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|fonse_treatment_closure=
|fonse_treatment_closure=
|top_motifs=NFY{A,B,C}:1.78051846714;GFI1:1.73301301888;ZNF143:1.68068116232;FOX{I1,J2}:1.62040512546;E2F1..5:1.36200035424;NANOG:1.30794546689;TFDP1:1.25322602233;NRF1:1.21827711601;SOX2:1.21184392524;SOX{8,9,10}:1.18580451119;ZNF384:1.17405399356;FOXQ1:1.12290161;MZF1:1.1179375924;TOPORS:1.06320395733;SOX17:1.00568839725;GZF1:0.952188135192;RREB1:0.938004589774;PATZ1:0.918046091486;HMGA1,2:0.877439101182;PAX6:0.870620829654;MAZ:0.831367809389;PRRX1,2:0.817378983503;EP300:0.809931685869;HOXA9_MEIS1:0.758265708285;HMX1:0.753194593672;NKX3-1:0.745479057408;ELK1,4_GABP{A,B1}:0.741711328505;DBP:0.718655101463;ADNP_IRX_SIX_ZHX:0.701898608697;BREu{core}:0.698322148214;ZNF238:0.686480137567;GATA4:0.679031775084;EN1,2:0.661419611531;RXR{A,B,G}:0.65411667237;ONECUT1,2:0.63900304404;LEF1_TCF7_TCF7L1,2:0.635870684261;NANOG{mouse}:0.621825434543;YY1:0.611295683814;GTF2I:0.602827960823;IKZF1:0.596748665203;IKZF2:0.546418227522;MYBL2:0.534481143396;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:0.523382458276;XCPE1{core}:0.522495250374;ZBTB16:0.519756542535;HIC1:0.509840326377;CRX:0.49314833499;ZIC1..3:0.485333293561;LHX3,4:0.455530483723;AHR_ARNT_ARNT2:0.453342903242;STAT1,3:0.444904171195;PAX8:0.424829426949;TFAP2{A,C}:0.393842286271;STAT5{A,B}:0.378706059994;HBP1_HMGB_SSRP1_UBTF:0.367271626654;FOXM1:0.362300184088;PAX1,9:0.357893930782;MED-1{core}:0.351814775754;HSF1,2:0.346889316023;PBX1:0.343599052468;CDC5L:0.341642419063;NKX2-1,4:0.340833135422;ZNF423:0.32946887194;SRF:0.326498694978;SP1:0.301199694234;SPZ1:0.279405403029;TEAD1:0.272699879938;TFAP2B:0.270896940466;VSX1,2:0.249213274245;POU2F1..3:0.248878681363;KLF4:0.245781671958;UFEwm:0.243821703228;CDX1,2,4:0.214063232002;GTF2A1,2:0.206755400888;OCT4_SOX2{dimer}:0.204397836566;GATA6:0.203631204615;bHLH_family:0.189626702098;PAX5:0.175940942881;EGR1..3:0.169881471037;RFX1:0.158570110711;RFX2..5_RFXANK_RFXAP:0.158292822767;EBF1:0.15453548577;HOX{A5,B5}:0.149829120414;MYB:0.149632756423;HES1:0.146319029503;ELF1,2,4:0.123710030512;HAND1,2:0.115658633497;FOXD3:0.113302771126;RBPJ:0.0960113451065;ZFP161:0.0876689470716;PRDM1:0.0806275717242;PITX1..3:0.077721871518;HIF1A:0.0561256455336;MTE{core}:0.0408829241926;FOX{F1,F2,J1}:0.0335337673847;POU5F1:0.0262847393522;TLX2:0.0181917282566;GLI1..3:0.00250231758724;CUX2:-0.0109271205196;RXR{A,B,G}_{NR1H2,PPAR}dimers:-0.0258598373897;GFI1B:-0.031201300831;JUN:-0.032868152703;SOX5:-0.0431289362278;TFCP2:-0.0582570850279;FOXA2:-0.0663812460634;FOX{D1,D2}:-0.0756034743146;PDX1:-0.0870716258536;HNF1A:-0.0887355395335;RORA:-0.110749079333;ATF2:-0.11567403471;ESR1:-0.121047523142;SPIB:-0.126880733579;NKX3-2:-0.132490126766;TLX1..3_NFIC{dimer}:-0.144889399972;PAX4:-0.159702532721;ZBTB6:-0.179354228478;ZNF148:-0.183754828357;REST:-0.192489739276;T:-0.195652342286;DMAP1_NCOR{1,2}_SMARC:-0.199018156294;NHLH1,2:-0.200339764631;TEF:-0.212239235973;CREB1:-0.216525697886;AIRE:-0.225054506252;POU1F1:-0.238350426995;POU6F1