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|fonse_treatment_closure=
|fonse_treatment_closure=
|top_motifs=HOX{A5,B5}:3.20313119147;SRF:2.38961543199;GATA4:2.08969672095;MEF2{A,B,C,D}:1.96117236344;GATA6:1.71068379222;RXR{A,B,G}:1.69822797862;HIF1A:1.43564618288;NR5A1,2:1.38215408251;EVI1:1.3191845153;NANOG{mouse}:1.29293445164;NFE2L1:1.150815354;TEAD1:1.14840468541;FOXL1:1.06912843954;POU3F1..4:0.999022794969;ZNF143:0.997774363697;E2F1..5:0.890487467002;IKZF2:0.868140908793;MZF1:0.862068799268;PRDM1:0.844183602467;NFY{A,B,C}:0.838841452548;GFI1:0.789725847619;PATZ1:0.783198256213;SOX17:0.778274282764;EN1,2:0.769532381701;IKZF1:0.76258528623;ALX1:0.751257523593;RREB1:0.736983246802;SOX{8,9,10}:0.727853668386;NKX2-1,4:0.685444271149;UFEwm:0.64577528394;TGIF1:0.589571433095;GFI1B:0.573811980401;SOX2:0.570958496842;HES1:0.565267777159;RXR{A,B,G}_{NR1H2,PPAR}dimers:0.559262705533;PITX1..3:0.550296601458;HMGA1,2:0.53563112316;NR3C1:0.530899316231;GCM1,2:0.524928165646;T:0.511586771946;EP300:0.486472900038;ZIC1..3:0.476721867359;SOX5:0.467426646361;ESRRA:0.457184483452;HOXA9_MEIS1:0.456839578281;NRF1:0.425049622378;TOPORS:0.407961694726;MAZ:0.395119711619;XCPE1{core}:0.395090354256;NFATC1..3:0.393221735725;KLF4:0.387004741142;TFDP1:0.342297237163;NR6A1:0.339290801656;TFAP2{A,C}:0.295264682106;HSF1,2:0.280319571447;MYBL2:0.279247296894;TFAP2B:0.266059948954;BREu{core}:0.262910286422;YY1:0.256752126015;CRX:0.242755657668;EBF1:0.221312484961;PDX1:0.220363940795;NANOG:0.195715569402;TFAP4:0.175328266105;PAX2:0.1699496518;EGR1..3:0.161566335948;ELF1,2,4:0.153551111746;TLX1..3_NFIC{dimer}:0.13939843358;FOSL2:0.116195053339;NKX3-1:0.108231191842;MYB:0.0788531272978;CUX2:0.0765435690154;TFCP2:0.0749796158195;ELK1,4_GABP{A,B1}:0.07492326861;PAX8:0.072151837235;SPIB:0.0719776030011;ATF2:0.0701163028916;MAFB:0.0691006301672;CDX1,2,4:0.0609596267806;ESR1:0.0489158024144;HAND1,2:0.0412634575167;HIC1:0.0410518291855;CDC5L:0.0233623007487;ATF4:0.0209326321798;ZFP161:0.00743854210218;HOX{A4,D4}:0.00230922097473;PAX4:-0.00531779997314;GTF2A1,2:-0.0125975669177;SP1:-0.0133709850413;TEF:-0.0202664660367;AR:-0.0217310767235;TBX4,5:-0.0244426090222;SPI1:-0.0309919583323;PAX5:-0.0354985964265;GTF2I:-0.0363781278028;RFX2..5_RFXANK_RFXAP:-0.0380480519649;JUN:-0.0528198591978;PAX1,9:-0.0589343136163;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:-0.0703577188405;NKX2-2,8:-0.0744890594072;RORA:-0.0849285112327;SMAD1..7,9:-0.0895439913596;MTF1:-0.0897867152561;CREB1:-0.133761467066;NHLH1,2:-0.136112435208;RBPJ:-0.152361770463;GZF1:-0.156771988623;FOXP1:-0.165368498086;FOXO1,3,4:-0.168795526677;FOX{I1,J2}:-0.180071475315;TBP:-0.187311748292;MTE{core}:-0.19395289612;ETS1,2:-0.204893746545;STAT1,3:-0.213704689183;ZBTB16:-0.225963590701;PBX1:-0.226251501608;ZBTB6:-0.230094760271;ARID5B:-0.245756335126;NKX6-1,2:-0.257621556485;ZNF238:-0.270817471009;AIRE:-0.2766024956;NR1H4:-0.278308037563;FOXD3:-0.284906082712;ZNF148:-0.288729671362;MED-1{core}:-0.289482002603;NFE2L2:-0.291881495384;RFX1:-0.293888595937;NKX3-2:-0.320040594541;NKX