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|fonse_treatment_closure=
|fonse_treatment_closure=
|top_motifs=FOX{F1,F2,J1}:3.1924189647;GATA6:2.76861702076;FOX{D1,D2}:2.35931638929;FOXA2:2.35023608653;NKX2-2,8:2.1689314718;CEBPA,B_DDIT3:1.97551969459;HNF1A:1.9543222139;HLF:1.77771753994;NFIL3:1.57515688906;STAT2,4,6:1.51782582568;ZNF423:1.45060613114;HNF4A_NR2F1,2:1.29727610627;PAX1,9:1.28361470663;EBF1:1.20726932866;ARID5B:1.11398313808;RXR{A,B,G}_{NR1H2,PPAR}dimers:1.05889266699;ONECUT1,2:1.05447026481;STAT5{A,B}:1.05135334161;NFY{A,B,C}:0.875488172091;TLX2:0.835717470272;E2F1..5:0.820854967686;NKX3-2:0.757935777548;GZF1:0.745064476379;NFIX:0.688806016325;CUX2:0.677315194191;SPIB:0.621282521375;NR6A1:0.619372732345;IRF1,2:0.587264474649;FOXM1:0.511834752833;RXRA_VDR{dimer}:0.506612873935;FOXO1,3,4:0.499146558009;SPI1:0.465412713065;DBP:0.455669746357;ELF1,2,4:0.372395737518;ETS1,2:0.354721542279;NFE2:0.318014199674;ZNF148:0.312447489157;IRF7:0.298067546553;PBX1:0.276994814607;MYB:0.274676982134;ALX4:0.270954892844;PDX1:0.26325690341;GCM1,2:0.226833616582;HMGA1,2:0.223772087996;EN1,2:0.194215708826;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:0.179391529028;NANOG{mouse}:0.160606479887;NFE2L2:0.155096970811;POU1F1:0.110485123878;FOXD3:0.0997241895538;GFI1:0.0959761834851;BACH2:0.0809695542174;RUNX1..3:0.064630329766;TBP:0.0591300226948;XCPE1{core}:0.0534465334885;HOXA9_MEIS1:0.0395452550883;TLX1..3_NFIC{dimer}:0.0368756690379;SNAI1..3:0.0299526737961;IKZF1:0.0177686471631;EVI1:0.0145940359283;PAX4:-0.015726682049;NR5A1,2:-0.0359683475032;MTF1:-0.0403117882516;RXR{A,B,G}:-0.0558039945569;ESRRA:-0.0700216248693;CDX1,2,4:-0.0951090460326;NFE2L1:-0.0989850718764;RORA:-0.104582285543;SP1:-0.136799507102;TEF:-0.161754496555;PPARG:-0.184421883496;TFCP2:-0.187543614515;RBPJ:-0.20219421023;T:-0.205301084217;SRF:-0.227228347906;AR:-0.241868301272;POU2F1..3:-0.244541903728;GFI1B:-0.268796844987;SOX{8,9,10}:-0.271047714232;LMO2:-0.281508510541;bHLH_family:-0.283635019456;VSX1,2:-0.288607988519;ZEB1:-0.297277538548;HOX{A5,B5}:-0.29728158961;NR1H4:-0.299705339761;DMAP1_NCOR{1,2}_SMARC:-0.310514156362;PAX2:-0.343707494581;ZBTB16:-0.366711765046;MYBL2:-0.394890557435;TP53:-0.395014654358;NR3C1:-0.400797270033;FOXL1:-0.405646182057;PAX5:-0.414317100325;HIF1A:-0.431372984066;AIRE:-0.431680342808;ATF5_CREB3:-0.435600442467;IKZF2:-0.436017597117;NFKB1_REL_RELA:-0.450835214873;FOXQ1:-0.450858343719;LHX3,4:-0.460432583574;TOPORS:-0.463983035926;TBX4,5:-0.465023286291;GTF2I:-0.512971270651;HMX1:-0.514333548361;SMAD1..7,9:-0.515283308988;TEAD1:-0.519032745022;RREB1:-0.527876477438;FOXP1:-0.533055516778;NKX2-1,4:-0.536336127224;BPTF:-0.537355865078;SREBF1,2:-0.545183410967;MYOD1:-0.546378502615;HSF1,2:-0.550823300621;PATZ1:-0.556550026849;PITX1..3:-0.557885172916;STAT1,3:-0.558866824054;NKX3-1:-0.574663857156;SOX17:-0.607884546572;TFAP4:-0.621384489188;MYFfamily:-0.635723194601;PAX6:-0.638038931578;LEF1_TCF7_TCF7L1,2:-0.671736387205;ZNF143:-0.678682809432;YY1:-0.681169133261;POU5F1:-0.681687124149;MAZ:-0.682690555