:-0.242962373814;ARID5B:-0.256315227502;TP53:-0.261569622732;RUNX1..3:-0.262162278148;EVI1:-0.266311240958;TFAP4:-0.268955175446;FOXP1:-0.278342994895;NR6A1:-0.283221600017;SPI1:-0.28859164271;MTF1:-0.306858902786;ETS1,2:-0.316588940645;SNAI1..3:-0.316986730078;POU3F1..4:-0.333335715534;NKX2-3_NKX2-5:-0.335550012135;ALX4:-0.336945477562;HNF4A_NR2F1,2:-0.340954039864;GCM1,2:-0.361026077544;ATF4:-0.365744112312;ATF5_CREB3:-0.39342400122;FOXP3:-0.405915504956;ATF6:-0.416267821051;TBP:-0.44574383078;NFIL3:-0.45404316385;NKX2-2,8:-0.466529416666;HOX{A4,D4}:-0.469497469839;SREBF1,2:-0.473624457323;BPTF:-0.48222484151;NFKB1_REL_RELA:-0.485795712229;NFIX:-0.499539539437;MEF2{A,B,C,D}:-0.524875659443;TAL1_TCF{3,4,12}:-0.531339306677;TGIF1:-0.532729785579;NKX6-1,2:-0.542005238228;FOXL1:-0.595492927485;NR1H4:-0.609696652877;HLF:-0.639313964847;MYFfamily:-0.654305897069;MYOD1:-0.669958836514;RXRA_VDR{dimer}:-0.674364093101;LMO2:-0.675060396446;FOXN1:-0.679776193204;ZEB1:-0.705714515123;ESRRA:-0.760747535479;NFATC1..3:-0.767905089306;TBX4,5:-0.807366515077;BACH2:-0.810112834278;FOSL2:-0.821657432322;FOS_FOS{B,L1}_JUN{B,D}:-0.828637875025;SMAD1..7,9:-0.840724982958;IRF7:-0.884564288712;NR3C1:-0.889529658399;NFE2L1:-0.891795062456;ALX1:-0.905549921797;NFE2:-0.962935686363;NR5A1,2:-0.976580649994;AR:-0.983970968904;PPARG:-0.999037821991;PAX2:-1.03329870403;IRF1,2:-1.06084754621;FOXO1,3,4:-1.07353896228;CEBPA,B_DDIT3:-1.13957147163;MAFB:-1.14078609148;STAT2,4,6:-1.17794658081;NFE2L2:-1.2951611519
|top_motifs=NFY{A,B,C}:1.78051846714;GFI1:1.73301301888;ZNF143:1.68068116232;FOX{I1,J2}:1.62040512546;E2F1..5:1.36200035424;NANOG:1.30794546689;TFDP1:1.25322602233;NRF1:1.21827711601;SOX2:1.21184392524;SOX{8,9,10}:1.18580451119;ZNF384:1.17405399356;FOXQ1:1.12290161;MZF1:1.1179375924;TOPORS:1.06320395733;SOX17:1.00568839725;GZF1:0.952188135192;RREB1:0.938004589774;PATZ1:0.918046091486;HMGA1,2:0.877439101182;PAX6:0.870620829654;MAZ:0.831367809389;PRRX1,2:0.817378983503;EP300:0.809931685869;HOXA9_MEIS1:0.758265708285;HMX1:0.753194593672;NKX3-1:0.745479057408;ELK1,4_GABP{A,B1}:0.741711328505;DBP:0.718655101463;ADNP_IRX_SIX_ZHX:0.701898608697;BREu{core}:0.698322148214;ZNF238:0.686480137567;GATA4:0.679031775084;EN1,2:0.661419611531;RXR{A,B,G}:0.65411667237;ONECUT1,2:0.63900304404;LEF1_TCF7_TCF7L1,2:0.635870684261;NANOG{mouse}:0.621825434543;YY1:0.611295683814;GTF2I:0.602827960823;IKZF1:0.596748665203;IKZF2:0.546418227522;MYBL2:0.534481143396;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:0.523382458276;XCPE1{core}:0.522495250374;ZBTB16:0.519756542535;HIC1:0.509840326377;CRX:0.49314833499;ZIC1..3:0.485333293561;LHX3,4:0.455530483723;AHR_ARNT_ARNT2:0.453342903242;STAT1,3:0.444904171195;PAX8:0.424829426949;TFAP2{A,C}:0.393842286271;STAT5{A,B}:0.378706059994;HBP1_HMGB_SSRP1_UBTF:0.367271626654;FOXM1:0.362300184088;PAX1,9:0.357893930782;MED-1{core}:0.351814775754;HSF1,2:0.346889316023;PBX1:0.343599052468;CDC5L:0.341642419063;NKX2-1,4:0.340833135422;ZNF423:0.32946887194;SRF:0.326498694978;SP1:0.301199694234;SPZ1:0.279405403029;TEAD1:0.272699879938;TFAP2B:0.270896940466;VSX1,2:0.249213274245;POU2F1..3:0.248878681363;KLF4:0.245781671958;UFEwm:0.243821703228;CDX1,2,4:0.214063232002;GTF2A1,2:0.206755400888;OCT4_SOX2{dimer}:0.204397836566;GATA6:0.203631204615;bHLH_family:0.189626702098;PAX5:0.175940942881;EGR1..3:0.169881471037;RFX1:0.158570110711;RFX2..5_RFXANK_RFXAP:0.158292822767;EBF1:0.15453548577;HOX{A5,B5}:0.149829120414;MYB:0.149632756423;HES1:0.146319029503;ELF1,2,4:0.123710030512;HAND1,2:0.115658633497;FOXD3:0.113302771126;RBPJ:0.0960113451065;ZFP161:0.0876689470716;PRDM1:0.0806275717242;PITX1..3:0.077721871518;HIF1A:0.0561256455336;MTE{core}:0.0408829241926;FOX{F1,F2,J1}:0.0335337673847;POU5F1:0.0262847393522;TLX2:0.0181917282566;GLI1..3:0.00250231758724;CUX2:-0.0109271205196;RXR{A,B,G}_{NR1H2,PPAR}dimers:-0.0258598373897;GFI1B:-0.031201300831;JUN:-0.032868152703;SOX5:-0.0431289362278;TFCP2:-0.0582570850279;FOXA2:-0.0663812460634;FOX{D1,D2}:-0.0756034743146;PDX1:-0.0870716258536;HNF1A:-0.0887355395335;RORA:-0.110749079333;ATF2:-0.11567403471;ESR1:-0.121047523142;SPIB:-0.126880733579;NKX3-2:-0.132490126766;TLX1..3_NFIC{dimer}:-0.144889399972;PAX4:-0.159702532721;ZBTB6:-0.179354228478;ZNF148:-0.183754828357;REST:-0.192489739276;T:-0.195652342286;DMAP1_NCOR{1,2}_SMARC:-0.199018156294;NHLH1,2:-0.200339764631;TEF:-0.212239235973;CREB1:-0.216525697886;AIRE:-0.225054506252;POU1F1:-0.238350426995;POU6F1:-0.242962373814;ARID5B:-0.256315227502;TP53:-0.261569622732;RUNX1..3:-0.262162278148;EVI1:-0.266311240958;TFAP4:-0.268955175446;FOXP1:-0.278342994895;NR6A1:-0.283221600017;SPI1:-0.28859164271;MTF1:-0.306858902786;ETS1,2:-0.316588940645;SNAI1..3:-0.316986730078;POU3F1..4:-0.333335715534;NKX2-3_NKX2-5:-0.335550012135;ALX4:-0.336945477562;HNF4A_NR2F1,2:-0.340954039864;GCM1,2:-0.361026077544;ATF4:-0.365744112312;ATF5_CREB3:-0.39342400122;FOXP3:-0.405915504956;ATF6:-0.416267821051;TBP:-0.44574383078;NFIL3:-0.45404316385;NKX2-2,8:-0.466529416666;HOX{A4,D4}:-0.469497469839;SREBF1,2:-0.473624457323;BPTF:-0.48222484151;NFKB1_REL_RELA:-0.485795712229;NFIX:-0.499539539437;MEF2{A,B,C,D}:-0.524875659443;TAL1_TCF{3,4,12}:-0.531339306677;TGIF1:-0.532729785579;NKX6-1,2:-0.542005238228;FOXL1:-0.595492927485;NR1H4:-0.609696652877;HLF:-0.639313964847;MYFfamily:-0.654305897069;MYOD1:-0.669958836514;RXRA_VDR{dimer}:-0.674364093101;LMO2:-0.675060396446;FOXN1:-0.679776193204;ZEB1:-0.705714515123;ESRRA:-0.760747535479;NFATC1..3:-0.767905089306;TBX4,5:-0.807366515077;BACH2:-0.810112834278;FOSL2:-0.821657432322;FOS_FOS{B,L1}_JUN{B,D}:-0.828637875025;SMAD1..7,9:-0.840724982958;IRF7:-0.884564288712;NR3C1:-0.889529658399;NFE2L1:-0.891795062456;ALX1:-0.905549921797;NFE2:-0.962935686363;NR5A1,2:-0.976580649994;AR:-0.983970968904;PPARG:-0.999037821991;PAX2:-1.03329870403;IRF1,2:-1.06084754621;FOXO1,3,4:-1.07353896228;CEBPA,B_DDIT3:-1.13957147163;MAFB:-1.14078609148;STAT2,4,6:-1.17794658081;NFE2L2:-1.2951611519
|comment=
|created_by=
|creation_date=
|def=
|has_quality=
|is_a=EFO:0002091;;FF:0000004;;FF:0000103;;FF:0011321
|namespace=FANTOM5
|part_of=
}}
}}