2-3_NKX2-5:-0.321898925085;FOXP3:-0.329889618502;SREBF1,2:-0.344213379732;ATF5_CREB3:-0.347759130539;PAX6:-0.349120403041;FOXA2:-0.359707562375;GLI1..3:-0.412655581788;OCT4_SOX2{dimer}:-0.413449545082;ZNF423:-0.413893414503;AHR_ARNT_ARNT2:-0.415787913654;ONECUT1,2:-0.442557175954;LEF1_TCF7_TCF7L1,2:-0.445967588306;ZNF384:-0.464185242689;HNF1A:-0.501035905414;RUNX1..3:-0.503379308587;HBP1_HMGB_SSRP1_UBTF:-0.524750411758;RXRA_VDR{dimer}:-0.56566276408;BACH2:-0.57012376534;FOX{F1,F2,J1}:-0.577693553178;PRRX1,2:-0.582909801823;HNF4A_NR2F1,2:-0.583148932208;HMX1:-0.583228874185;NFE2:-0.593159193182;MYFfamily:-0.605139603903;NFIL3:-0.622216097286;NFKB1_REL_RELA:-0.637861415467;IRF7:-0.642647741264;TP53:-0.644372577084;POU2F1..3:-0.644747287609;REST:-0.646079550559;FOX{D1,D2}:-0.651339071766;TLX2:-0.668916315837;VSX1,2:-0.688540972469;bHLH_family:-0.696859358881;DBP:-0.741378832204;LHX3,4:-0.751127412164;STAT5{A,B}:-0.860780280612;HLF:-0.864397911789;FOXN1:-0.86963694092;FOS_FOS{B,L1}_JUN{B,D}:-0.872438137571;POU5F1:-0.955791223491;IRF1,2:-0.957797460308;ALX4:-0.995016597333;SNAI1..3:-0.996202712148;FOXQ1:-1.02237353647;ZEB1:-1.03118184948;MYOD1:-1.04930831541;POU6F1:-1.07313339931;POU1F1:-1.07600217249;ADNP_IRX_SIX_ZHX:-1.0781699294;BPTF:-1.08664980852;DMAP1_NCOR{1,2}_SMARC:-1.13896808094;FOXM1:-1.17804373492;ATF6:-1.18632864104;PPARG:-1.25713267565;LMO2:-1.26066381002;NFIX:-1.36387538908;SPZ1:-1.44144913618;CEBPA,B_DDIT3:-1.48560820305;TAL1_TCF{3,4,12}:-1.4967097031;STAT2,4,6:-1.56482388887
|top_motifs=HOX{A5,B5}:3.20313119147;SRF:2.38961543199;GATA4:2.08969672095;MEF2{A,B,C,D}:1.96117236344;GATA6:1.71068379222;RXR{A,B,G}:1.69822797862;HIF1A:1.43564618288;NR5A1,2:1.38215408251;EVI1:1.3191845153;NANOG{mouse}:1.29293445164;NFE2L1:1.150815354;TEAD1:1.14840468541;FOXL1:1.06912843954;POU3F1..4:0.999022794969;ZNF143:0.997774363697;E2F1..5:0.890487467002;IKZF2:0.868140908793;MZF1:0.862068799268;PRDM1:0.844183602467;NFY{A,B,C}:0.838841452548;GFI1:0.789725847619;PATZ1:0.783198256213;SOX17:0.778274282764;EN1,2:0.769532381701;IKZF1:0.76258528623;ALX1:0.751257523593;RREB1:0.736983246802;SOX{8,9,10}:0.727853668386;NKX2-1,4:0.685444271149;UFEwm:0.64577528394;TGIF1:0.589571433095;GFI1B:0.573811980401;SOX2:0.570958496842;HES1:0.565267777159;RXR{A,B,G}_{NR1H2,PPAR}dimers:0.559262705533;PITX1..3:0.550296601458;HMGA1,2:0.53563112316;NR3C1:0.530899316231;GCM1,2:0.524928165646;T:0.511586771946;EP300:0.486472900038;ZIC1..3:0.476721867359;SOX5:0.467426646361;ESRRA:0.457184483452;HOXA9_MEIS1:0.456839578281;NRF1:0.425049622378;TOPORS:0.407961694726;MAZ:0.395119711619;XCPE1{core}:0.395090354256;NFATC1..3:0.393221735725;KLF4:0.387004741142;TFDP1:0.342297237163;NR6A1:0.339290801656;TFAP2{A,C}:0.295264682106;HSF1,2:0.280319571447;MYBL2:0.279247296894;TFAP2B:0.266059948954;BREu{core}:0.262910286422;YY1:0.256752126015;CRX:0.242755657668;EBF1:0.221312484961;PDX1:0.220363940795;NANOG:0.195715569402;TFAP4:0.175328266105;PAX2:0.1699496518;EGR1..3:0.161566335948;ELF1,2,4:0.153551111746;TLX1..3_NFIC{dimer}:0.13939843358;FOSL2:0.116195053339;NKX3-1:0.108