794;OCT4_SOX2{dimer}:-0.685177470089;MEF2{A,B,C,D}:-0.693255576915;CREB1:-0.713038940092;FOS_FOS{B,L1}_JUN{B,D}:-0.736390520173;FOXP3:-0.738236886702;EGR1..3:-0.754610009265;BREu{core}:-0.763161700573;GLI1..3:-0.790352165155;NHLH1,2:-0.791431607173;UFEwm:-0.801250481133;AHR_ARNT_ARNT2:-0.809770300002;TFDP1:-0.820115989508;PRRX1,2:-0.820665668363;ADNP_IRX_SIX_ZHX:-0.82095125774;REST:-0.821964910869;MZF1:-0.831807230463;ATF4:-0.837485078041;TGIF1:-0.853804189547;TAL1_TCF{3,4,12}:-0.869991649299;EP300:-0.874628879071;SPZ1:-0.874679431755;ELK1,4_GABP{A,B1}:-0.878837418114;POU3F1..4:-0.91580588105;RFX1:-0.92729910752;NRF1:-0.938015630041;KLF4:-0.938903825033;HAND1,2:-0.954835775148;MED-1{core}:-0.959719521244;NKX2-3_NKX2-5:-0.972330059736;ESR1:-0.972473033074;SOX2:-1.03835865671;MAFB:-1.03952134567;TFAP2{A,C}:-1.06665811244;ZIC1..3:-1.0680465814;HIC1:-1.07442296181;PRDM1:-1.07723344084;ZBTB6:-1.0857310216;HOX{A4,D4}:-1.10739298116;TFAP2B:-1.10918802266;JUN:-1.12845739302;CRX:-1.13201035506;FOXN1:-1.13860365841;ZFP161:-1.15646056327;RFX2..5_RFXANK_RFXAP:-1.17873801822;ZNF238:-1.19432114049;FOX{I1,J2}:-1.23597260639;HES1:-1.2422647712;MTE{core}:-1.26077823908;ATF6:-1.31581633031;ATF2:-1.33719584314;GATA4:-1.3517482347;PAX8:-1.36227398083;CDC5L:-1.39089497609;FOSL2:-1.45405497736;SOX5:-1.51454459012;ZNF384:-1.55391773795;GTF2A1,2:-1.56174073404;ALX1:-1.60000547108;NFATC1..3:-1.60050926569;POU6F1:-1.61982950732;HBP1_HMGB_SSRP1_UBTF:-1.77777820645;NANOG:-1.81441577675;NKX6-1,2:-1.94707309075
|top_motifs=FOX{F1,F2,J1}:3.1924189647;GATA6:2.76861702076;FOX{D1,D2}:2.35931638929;FOXA2:2.35023608653;NKX2-2,8:2.1689314718;CEBPA,B_DDIT3:1.97551969459;HNF1A:1.9543222139;HLF:1.77771753994;NFIL3:1.57515688906;STAT2,4,6:1.51782582568;ZNF423:1.45060613114;HNF4A_NR2F1,2:1.29727610627;PAX1,9:1.28361470663;EBF1:1.20726932866;ARID5B:1.11398313808;RXR{A,B,G}_{NR1H2,PPAR}dimers:1.05889266699;ONECUT1,2:1.05447026481;STAT5{A,B}:1.05135334161;NFY{A,B,C}:0.875488172091;TLX2:0.835717470272;E2F1..5:0.820854967686;NKX3-2:0.757935777548;GZF1:0.745064476379;NFIX:0.688806016325;CUX2:0.677315194191;SPIB:0.621282521375;NR6A1:0.619372732345;IRF1,2:0.587264474649;FOXM1:0.511834752833;RXRA_VDR{dimer}:0.506612873935;FOXO1,3,4:0.499146558009;SPI1:0.465412713065;DBP:0.455669746357;ELF1,2,4:0.372395737518;ETS1,2:0.354721542279;NFE2:0.318014199674;ZNF148:0.312447489157;IRF7:0.298067546553;PBX1:0.276994814607;MYB:0.274676982134;ALX4:0.270954892844;PDX1:0.26325690341;GCM1,2:0.226833616582;HMGA1,2:0.223772087996;EN1,2:0.194215708826;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:0.179391529028;NANOG{mouse}:0.160606479887;NFE2L2:0.155096970811;POU1F1:0.110485123878;FOXD3:0.0997241895538;GFI1:0.0959761834851;BACH2:0.0809695542174;RUNX1..3:0.064630329766;TBP:0.0591300226948;XCPE1{core}:0.0534465334885;HOXA9_MEIS1:0.0395452550883;TLX1..3_NFIC{dimer}:0.0368756690379;SNAI1..3:0.0299526737961;IKZF1:0.0177686471631;EVI1:0.0145940359283;PAX4:-0.015726682049;NR5A1,2:-0.0359683475032;MTF1:-0.0403117882516;RXR{A,B,G}:-0.0558039945569;ESRRA:-0.0700216248693;CDX