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|fonse_treatment_closure=
|fonse_treatment_closure=
|top_motifs=HOX{A5,B5}:3.71065490525;GATA4:3.14312851544;EVI1:2.67523938171;IKZF2:2.32138653622;SRF:2.17496995833;MEF2{A,B,C,D}:1.96264023617;NR3C1:1.73944018761;ALX1:1.67873384698;GATA6:1.65732888735;UFEwm:1.60408363884;NR5A1,2:1.46452788795;PITX1..3:1.43401050173;POU3F1..4:1.41037805444;NKX2-1,4:1.38029846185;PRDM1:1.35617653943;HIF1A:1.34154541339;NKX2-2,8:1.31386375613;FOXL1:1.29542239316;RXR{A,B,G}:1.28167986672;TEAD1:1.24558140414;T:1.03260323945;KLF4:1.0124313107;GFI1:0.974244210768;NKX3-1:0.922304743858;NFE2L1:0.916231347174;MZF1:0.866983660604;FOXP1:0.803757117472;HMGA1,2:0.76933438401;NR6A1:0.752147054589;CDC5L:0.750085042591;ZNF384:0.738360766586;PATZ1:0.724954349408;E2F1..5:0.72125110107;ZBTB16:0.704879708503;TOPORS:0.676745899332;CDX1,2,4:0.67156780241;MYBL2:0.656805890839;NFATC1..3:0.655808353158;RREB1:0.646786467264;NANOG{mouse}:0.637412998907;RXR{A,B,G}_{NR1H2,PPAR}dimers:0.637321549414;ZNF143:0.634327316638;CUX2:0.607669116816;NKX6-1,2:0.582489930733;SOX5:0.559986631719;NFY{A,B,C}:0.549136269762;TEF:0.544216181023;GCM1,2:0.542582148311;IKZF1:0.534383946958;SOX{8,9,10}:0.513735494708;SOX17:0.510650077829;EN1,2:0.452074484168;PAX4:0.421439400047;MAZ:0.359984760749;GFI1B:0.338121929751;ESRRA:0.32771081304;EBF1:0.324662242848;TGIF1:0.323568299788;SOX2:0.314814834072;TFAP4:0.310602362821;TLX1..3_NFIC{dimer}:0.23935295886;NRF1:0.166712025884;POU1F1:0.164392581377;PDX1:0.160326595447;FOX{I1,J2}:0.156323387034;ATF2:0.155297169657;ZIC1..3:0.150728502066;SPIB:0.141110043425;NANOG:0.10995434874;BREu{core}:0.108970668489;GTF2A1,2:0.10454848297;FOXD3:0.0822833696887;HOX{A4,D4}:0.0454822339103;EP300:0.0342209437013;ARID5B:0.0316184872051;STAT1,3:0.00754494894442;CRX:-0.00331952973318;TFDP1:-0.0096008692651;HOXA9_MEIS1:-0.0204695806407;XCPE1{core}:-0.039746690988;FOXO1,3,4:-0.0482887240511;FOSL2:-0.0522491800461;MYB:-0.080901971018;SPI1:-0.0894888277786;TBP:-0.0934537963821;AIRE:-0.102360101523;ZFP161:-0.113661373409;GTF2I:-0.114146597353;NHLH1,2:-0.117297973573;NKX3-2:-0.119593464361;ELF1,2,4:-0.123697291109;HBP1_HMGB_SSRP1_UBTF:-0.123725401866;NFE2L2:-0.138729704236;ONECUT1,2:-0.157993611943;HIC1:-0.158835703558;YY1:-0.165908116384;FOXP3:-0.184