231191842;MYB:0.0788531272978;CUX2:0.0765435690154;TFCP2:0.0749796158195;ELK1,4_GABP{A,B1}:0.07492326861;PAX8:0.072151837235;SPIB:0.0719776030011;ATF2:0.0701163028916;MAFB:0.0691006301672;CDX1,2,4:0.0609596267806;ESR1:0.0489158024144;HAND1,2:0.0412634575167;HIC1:0.0410518291855;CDC5L:0.0233623007487;ATF4:0.0209326321798;ZFP161:0.00743854210218;HOX{A4,D4}:0.00230922097473;PAX4:-0.00531779997314;GTF2A1,2:-0.0125975669177;SP1:-0.0133709850413;TEF:-0.0202664660367;AR:-0.0217310767235;TBX4,5:-0.0244426090222;SPI1:-0.0309919583323;PAX5:-0.0354985964265;GTF2I:-0.0363781278028;RFX2..5_RFXANK_RFXAP:-0.0380480519649;JUN:-0.0528198591978;PAX1,9:-0.0589343136163;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:-0.0703577188405;NKX2-2,8:-0.0744890594072;RORA:-0.0849285112327;SMAD1..7,9:-0.0895439913596;MTF1:-0.0897867152561;CREB1:-0.133761467066;NHLH1,2:-0.136112435208;RBPJ:-0.152361770463;GZF1:-0.156771988623;FOXP1:-0.165368498086;FOXO1,3,4:-0.168795526677;FOX{I1,J2}:-0.180071475315;TBP:-0.187311748292;MTE{core}:-0.19395289612;ETS1,2:-0.204893746545;STAT1,3:-0.213704689183;ZBTB16:-0.225963590701;PBX1:-0.226251501608;ZBTB6:-0.230094760271;ARID5B:-0.245756335126;NKX6-1,2:-0.257621556485;ZNF238:-0.270817471009;AIRE:-0.2766024956;NR1H4:-0.278308037563;FOXD3:-0.284906082712;ZNF148:-0.288729671362;MED-1{core}:-0.289482002603;NFE2L2:-0.291881495384;RFX1:-0.293888595937;NKX3-2:-0.320040594541;NKX2-3_NKX2-5:-0.321898925085;FOXP3:-0.329889618502;SREBF1,2:-0.344213379732;ATF5_CREB3:-0.347759130539;PAX6:-0.349120403041;FOXA2:-0.359707562375;GLI1..3:-0.412655581788;OCT4_SOX2{dimer}:-0.413449545082;ZNF423:-0.413893414503;AHR_ARNT_ARNT2:-0.415787913654;ONECUT1,2:-0.442557175954;LEF1_TCF7_TCF7L1,2:-0.445967588306;ZNF384:-0.464185242689;HNF1A:-0.501035905414;RUNX1..3:-0.503379308587;HBP1_HMGB_SSRP1_UBTF:-0.524750411758;RXRA_VDR{dimer}:-0.56566276408;BACH2:-0.57012376534;FOX{F1,F2,J1}:-0.577693553178;PRRX1,2:-0.582909801823;HNF4A_NR2F1,2:-0.583148932208;HMX1:-0.583228874185;NFE2:-0.593159193182;MYFfamily:-0.605139603903;NFIL3:-0.622216097286;NFKB1_REL_RELA:-0.637861415467;IRF7:-0.642647741264;TP53:-0.644372577084;POU2F1..3:-0.644747287609;REST:-0.646079550559;FOX{D1,D2}:-0.651339071766;TLX2:-0.668916315837;VSX1,2:-0.688540972469;bHLH_family:-0.696859358881;DBP:-0.741378832204;LHX3,4:-0.751127412164;STAT5{A,B}:-0.860780280612;HLF:-0.864397911789;FOXN1:-0.86963694092;FOS_FOS{B,L1}_JUN{B,D}:-0.872438137571;POU5F1:-0.955791223491;IRF1,2:-0.957797460308;ALX4:-0.995016597333;SNAI1..3:-0.996202712148;FOXQ1:-1.02237353647;ZEB1:-1.03118184948;MYOD1:-1.04930831541;POU6F1:-1.07313339931;POU1F1:-1.07600217249;ADNP_IRX_SIX_ZHX:-1.0781699294;BPTF:-1.08664980852;DMAP1_NCOR{1,2}_SMARC:-1.13896808094;FOXM1:-1.17804373492;ATF6:-1.18632864104;PPARG:-1.25713267565;LMO2:-1.26066381002;NFIX:-1.36387538908;SPZ1:-1.44144913618;CEBPA,B_DDIT3:-1.48560820305;TAL1_TCF{3,4,12}:-1.4967097031;STAT2,4,6:-1.56482388887
|comment=
|created_by=
|creation_date=
|def=
|has_quality=
|is_a=EFO:0002091;;FF:0000004;;FF:0000103;;FF:0011313
|namespace=FANTOM5
|part_of=
}}
}}