1,2,4:-0.0951090460326;NFE2L1:-0.0989850718764;RORA:-0.104582285543;SP1:-0.136799507102;TEF:-0.161754496555;PPARG:-0.184421883496;TFCP2:-0.187543614515;RBPJ:-0.20219421023;T:-0.205301084217;SRF:-0.227228347906;AR:-0.241868301272;POU2F1..3:-0.244541903728;GFI1B:-0.268796844987;SOX{8,9,10}:-0.271047714232;LMO2:-0.281508510541;bHLH_family:-0.283635019456;VSX1,2:-0.288607988519;ZEB1:-0.297277538548;HOX{A5,B5}:-0.29728158961;NR1H4:-0.299705339761;DMAP1_NCOR{1,2}_SMARC:-0.310514156362;PAX2:-0.343707494581;ZBTB16:-0.366711765046;MYBL2:-0.394890557435;TP53:-0.395014654358;NR3C1:-0.400797270033;FOXL1:-0.405646182057;PAX5:-0.414317100325;HIF1A:-0.431372984066;AIRE:-0.431680342808;ATF5_CREB3:-0.435600442467;IKZF2:-0.436017597117;NFKB1_REL_RELA:-0.450835214873;FOXQ1:-0.450858343719;LHX3,4:-0.460432583574;TOPORS:-0.463983035926;TBX4,5:-0.465023286291;GTF2I:-0.512971270651;HMX1:-0.514333548361;SMAD1..7,9:-0.515283308988;TEAD1:-0.519032745022;RREB1:-0.527876477438;FOXP1:-0.533055516778;NKX2-1,4:-0.536336127224;BPTF:-0.537355865078;SREBF1,2:-0.545183410967;MYOD1:-0.546378502615;HSF1,2:-0.550823300621;PATZ1:-0.556550026849;PITX1..3:-0.557885172916;STAT1,3:-0.558866824054;NKX3-1:-0.574663857156;SOX17:-0.607884546572;TFAP4:-0.621384489188;MYFfamily:-0.635723194601;PAX6:-0.638038931578;LEF1_TCF7_TCF7L1,2:-0.671736387205;ZNF143:-0.678682809432;YY1:-0.681169133261;POU5F1:-0.681687124149;MAZ:-0.682690555794;OCT4_SOX2{dimer}:-0.685177470089;MEF2{A,B,C,D}:-0.693255576915;CREB1:-0.713038940092;FOS_FOS{B,L1}_JUN{B,D}:-0.736390520173;FOXP3:-0.738236886702;EGR1..3:-0.754610009265;BREu{core}:-0.763161700573;GLI1..3:-0.790352165155;NHLH1,2:-0.791431607173;UFEwm:-0.801250481133;AHR_ARNT_ARNT2:-0.809770300002;TFDP1:-0.820115989508;PRRX1,2:-0.820665668363;ADNP_IRX_SIX_ZHX:-0.82095125774;REST:-0.821964910869;MZF1:-0.831807230463;ATF4:-0.837485078041;TGIF1:-0.853804189547;TAL1_TCF{3,4,12}:-0.869991649299;EP300:-0.874628879071;SPZ1:-0.874679431755;ELK1,4_GABP{A,B1}:-0.878837418114;POU3F1..4:-0.91580588105;RFX1:-0.92729910752;NRF1:-0.938015630041;KLF4:-0.938903825033;HAND1,2:-0.954835775148;MED-1{core}:-0.959719521244;NKX2-3_NKX2-5:-0.972330059736;ESR1:-0.972473033074;SOX2:-1.03835865671;MAFB:-1.03952134567;TFAP2{A,C}:-1.06665811244;ZIC1..3:-1.0680465814;HIC1:-1.07442296181;PRDM1:-1.07723344084;ZBTB6:-1.0857310216;HOX{A4,D4}:-1.10739298116;TFAP2B:-1.10918802266;JUN:-1.12845739302;CRX:-1.13201035506;FOXN1:-1.13860365841;ZFP161:-1.15646056327;RFX2..5_RFXANK_RFXAP:-1.17873801822;ZNF238:-1.19432114049;FOX{I1,J2}:-1.23597260639;HES1:-1.2422647712;MTE{core}:-1.26077823908;ATF6:-1.31581633031;ATF2:-1.33719584314;GATA4:-1.3517482347;PAX8:-1.36227398083;CDC5L:-1.39089497609;FOSL2:-1.45405497736;SOX5:-1.51454459012;ZNF384:-1.55391773795;GTF2A1,2:-1.56174073404;ALX1:-1.60000547108;NFATC1..3:-1.60050926569;POU6F1:-1.61982950732;HBP1_HMGB_SSRP1_UBTF:-1.77777820645;NANOG:-1.81441577675;NKX6-1,2:-1.94707309075
|comment=
|created_by=
|creation_date=
|def=
|has_quality=
|is_a=EFO:0002091;;FF:0000004;;FF:0000103;;FF:0011376
|namespace=FANTOM5
|part_of=
}}
}}