549965351;HES1:-0.189928030851;PAX8:-0.203106013872;MAFB:-0.204989466956;PAX5:-0.205312095507;HSF1,2:-0.212541093329;PAX2:-0.213910489121;OCT4_SOX2{dimer}:-0.217388162363;ZNF238:-0.226327267041;GLI1..3:-0.227446466686;TFCP2:-0.228290764478;FOXA2:-0.253285980137;EGR1..3:-0.273082947313;ELK1,4_GABP{A,B1}:-0.273856268044;SMAD1..7,9:-0.277457889993;HAND1,2:-0.288594057147;RFX2..5_RFXANK_RFXAP:-0.299820086203;NKX2-3_NKX2-5:-0.30501464909;CREB1:-0.317529687539;ETS1,2:-0.318667748111;TFAP2{A,C}:-0.321398593633;TFAP2B:-0.332266188728;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:-0.332375937063;FOX{F1,F2,J1}:-0.336961667665;DBP:-0.339997942536;SP1:-0.36805098369;MTE{core}:-0.370010889276;VSX1,2:-0.376818125563;AHR_ARNT_ARNT2:-0.377741269678;ATF4:-0.39932249139;NR1H4:-0.410414366368;JUN:-0.413827729895;TBX4,5:-0.416067823859;RFX1:-0.429891850446;RORA:-0.443949363157;LEF1_TCF7_TCF7L1,2:-0.449782017106;BPTF:-0.45601954788;AR:-0.459698837579;HNF1A:-0.464829671078;bHLH_family:-0.48896373056;ZBTB6:-0.491745783386;MTF1:-0.501733966286;ESR1:-0.523239173215;MED-1{core}:-0.529000603364;ZNF148:-0.533778569229;PAX1,9:-0.580774867765;HNF4A_NR2F1,2:-0.580800989118;MYFfamily:-0.583193292088;IRF1,2:-0.591073701468;NFE2:-0.592052095027;TP53:-0.610399509787;RUNX1..3:-0.619694315225;GZF1:-0.628758249634;FOX{D1,D2}:-0.632234377667;REST:-0.697384766013;PAX6:-0.702047974932;IRF7:-0.703493358433;FOXQ1:-0.726021196453;POU5F1:-0.740420084425;HLF:-0.751945253448;ATF5_CREB3:-0.756350928774;BACH2:-0.762026876259;NFKB1_REL_RELA:-0.763284112252;RXRA_VDR{dimer}:-0.772917255312;PBX1:-0.777811574041;ALX4:-0.780342489883;PRRX1,2:-0.788505594483;ZNF423:-0.822136525588;SREBF1,2:-0.840411204501;NFIL3:-0.848996408343;POU2F1..3:-0.88249428614;POU6F1:-0.945317607076;STAT5{A,B}:-0.951097726493;HMX1:-0.97905762416;ZEB1:-0.984291782866;LHX3,4:-0.998342099945;SNAI1..3:-1.03747183138;TLX2:-1.05398451469;FOS_FOS{B,L1}_JUN{B,D}:-1.07287464552;DMAP1_NCOR{1,2}_SMARC:-1.11462057806;FOXN1:-1.14501359091;ADNP_IRX_SIX_ZHX:-1.16581234109;PPARG:-1.16951894152;RBPJ:-1.18259732325;CEBPA,B_DDIT3:-1.20301082084;NFIX:-1.23847722456;LMO2:-1.24203084429;MYOD1:-1.2658994222;ATF6:-1.43814584297;TAL1_TCF{3,4,12}:-1.44827590843;FOXM1:-1.50536560395;STAT2,4,6:-1.53132582689;SPZ1:-1.57569635422