Revision as of 16:01, 7 March 2012


Name:heart, 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
tissueheart
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

CNhs10586

00
10
100.0818
1000
1000-0.0355
10010.111
10020.299
1003-0.104
10040
1005-0.0765
10060.148
1007-0.00469
10080
10090.00991
1010.0599
10100
10110
10120
1013-0.217
10140.266
10150.213
10160.194
10170
10180
10190
1020
10200
10210.0219
10220.0818
10230
1024-0.0578
10250
10260
10270
10280
1029-0.0323
103-0.0376
10300
10310.369
1032-0.0808
1033-0.0752
10340
10350.262
1036-0.0341
10370
1038-0.0594
10390.00245
1040
10400.171
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: CNhs10586

Jaspar motifP-value
MA0002.20.0163
MA0003.10.74
MA0004.10.919
MA0006.10.992
MA0007.10.237
MA0009.10.74
MA0014.10.723
MA0017.10.00773
MA0018.20.351
MA0019.10.838
MA0024.14.52952e-7
MA0025.10.91
MA0027.10.0636
MA0028.10.168
MA0029.10.349
MA0030.10.386
MA0031.10.0705
MA0035.20.0105
MA0038.10.623
MA0039.20.146
MA0040.10.0831
MA0041.10.62
MA0042.10.58
MA0043.10.362
MA0046.14.94381e-12
MA0047.20.0915
MA0048.10.0979
MA0050.11.28295e-8
MA0051.10.00151
MA0052.14.1134e-23
MA0055.10.00658
MA0057.10.597
MA0058.10.689
MA0059.10.924
MA0060.14.65451e-6
MA0061.10.0974
MA0062.20.766
MA0065.20.0367
MA0066.10.521
MA0067.10.844
MA0068.10.177
MA0069.10.4
MA0070.10.615
MA0071.10.797
MA0072.10.251
MA0073.10.755
MA0074.10.433
MA0076.10.607
MA0077.10.493
MA0078.10.201
MA0079.20.128
MA0080.20.0194
MA0081.10.874
MA0083.11.64828e-18
MA0084.10.821
MA0087.10.945
MA0088.10.265
MA0090.10.00882
MA0091.10.504
MA0092.10.387
MA0093.10.872
MA0099.27.64459e-6
MA0100.10.505
MA0101.10.468
MA0102.20.0219
MA0103.17.07196e-7
MA0104.20.679
MA0105.10.0731
MA0106.10.261
MA0107.10.322
MA0108.20.148
MA0111.10.234
MA0112.20.233
MA0113.10.433
MA0114.13.60077e-4
MA0115.10.551
MA0116.10.00612
MA0117.10.332
MA0119.10.808
MA0122.10.534
MA0124.10.29
MA0125.10.179
MA0131.10.689
MA0135.10.239
MA0136.10.0572
MA0137.20.32
MA0138.20.0349
MA0139.10.063
MA0140.11.23982e-4
MA0141.10.198
MA0142.10.312
MA0143.10.36
MA0144.10.614
MA0145.10.108
MA0146.10.87
MA0147.10.977
MA0148.10.0716
MA0149.10.0809
MA0150.10.0067
MA0152.10.632
MA0153.14.53726e-8
MA0154.10.0315
MA0155.10.418
MA0156.10.0217
MA0157.10.0683
MA0159.10.748
MA0160.10.327
MA0162.10.574
MA0163.10.973
MA0164.10.665
MA0258.10.16
MA0259.10.61



