,2:0.408357843039;ESR1:0.39368613306;STAT2,4,6:0.389557479686;MYOD1:0.380013731447;MAZ:0.355404784154;IRF1,2:0.348678973949;STAT1,3:0.318231627328;NANOG:0.287867209887;AR:0.264495359272;POU6F1:0.256526267734;FOX{I1,J2}:0.246629956748;ETS1,2:0.235835677746;RBPJ:0.217903276692;EP300:0.215518920618;CEBPA,B_DDIT3:0.215506118612;CUX2:0.212934032058;HIF1A:0.193146747145;HAND1,2:0.177112275341;NR6A1:0.168313018482;LMO2:0.163151507452;GFI1B:0.163148218353;ELF1,2,4:0.136997834694;LEF1_TCF7_TCF7L1,2:0.122759671869;TEAD1:0.112754490732;GTF2I:0.0971068668224;GTF2A1,2:0.0962953716645;NKX2-1,4:0.0808194734256;FOXN1:0.0732771787311;EBF1:0.0478685482805;FOS_FOS{B,L1}_JUN{B,D}:0.0401816788506;T:0.036445211498;DBP:0.0227572997904;MYFfamily:0.0108361353093;PRRX1,2:-0.00883862145736;REST:-0.0172544850238;PBX1:-0.0294603626879;NR5A1,2:-0.0486007340711;FOXQ1:-0.0510578868716;PAX6:-0.059757817745;E2F1..5:-0.0772604094091;ZBTB6:-0.0814909040964;SMAD1..7,9:-0.0855738203417;IRF7:-0.0856776638551;IKZF1:-0.105879141094;NKX3-2:-0.108089956673;EVI1:-0.108225574581;ARID5B:-0.111432539995;VSX1,2:-0.124885448567;RREB1:-0.159013881044;FOXL1:-0.160145963832;MTF1:-0.167763169276;HES1:-0.180629789003;SPI1:-0.182408112243;FOX{F1,F2,J1}:-0.18580207788;ZNF143:-0.198161673675;YY1:-0.209322891506;HIC1:-0.219048210348;bHLH_family:-0.22166268343;IKZF2:-0.229642395462;ELK1,4_GABP{A,B1}:-0.231622136763;PAX8:-0.232492957074;PAX1,9:-0.235836861167;PAX5:-0.237562582563;PATZ1:-0.239823489245;NKX2-3_NKX2-5:-0.241896439854;BACH2:-0.256301089093;PAX2:-0.256753929536;NFKB1_REL_RELA:-0.265165665593;FOXO1,3,4:-0.280694574015;SOX17:-0.287278705105;HLF:-0.29523597372;OCT4_SOX2{dimer}:-0.302381441604;ZIC1..3:-0.303847180612;LHX3,4:-0.31293898517;NANOG{mouse}:-0.315278365099;AIRE:-0.327500996335;HMGA1,2:-0.350272604776;JUN:-0.367552715396;SPIB:-0.383225531867;STAT5{A,B}:-0.39486632326;MED-1{core}:-0.395394906023;ATF5_CREB3:-0.404296856375;EN1,2:-0.406582789708;NFE2:-0.419067106853;RXR{A,B,G}:-0.428267112764;NKX2-2,8:-0.428374148169;TAL1_TCF{3,4,12}:-0.430382254977;MTE{core}:-0.430550972887;BREu{core}:-0.430987621566;ALX4:-0.432400155348;ATF2:-0.434062478843;SPZ1:-0.442550624664;TGIF1:-0.459911961522;POU2F1..3:-0.463201347233;HOXA9_MEIS1:-0.464248930284;NKX3-1:-0.490885088626;GLI1..3:-0.493937594601;TFAP2B:-0.501337393375;MYB:-0.506564462903;SOX5:-0.518048095702;MAFB:-0.51883562546;HBP1_HMGB_SSRP1_UBTF:-0.531141923835;PPARG:-0.534672627603;RFX1:-0.535519620931;EGR1..3:-0.545770541847;TFDP1:-0.550676974692;FOXD3:-0.560457922296;KLF4:-0.562110001136;SOX2:-0.568010349458;RUNX1..3:-0.572564932112;ZFP161:-0.582800561332;NFE2L2:-0.588098643508;NHLH1,2:-0.591892504155;TFAP2{A,C}:-0.614199676459;MEF2{A,B,C,D}:-0.636487811663