|top_motifs=HOX{A5,B5}:3.71065490525;GATA4:3.14312851544;EVI1:2.67523938171;IKZF2:2.32138653622;SRF:2.17496995833;MEF2{A,B,C,D}:1.96264023617;NR3C1:1.73944018761;ALX1:1.67873384698;GATA6:1.65732888735;UFEwm:1.60408363884;NR5A1,2:1.46452788795;PITX1..3:1.43401050173;POU3F1..4:1.41037805444;NKX2-1,4:1.38029846185;PRDM1:1.35617653943;HIF1A:1.34154541339;NKX2-2,8:1.31386375613;FOXL1:1.29542239316;RXR{A,B,G}:1.28167986672;TEAD1:1.24558140414;T:1.03260323945;KLF4:1.0124313107;GFI1:0.974244210768;NKX3-1:0.922304743858;NFE2L1:0.916231347174;MZF1:0.866983660604;FOXP1:0.803757117472;HMGA1,2:0.76933438401;NR6A1:0.752147054589;CDC5L:0.750085042591;ZNF384:0.738360766586;PATZ1:0.724954349408;E2F1..5:0.72125110107;ZBTB16:0.704879708503;TOPORS:0.676745899332;CDX1,2,4:0.67156780241;MYBL2:0.656805890839;NFATC1..3:0.655808353158;RREB1:0.646786467264;NANOG{mouse}:0.637412998907;RXR{A,B,G}_{NR1H2,PPAR}dimers:0.637321549414;ZNF143:0.634327316638;CUX2:0.607669116816;NKX6-1,2:0.582489930733;SOX5:0.559986631719;NFY{A,B,C}:0.549136269762;TEF:0.544216181023;GCM1,2:0.542582148311;IKZF1:0.534383946958;SOX{8,9,10}:0.513735494708;SOX17:0.510650077829;EN1,2:0.452074484168;PAX4:0.421439400047;MAZ:0.359984760749;GFI1B:0.338121929751;ESRRA:0.32771081304;EBF1:0.324662242848;TGIF1:0.323568299788;SOX2:0.314814834072;TFAP4:0.310602362821;TLX1..3_NFIC{dimer}:0.23935295886;NRF1:0.166712025884;POU1F1:0.164392581377;PDX1:0.160326595447;FOX{I1,J2}:0.156323387034;ATF2:0.155297169657;ZIC1..3:0.150728502066;SPIB:0.141110043425;NANOG:0.10995434874;BREu{core}:0.108970668489;GTF2A1,2:0.10454848297;FOXD3:0.0822833696887;HOX{A4,D4}:0.0454822339103;EP300:0.0342209437013;ARID5B:0.0316184872051;STAT1,3:0.00754494894442;CRX:-0.00331952973318;TFDP1:-0.0096008692651;HOXA9_MEIS1:-0.0204695806407;XCPE1{core}:-0.039746690988;FOXO1,3,4:-0.0482887240511;FOSL2:-0.0522491800461;MYB:-0.080901971018;SPI1:-0.0894888277786;TBP:-0.0934537963821;AIRE:-0.102360101523;ZFP161:-0.113661373409;GTF2I:-0.114146597353;NHLH1,2:-0.117297973573;NKX3-2:-0.119593464361;ELF1,2,4:-0.123697291109;HBP1_HMGB_SSRP1_UBTF:-0.123725401866;NFE2L2:-0.138729704236;ONECUT1,2:-0.157993611943;HIC1:-0.158835703558;YY1:-0.165908116384;FOXP3:-0.184549965351;HES1:-0.189928030851;PAX8:-0.203106013872;MAFB:-0.204989466956;PAX5:-0.205312095507;HSF1,2:-0.212541093329;PAX2:-0.213