Revision as of 16:02, 7 March 2012


Name:liver, 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
tissueliver
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

CNhs10579

00
10
100
1000
10000
1001-0.0749
1002-0.116
1003-0.123
10040
10050.345
1006-0.071
1007-0.126
10080
1009-0.0572
1010.0025
10100
1011-0.298
10120
10130.276
10140.11
1015-0.203
1016-0.2
10170
10180
10190
1020
10200
10210.11
10220.128
10230
1024-0.0297
10250.436
10260
10270
10280
1029-0.00495
103-0.0528
10300
1031-0.139
1032-0.177
10330
10340.638
10350
10360.0866
10370
1038-0.101
10390.223
1040
1040-0.106
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: CNhs10579

Jaspar motifP-value
MA0002.20.00198
MA0003.10.216
MA0004.10.872
MA0006.10.241
MA0007.10.481
MA0009.10.553
MA0014.10.54
MA0017.11.58421e-14
MA0018.23.86768e-5
MA0019.10.286
MA0024.10.644
MA0025.10.307
MA0027.10.339
MA0028.10.866
MA0029.10.0289
MA0030.10.00244
MA0031.10.00268
MA0035.21.97636e-10
MA0038.10.504
MA0039.20.0151
MA0040.10.0603
MA0041.10.538
MA0042.10.961
MA0043.10.142
MA0046.11.07504e-62
MA0047.23.25368e-10
MA0048.10.278
MA0050.10.00234
MA0051.10.0127
MA0052.19.10054e-4
MA0055.10.326
MA0057.10.486
MA0058.10.755
MA0059.10.315
MA0060.10.314
MA0061.10.147
MA0062.20.922
MA0065.23.181e-8
MA0066.10.0904
MA0067.10.223
MA0068.10.716
MA0069.10.165
MA0070.10.374
MA0071.10.0202
MA0072.10.00583
MA0073.10.732
MA0074.10.383
MA0076.10.454
MA0077.10.0577
MA0078.10.296
MA0079.20.366
MA0080.29.238e-6
MA0081.10.356
MA0083.10.226
MA0084.10.136
MA0087.10.0728
MA0088.10.147
MA0090.10.878
MA0091.10.93
MA0092.10.0985
MA0093.10.901
MA0099.20.777
MA0100.10.781
MA0101.10.566
MA0102.20.00622
MA0103.10.243
MA0104.20.885
MA0105.10.00349
MA0106.10.376
MA0107.10.642
MA0108.20.261
MA0111.10.782
MA0112.21.53651e-4
MA0113.10.184
MA0114.14.65229e-13
MA0115.13.93668e-7
MA0116.10.00902
MA0117.10.996
MA0119.10.00301
MA0122.10.35
MA0124.10.783
MA0125.10.499
MA0131.10.805
MA0135.10.712
MA0136.10.00218
MA0137.20.159
MA0138.20.997
MA0139.10.162
MA0140.11.13367e-25
MA0141.10.0055
MA0142.10.288
MA0143.10.242
MA0144.10.332
MA0145.10.194
MA0146.10.092
MA0147.10.98
MA0148.12.91512e-11
MA0149.10.0381
MA0150.10.00892
MA0152.10.735
MA0153.12.24986e-47
MA0154.10.0171
MA0155.10.659
MA0156.10.0266
MA0157.10.00364
MA0159.10.00695
MA0160.10.00363
MA0162.10.321
MA0163.14.21991e-4
MA0164.10.611
MA0258.10.016
MA0259.10.857