;TEF:-0.639235314852;ZNF384:-0.641061443063;CREB1:-0.649200545253;MZF1:-0.663514318664;NRF1:-0.671817638575;NFATC1..3:-0.678779840861;HSF1,2:-0.73013617569;NFIL3:-0.75099864557;AHR_ARNT_ARNT2:-0.760426155451;POU3F1..4:-0.763390337219;SOX{8,9,10}:-0.775849805957;NR3C1:-0.785510035269;RORA:-0.78658404102;UFEwm:-0.816456688199;PRDM1:-0.825313813214;CDC5L:-0.826106952155;ATF4:-0.827593421237;POU1F1:-0.834247077891;GATA4:-0.839724941456;RFX2..5_RFXANK_RFXAP:-0.854970307579;PAX4:-0.875032068291;FOXP1:-0.898902522999;PITX1..3:-0.899122316391;NKX6-1,2:-0.927148012375;POU5F1:-0.945705483545;BPTF:-0.960219823223;NFE2L1:-1.08642431283;FOXP3:-1.12063014323;ALX1:-1.24230270036;CRX:-1.29566655198;HOX{A5,B5}:-1.45711618598;ZBTB16:-1.56268049021;HOX{A4,D4}:-1.59040062196
|top_motifs=ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:2.24929551089;HNF4A_NR2F1,2:2.20894038856;HNF1A:1.84647819067;SREBF1,2:1.8148844119;ESRRA:1.66598223455;ATF6:1.46132461389;SNAI1..3:1.3497811091;PDX1:1.23690850305;NFIX:1.23423230935;XCPE1{core}:1.22593454566;RXRA_VDR{dimer}:1.16386361392;GZF1:1.00930639657;SRF:0.980608767431;DMAP1_NCOR{1,2}_SMARC:0.967879282627;TBX4,5:0.932374311277;FOXM1:0.922272366375;ZNF423:0.905647432433;CDX1,2,4:0.891820318996;TLX1..3_NFIC{dimer}:0.886810574232;ZEB1:0.831831182253;SP1:0.815509481732;MYBL2:0.772464388476;TBP:0.756433752184;FOXA2:0.74318237869;TOPORS:0.741325718045;RXR{A,B,G}_{NR1H2,PPAR}dimers:0.738040193835;ZNF148:0.716319459464;NR1H4:0.689505666645;NFY{A,B,C}:0.651976263042;GATA6:0.647199612735;GFI1:0.627275257855;HMX1:0.53650721762;FOX{D1,D2}:0.53605413393;TP53:0.53230293371;ZNF238:0.515773581359;ADNP_IRX_SIX_ZHX:0.496881539206;FOSL2:0.492591167178;TLX2:0.482380419061;TFCP2:0.480365371623;TFAP4:0.436553882558;GCM1,2:0.4230804688;ONECUT1,2:0.408357843039;ESR1:0.39368613306;STAT2,4,6:0.389557479686;MYOD1:0.380013731447;MAZ:0.355404784154;IRF1,2:0.348678973949;STAT1,3:0.318231627328;NANOG:0.287867209887;AR:0.264495359272;POU6F1:0.256526267734;FOX{I1,J2}:0.246629956748;ETS1,2:0.235835677746;RBPJ:0.217903276692;EP300:0.215518920618;CEBPA,B_DDIT3:0.215506118612;CUX2:0.212934032058;HIF1A:0.193146747145;HAND1,2:0.177112275341;NR6A1:0.168313018482;LMO2:0.163151507452;GFI1B:0.163148218353;ELF1,2,4:0.136997834694;LEF1_TCF7_TCF7L1,2:0.122759671869;TEAD1:0.112754490732;GTF2I:0.0971068668224;GTF2A1,2:0.0962953716645;NKX2-1,4:0.0808194734256;FOXN1:0.0732771787311;EBF1:0.0478685482805;FOS_FOS{B,L1}_JUN{B,D}:0.0401816788506;T:0.036445211498;DBP:0.0227572997904;MYFfamily:0.0108361353093;PRRX1,2:-0.00883862145736;REST:-0.0172544850238;PBX1:-0.0294603626879;NR5A1,2:-0.0486007340711;FOXQ1:-0.0510578868716;PAX6:-0.059757817745;E2F1..5:-0.0772604094091;ZBTB6:-0.0814909040