910489121;OCT4_SOX2{dimer}:-0.217388162363;ZNF238:-0.226327267041;GLI1..3:-0.227446466686;TFCP2:-0.228290764478;FOXA2:-0.253285980137;EGR1..3:-0.273082947313;ELK1,4_GABP{A,B1}:-0.273856268044;SMAD1..7,9:-0.277457889993;HAND1,2:-0.288594057147;RFX2..5_RFXANK_RFXAP:-0.299820086203;NKX2-3_NKX2-5:-0.30501464909;CREB1:-0.317529687539;ETS1,2:-0.318667748111;TFAP2{A,C}:-0.321398593633;TFAP2B:-0.332266188728;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:-0.332375937063;FOX{F1,F2,J1}:-0.336961667665;DBP:-0.339997942536;SP1:-0.36805098369;MTE{core}:-0.370010889276;VSX1,2:-0.376818125563;AHR_ARNT_ARNT2:-0.377741269678;ATF4:-0.39932249139;NR1H4:-0.410414366368;JUN:-0.413827729895;TBX4,5:-0.416067823859;RFX1:-0.429891850446;RORA:-0.443949363157;LEF1_TCF7_TCF7L1,2:-0.449782017106;BPTF:-0.45601954788;AR:-0.459698837579;HNF1A:-0.464829671078;bHLH_family:-0.48896373056;ZBTB6:-0.491745783386;MTF1:-0.501733966286;ESR1:-0.523239173215;MED-1{core}:-0.529000603364;ZNF148:-0.533778569229;PAX1,9:-0.580774867765;HNF4A_NR2F1,2:-0.580800989118;MYFfamily:-0.583193292088;IRF1,2:-0.591073701468;NFE2:-0.592052095027;TP53:-0.610399509787;RUNX1..3:-0.619694315225;GZF1:-0.628758249634;FOX{D1,D2}:-0.632234377667;REST:-0.697384766013;PAX6:-0.702047974932;IRF7:-0.703493358433;FOXQ1:-0.726021196453;POU5F1:-0.740420084425;HLF:-0.751945253448;ATF5_CREB3:-0.756350928774;BACH2:-0.762026876259;NFKB1_REL_RELA:-0.763284112252;RXRA_VDR{dimer}:-0.772917255312;PBX1:-0.777811574041;ALX4:-0.780342489883;PRRX1,2:-0.788505594483;ZNF423:-0.822136525588;SREBF1,2:-0.840411204501;NFIL3:-0.848996408343;POU2F1..3:-0.88249428614;POU6F1:-0.945317607076;STAT5{A,B}:-0.951097726493;HMX1:-0.97905762416;ZEB1:-0.984291782866;LHX3,4:-0.998342099945;SNAI1..3:-1.03747183138;TLX2:-1.05398451469;FOS_FOS{B,L1}_JUN{B,D}:-1.07287464552;DMAP1_NCOR{1,2}_SMARC:-1.11462057806;FOXN1:-1.14501359091;ADNP_IRX_SIX_ZHX:-1.16581234109;PPARG:-1.16951894152;RBPJ:-1.18259732325;CEBPA,B_DDIT3:-1.20301082084;NFIX:-1.23847722456;LMO2:-1.24203084429;MYOD1:-1.2658994222;ATF6:-1.43814584297;TAL1_TCF{3,4,12}:-1.44827590843;FOXM1:-1.50536560395;STAT2,4,6:-1.53132582689;SPZ1:-1.57569635422
|comment=
|created_by=
|creation_date=
|def=
|has_quality=
|is_a=EFO:0002091;;FF:0000004;;FF:0000103;;FF:0011318
|namespace=FANTOM5
|part_of=
}}
}}