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: CNhs10586

Novel motifP-value
10.258
100.299
1000.773
1010.83
1020.643
1030.012
1040.49
1050.645
1060.174
1070.368
1080.949
1090.712
110.14
1100.886
1110.95
1120.173
1130.863
1140.207
1150.482
1160.163
1170.456
1180.816
1190.103
120.463
1200.172
1210.767
1220.578
1230.0419
1240.431
1250.446
1260.972
1270.17
1280.0327
1290.205
130.077
1300.393
1310.406
1320.577
1330.596
1340.683
1350.833
1360.458
1370.579
1380.147
1390.58
140.617
1400.338
1410.142
1420.93
1430.237
1440.225
1450.547
1460.426
1470.75
1480.226
1490.856
150.178
1500.836
1510.0943
1520.609
1530.282
1540.495
1550.708
1560.165
1570.405
1580.391
1590.623
1600.952
1610.874
1620.997
1630.887
1640.892
1650.307
1660.657
1670.552
1680.706
1690.818
170.0882
180.149
190.87
20.583
200.146
210.556
220.879
230.0654
240.496
250.372
260.222
270.187
280.344
290.925
30.218
300.34
310.423
320.107
330.242
340.398
350.0692
360.0932
370.797
380.313
390.289
40.622
400.0108
410.751
420.349
430.191
440.831
450.406
460.476
470.294
480.284
490.157
50.676
500.681
510.61
520.849
530.49
540.529
550.46
560.613
570.829
580.422
590.668
60.105
600.599
610.654
620.192
630.364
640.377
650.148
660.604
670.714
680.247
690.405
70.913
700.00565
710.947
720.138
730.869
740.34
750.223
760.5
770.129
780.801
790.0299
80.506
800.0461
810.285
820.265
830.44
840.456
850.233
860.886
870.105
880.286
890.286
90.934
900.203
910.535
920.118
930.333
940.801
950.701
960.731
970.154
980.182
990.28



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: CNhs10586


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
0000025 (tube)
0000061 (anatomical structure)
0000062 (organ)
0000119 (cell layer)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000479 (tissue)
0000480 (anatomical group)
0000481 (multi-tissue structure)
0000483 (epithelium)
0000922 (embryo)
0000923 (germ layer)
0000926 (mesoderm)
0000948 (heart)
0001009 (circulatory system)
0001048 (primordium)
0001062 (anatomical entity)
0002050 (embryonic structure)
0002532 (epiblast (generic))
0003081 (lateral plate mesoderm)
0003084 (heart primordium)
0003914 (epithelial tube)
0004120 (mesoderm-derived structure)
0004140 (primary heart field)
0004141 (heart tube)
0004291 (heart rudiment)
0004535 (cardiovascular system)
0004872 (splanchnic layer of lateral plate mesoderm)
0005291 (embryonic tissue)
0005423 (developing anatomical structure)
0005498 (primitive heart tube)
0007005 (cardiac mesoderm)
0007100 (primary circulatory organ)

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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