964;SMAD1..7,9:-0.0855738203417;IRF7:-0.0856776638551;IKZF1:-0.105879141094;NKX3-2:-0.108089956673;EVI1:-0.108225574581;ARID5B:-0.111432539995;VSX1,2:-0.124885448567;RREB1:-0.159013881044;FOXL1:-0.160145963832;MTF1:-0.167763169276;HES1:-0.180629789003;SPI1:-0.182408112243;FOX{F1,F2,J1}:-0.18580207788;ZNF143:-0.198161673675;YY1:-0.209322891506;HIC1:-0.219048210348;bHLH_family:-0.22166268343;IKZF2:-0.229642395462;ELK1,4_GABP{A,B1}:-0.231622136763;PAX8:-0.232492957074;PAX1,9:-0.235836861167;PAX5:-0.237562582563;PATZ1:-0.239823489245;NKX2-3_NKX2-5:-0.241896439854;BACH2:-0.256301089093;PAX2:-0.256753929536;NFKB1_REL_RELA:-0.265165665593;FOXO1,3,4:-0.280694574015;SOX17:-0.287278705105;HLF:-0.29523597372;OCT4_SOX2{dimer}:-0.302381441604;ZIC1..3:-0.303847180612;LHX3,4:-0.31293898517;NANOG{mouse}:-0.315278365099;AIRE:-0.327500996335;HMGA1,2:-0.350272604776;JUN:-0.367552715396;SPIB:-0.383225531867;STAT5{A,B}:-0.39486632326;MED-1{core}:-0.395394906023;ATF5_CREB3:-0.404296856375;EN1,2:-0.406582789708;NFE2:-0.419067106853;RXR{A,B,G}:-0.428267112764;NKX2-2,8:-0.428374148169;TAL1_TCF{3,4,12}:-0.430382254977;MTE{core}:-0.430550972887;BREu{core}:-0.430987621566;ALX4:-0.432400155348;ATF2:-0.434062478843;SPZ1:-0.442550624664;TGIF1:-0.459911961522;POU2F1..3:-0.463201347233;HOXA9_MEIS1:-0.464248930284;NKX3-1:-0.490885088626;GLI1..3:-0.493937594601;TFAP2B:-0.501337393375;MYB:-0.506564462903;SOX5:-0.518048095702;MAFB:-0.51883562546;HBP1_HMGB_SSRP1_UBTF:-0.531141923835;PPARG:-0.534672627603;RFX1:-0.535519620931;EGR1..3:-0.545770541847;TFDP1:-0.550676974692;FOXD3:-0.560457922296;KLF4:-0.562110001136;SOX2:-0.568010349458;RUNX1..3:-0.572564932112;ZFP161:-0.582800561332;NFE2L2:-0.588098643508;NHLH1,2:-0.591892504155;TFAP2{A,C}:-0.614199676459;MEF2{A,B,C,D}:-0.636487811663;TEF:-0.639235314852;ZNF384:-0.641061443063;CREB1:-0.649200545253;MZF1:-0.663514318664;NRF1:-0.671817638575;NFATC1..3:-0.678779840861;HSF1,2:-0.73013617569;NFIL3:-0.75099864557;AHR_ARNT_ARNT2:-0.760426155451;POU3F1..4:-0.763390337219;SOX{8,9,10}:-0.775849805957;NR3C1:-0.785510035269;RORA:-0.78658404102;UFEwm:-0.816456688199;PRDM1:-0.825313813214;CDC5L:-0.826106952155;ATF4:-0.827593421237;POU1F1:-0.834247077891;GATA4:-0.839724941456;RFX2..5_RFXANK_RFXAP:-0.854970307579;PAX4:-0.875032068291;FOXP1:-0.898902522999;PITX1..3:-0.899122316391;NKX6-1,2:-0.927148012375;POU5F1:-0.945705483545;BPTF:-0.960219823223;NFE2L1:-1.08642431283;FOXP3:-1.12063014323;ALX1:-1.24230270036;CRX:-1.29566655198;HOX{A5,B5}:-1.45711618598;ZBTB16:-1.56268049021;HOX{A4,D4}:-1.59040062196
|comment=fantom:1289-20F7
|created_by=
|creation_date=
|def=
|has_quality=
|is_a=EFO:0002091;;FF:0000004;;FF:0000103;;FF:0011511
|namespace=FANTOM5
|part_of=
}}
}}