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: CNhs10579

Novel motifP-value
10.159
100.24
1000.718
1010.813
1020.216
1030.0152
1040.646
1050.442
1060.0306
1070.0261
1080.46
1090.0241
110.105
1100.0864
1110.102
1120.0106
1130.92
1140.134
1150.938
1160.851
1170.052
1180.141
1190.0934
120.592
1200.621
1210.735
1220.583
1230.179
1240.299
1250.592
1260.306
1270.328
1280.0341
1290.747
136.06525e-4
1300.429
1310.0678
1320.895
1330.785
1340.842
1350.981
1360.211
1370.316
1380.446
1390.987
140.695
1400.154
1410.839
1420.237
1430.204
1440.93
1450.0593
1460.223
1470.936
1480.6
1490.604
150.0937
1500.149
1510.303
1520.154
1530.36
1540.648
1550.556
1560.0431
1570.86
1580.811
1590.287
1600.0622
1610.3
1620.698
1630.618
1640.014
1650.505
1660.924
1670.698
1680.71
1690.00732
170.0815
180.819
190.0765
20.639
200.545
210.949
220.137
230.17
240.227
250.734
263.52945e-4
270.352
280.396
290.0784
30.025
300.686
310.47
320.348
330.182
340.745
350.804
360.0667
370.119
380.399
390.457
40.54
400.0754
411
420.107
430.0505
440.182
450.66
460.0731
470.274
480.187
490.0627
50.0958
500.43
510.333
520.218
530.781
540.377
550.347
560.332
570.671
580.539
590.0691
60.972
600.072
610.292
620.118
630.104
640.408
650.169
660.6
670.929
680.476
690.857
70.0795
700.403
710.0335
720.416
730.2
740.608
750.0398
760.988
770.395
780.0133
790.812
80.0422
800.0201
810.848
820.208
830.363
840.86
850.208
860.255
870.106
880.755
890.37
90.528
900.363
910.148
920.154
930.726
940.728
950.087
960.189
970.854
980.142
990.185



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: CNhs10579


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
0000015 (anatomical boundary)
0000061 (anatomical structure)
0000062 (organ)
0000077 (mixed endoderm/mesoderm-derived structure)
0000465 (material anatomical entity)
0000466 (immaterial anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000475 (organism subdivision)
0000479 (tissue)
0000480 (anatomical group)
0000481 (multi-tissue structure)
0000916 (abdomen)
0000922 (embryo)
0000923 (germ layer)
0000925 (endoderm)
0000926 (mesoderm)
0000949 (endocrine system)
0001007 (digestive system)
0001041 (foregut)
0001048 (primordium)
0001062 (anatomical entity)
0001555 (digestive tract)
0002050 (embryonic structure)
0002100 (trunk)
0002107 (liver)
0002330 (exocrine system)
0002365 (exocrine gland)
0002368 (endocrine gland)
0002405 (immune system)
0002417 (abdominal segment of trunk)
0002423 (hepatobiliary system)
0002530 (gland)
0002532 (epiblast (generic))
0003104 (mesenchyme)
0003894 (liver primordium)
0004119 (endoderm-derived structure)
0004120 (mesoderm-derived structure)
0004161 (septum transversum)
0004185 (endodermal part of digestive tract)
0004921 (subdivision of digestive tract)
0005057 (immune organ)
0005172 (abdomen element)
0005173 (abdominal segment element)
0005177 (trunk region element)
0005256 (trunk mesenchyme)
0005423 (developing anatomical structure)
0006235 (foregut-midgut junction)
0006925 (digestive gland)
0007026 (primitive gut)
0008835 (hepatic diverticulum)
0008836 (liver bud)
0009142 (entire embryonic mesenchyme)

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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