Revision as of 16:01, 7 March 2012


Name:heart, embryo E12
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 stage12 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

CNhs11015

00
10
100.0915
1000
10000
10010.26
10020.465
10030.00475
10040
1005-0.0389
10060.231
10070.0156
10080
10090.00751
1010.0744
10100
1011-0.0226
10120
1013-0.217
10140.539
10150.226
10160.161
10170
10180
10190
1020
10200
10210
10220.137
10230
1024-0.0361
10250.0915
10260
10270
10280
10290.238
1030.015
10300
10310.419
1032-0.0166
10330.00343
10340
10350.422
1036-0.0466
10370
1038-0.0129
10390.00774
1040
10400.0717
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: CNhs11015

Jaspar motifP-value
MA0002.20.0217
MA0003.10.523
MA0004.10.95
MA0006.10.81
MA0007.10.071
MA0009.10.855
MA0014.10.563
MA0017.10.0708
MA0018.20.155
MA0019.10.311
MA0024.18.73799e-5
MA0025.10.102
MA0027.10.0265
MA0028.10.853
MA0029.10.295
MA0030.10.0441
MA0031.10.0217
MA0035.20.0671
MA0038.10.831
MA0039.20.0128
MA0040.10.0868
MA0041.10.111
MA0042.10.205
MA0043.10.545
MA0046.18.38694e-13
MA0047.20.0152
MA0048.10.0274
MA0050.12.51774e-6
MA0051.10.00207
MA0052.14.11157e-13
MA0055.10.0158
MA0057.10.614
MA0058.10.645
MA0059.10.101
MA0060.10.316
MA0061.10.651
MA0062.20.00131
MA0065.20.174
MA0066.10.779
MA0067.10.15
MA0068.10.215
MA0069.10.209
MA0070.10.684
MA0071.10.919
MA0072.10.0927
MA0073.10.955
MA0074.10.626
MA0076.10.0798
MA0077.10.748
MA0078.10.22
MA0079.20.285
MA0080.20.00823
MA0081.10.844
MA0083.11.49213e-15
MA0084.10.77
MA0087.10.944
MA0088.10.326
MA0090.10.0119
MA0091.10.747
MA0092.10.71
MA0093.10.872
MA0099.25.48723e-8
MA0100.10.96
MA0101.10.104
MA0102.20.00928
MA0103.19.17424e-7
MA0104.20.262
MA0105.10.0151
MA0106.10.878
MA0107.10.124
MA0108.20.67
MA0111.10.499
MA0112.20.267
MA0113.10.465
MA0114.10.00365
MA0115.10.938
MA0116.10.889
MA0117.10.535
MA0119.10.0699
MA0122.10.924
MA0124.10.258
MA0125.10.826
MA0131.10.687
MA0135.10.23
MA0136.10.00841
MA0137.20.0393
MA0138.20.0411
MA0139.10.585
MA0140.17.87409e-4
MA0141.10.0257
MA0142.10.579
MA0143.10.554
MA0144.10.0707
MA0145.10.293
MA0146.10.559
MA0147.10.259
MA0148.10.0706
MA0149.10.0912
MA0150.10.00181
MA0152.10.658
MA0153.11.10387e-7
MA0154.10.711
MA0155.10.188
MA0156.11.14178e-5
MA0157.10.0442
MA0159.10.394
MA0160.10.846
MA0162.10.293
MA0163.10.0143
MA0164.10.816
MA0258.10.628
MA0259.10.473



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: CNhs11015

Novel motifP-value
10.742
100.923
1000.905
1010.757
1020.298
1030.329
1040.565
1050.846
1060.775
1070.924
1080.8
1090.984
110.195
1100.269
1110.607
1120.392
1130.503
1140.938
1150.535
1160.651
1170.396
1180.457
1190.357
120.388
1200.372
1210.845
1220.289
1230.0681
1240.937
1250.749
1260.732
1270.248
1280.296
1290.355
130.00201
1300.244
1310.458
1320.315
1330.692
1340.587
1350.721
1360.0227
1370.87
1380.153
1390.932
140.483
1400.747
1410.209
1420.738
1430.646
1440.0878
1450.0637
1460.183
1470.871
1480.622
1490.989
150.237
1500.738
1510.172
1520.281
1530.264
1540.742
1550.686
1560.0143
1570.435
1580.431
1590.171
1600.274
1610.66
1620.77
1630.564
1640.394
1650.197
1660.37
1670.765
1680.686
1690.113
170.234
180.525
190.178
20.526
200.146
210.444
220.634
230.196
240.472
250.328
260.0253
270.19
280.476
290.207
30.961
300.0936
310.758
320.482
330.135
340.772
350.91
360.156
370.66
380.173
390.351
40.573
400.00488
410.871
420.899
430.643
440.468
450.0729
460.643
470.586
480.414
490.818
50.943
500.485
510.975
520.786
530.552
540.833
550.201
560.999
570.287
580.638
590.4
60.194
600.722
610.415
620.569
630.865
640.469
650.168
660.614
670.607
680.789
690.212
70.56
700.0224
710.00663
720.0651
730.813
740.968
750.785
760.346
770.317
780.647
790.201
80.616
800.0119
810.771
820.981
830.934
840.968
850.883
860.763
874.15479e-5
880.315
890.128
90.974
900.706
910.256
920.998
930.636
940.182
950.646
960.394
970.14
980.307
990.663



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: CNhs11015


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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