Revision as of 15:51, 7 March 2012


Name:intestine, embryo E18
Species:Mouse (Mus musculus)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissueintestine
dev stage18 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

CNhs10526

00
10
100
1000
10000.0756
10010
10020.168
1003-0.0672
10040
10050.266
1006-0.00239
1007-0.039
10080.0756
10090.0555
101-0.0482
10100.0756
1011-0.0106
10120
10130.161
10140.111
1015-0.0385
1016-0.0487
10170
10180.335
10190
1020
10200
10210
1022-0.0777
10230
10240.0946
10250.626
10260
10270.0147
10280
10290.22
1030.0756
10300
10310.174
10320.199
10330
10340
10350
1036-0.105
10370
1038-0.0724
1039-0.0487
1040
1040-0.0452
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: CNhs10526

Jaspar motifP-value
MA0002.20.199
MA0003.10.144
MA0004.10.32
MA0006.10.0537
MA0007.10.546
MA0009.10.764
MA0014.10.544
MA0017.19.03868e-33
MA0018.20.00652
MA0019.10.133
MA0024.10.109
MA0025.10.15
MA0027.10.12
MA0028.10.404
MA0029.10.96
MA0030.10.247
MA0031.10.334
MA0035.23.31046e-10
MA0038.10.377
MA0039.27.50531e-5
MA0040.10.0628
MA0041.10.163
MA0042.10.393
MA0043.10.00425
MA0046.18.99535e-109
MA0047.24.89959e-5
MA0048.10.891
MA0050.10.0476
MA0051.10.108
MA0052.10.00626
MA0055.10.528
MA0057.10.192
MA0058.10.0462
MA0059.10.95
MA0060.10.0296
MA0061.10.679
MA0062.20.368
MA0065.28.22535e-11
MA0066.10.284
MA0067.10.3
MA0068.10.354
MA0069.10.032
MA0070.10.579
MA0071.10.93
MA0072.10.614
MA0073.10.775
MA0074.10.116
MA0076.10.271
MA0077.10.441
MA0078.10.24
MA0079.20.28
MA0080.20.02
MA0081.10.11
MA0083.10.0157
MA0084.10.619
MA0087.10.989
MA0088.10.343
MA0090.10.331
MA0091.10.646
MA0092.10.194
MA0093.10.214
MA0099.20.142
MA0100.10.00867
MA0101.10.592
MA0102.20.328
MA0103.13.93249e-5
MA0104.20.288
MA0105.10.632
MA0106.10.386
MA0107.10.484
MA0108.27.75867e-5
MA0111.10.346
MA0112.20.00535
MA0113.10.762
MA0114.13.50262e-39
MA0115.12.45094e-8
MA0116.10.35
MA0117.10.741
MA0119.10.189
MA0122.10.775
MA0124.10.322
MA0125.10.488
MA0131.10.774
MA0135.10.0037
MA0136.10.111
MA0137.20.0845
MA0138.20.374
MA0139.10.0105
MA0140.11.23902e-4
MA0141.10.00495
MA0142.10.0239
MA0143.10.122
MA0144.10.0148
MA0145.10.0126
MA0146.10.102
MA0147.10.0957
MA0148.11.82876e-6
MA0149.10.0819
MA0150.10.801
MA0152.10.755
MA0153.11.46858e-68
MA0154.10.0511
MA0155.10.0693
MA0156.10.0537
MA0157.10.611
MA0159.10.0236
MA0160.10.0218
MA0162.10.34
MA0163.10.0672
MA0164.10.613
MA0258.10.131
MA0259.10.217



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: CNhs10526

Novel motifP-value
10.617
100.752
1000.44
1010.697
1020.39
1030.228
1040.969
1050.331
1060.0422
1070.0436
1080.983
1090.0407
110.366
1100.613
1110.564
1120.0498
1130.56
1140.753
1150.934
1160.245
1170.998
1180.685
1190.227
120.726
1200.624
1210.534
1220.988
1230.213
1240.399
1250.446
1260.0936
1270.408
1280.221
1290.705
137.92339e-4
1300.831
1310.1
1320.202
1330.214
1340.641
1350.578
1360.0728
1370.694
1380.101
1390.145
140.774
1400.0536
1410.332
1420.294
1430.046
1440.262
1450.181
1460.116
1470.625
1480.227
1490.137
150.579
1500.248
1510.656
1520.03
1530.0423
1540.439
1550.76
1560.0104
1570.354
1580.212
1590.759
1600.0781
1610.369
1620.39
1630.141
1640.418
1650.609
1660.788
1670.28
1680.218
1690.0722
170.253
180.177
190.0435
20.0859
200.316
210.835
220.171
230.292
240.803
250.784
260.0403
270.437
280.971
290.758
30.605
300.123
310.766
320.198
330.253
340.265
350.604
360.924
370.134
380.35
390.443
40.186
400.0988
410.56
420.868
430.327
440.584
450.0881
460.65
470.485
480.436
490.682
50.881
500.442
510.689
520.0384
530.549
540.667
550.224
560.393
570.135
580.562
590.12
60.754
600.0569
610.464
620.915
630.499
640.526
650.226
660.869
670.0711
680.894
690.611
70.0758
700.616
710.23
720.286
730.166
740.906
750.528
760.164
770.0118
780.0466
790.981
80.932
800.595
810.782
820.305
830.926
840.237
850.192
860.521
870.0908
880.652
890.149
90.652
900.641
910.463
920.607
930.513
940.0966
950.203
960.352
970.517
980.935
990.0271



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: CNhs10526


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)
0000160 (intestine)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000479 (tissue)
0000480 (anatomical group)
0000481 (multi-tissue structure)
0000922 (embryo)
0000923 (germ layer)
0000925 (endoderm)
0001007 (digestive system)
0001062 (anatomical entity)
0001555 (digestive tract)
0002050 (embryonic structure)
0002532 (epiblast (generic))
0004119 (endoderm-derived structure)
0004185 (endodermal part of digestive tract)
0004921 (subdivision of digestive tract)
0005409 (gastrointestinal system)
0005423 (developing anatomical structure)
0007026 (primitive gut)

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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