Revision as of 16:01, 7 March 2012


Name:stomach, 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
tissuestomach
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

CNhs10588

00
10
100
1000
1000-0.0119
1001-0.0668
10020.481
1003-0.132
10040
1005-0.136
1006-0.00645
10070.17
10080
10090
1010.14
10100
10110
10120
1013-0.217
10140.343
10150.406
10160.315
10170
10180
10190
1020
10200
10210.0151
1022-0.124
10230
1024-0.0173
10250.665
10260
10270.0638
10280
1029-0.0838
1030
10300
10310.285
1032-0.0606
10330.0441
10340
10350
10360.164
10370
10380.0106
1039-0.18
1040
10400.161
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: CNhs10588

Jaspar motifP-value
MA0002.20.00101
MA0003.10.251
MA0004.10.678
MA0006.10.362
MA0007.10.358
MA0009.10.606
MA0014.10.418
MA0017.13.79694e-4
MA0018.20.379
MA0019.10.791
MA0024.15.09002e-6
MA0025.10.0898
MA0027.10.0423
MA0028.10.0605
MA0029.10.515
MA0030.10.669
MA0031.10.374
MA0035.20.275
MA0038.10.00823
MA0039.20.461
MA0040.10.764
MA0041.10.337
MA0042.10.653
MA0043.10.0679
MA0046.10.0536
MA0047.20.725
MA0048.10.238
MA0050.11.15441e-6
MA0051.13.75459e-5
MA0052.18.6983e-6
MA0055.10.0419
MA0057.10.0891
MA0058.10.494
MA0059.10.692
MA0060.16.80594e-18
MA0061.10.0973
MA0062.20.12
MA0065.20.00109
MA0066.10.0795
MA0067.10.429
MA0068.10.613
MA0069.10.946
MA0070.10.366
MA0071.10.111
MA0072.10.158
MA0073.10.979
MA0074.10.764
MA0076.10.0379
MA0077.10.0281
MA0078.10.572
MA0079.20.552
MA0080.29.4604e-7
MA0081.10.646
MA0083.10.197
MA0084.10.383
MA0087.10.936
MA0088.10.98
MA0090.10.533
MA0091.10.714
MA0092.10.433
MA0093.10.624
MA0099.24.92676e-4
MA0100.10.592
MA0101.10.635
MA0102.20.61
MA0103.10.0141
MA0104.20.233
MA0105.10.00769
MA0106.10.193
MA0107.10.291
MA0108.20.0456
MA0111.10.568
MA0112.23.30863e-6
MA0113.10.817
MA0114.10.00281
MA0115.10.0534
MA0116.10.0093
MA0117.10.101
MA0119.10.012
MA0122.10.929
MA0124.10.757
MA0125.10.0499
MA0131.10.179
MA0135.10.203
MA0136.10.036
MA0137.20.346
MA0138.20.0019
MA0139.10.282
MA0140.10.337
MA0141.10.00162
MA0142.10.754
MA0143.10.0155
MA0144.10.293
MA0145.10.0221
MA0146.10.853
MA0147.10.371
MA0148.10.123
MA0149.10.0259
MA0150.10.00348
MA0152.10.755
MA0153.10.599
MA0154.10.00554
MA0155.10.952
MA0156.10.811
MA0157.10.3
MA0159.10.0231
MA0160.10.0423
MA0162.10.662
MA0163.10.0876
MA0164.10.691
MA0258.12.91149e-4
MA0259.10.573



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: CNhs10588

Novel motifP-value
10.0661
100.341
1000.939
1010.47
1020.754
1030.0691
1040.901
1050.276
1060.00974
1070.0517
1080.96
1090.211
110.137
1100.198
1110.091
1120.0843
1130.424
1140.0138
1150.701
1160.62
1170.419
1180.806
1190.0489
120.98
1200.806
1210.706
1220.936
1230.107
1240.368
1250.387
1260.733
1270.0884
1280.0272
1290.0315
130.441
1300.589
1310.179
1320.646
1330.493
1340.522
1350.943
1360.408
1370.679
1380.728
1390.00441
140.333
1400.059
1410.281
1420.327
1430.452
1440.692
1450.51
1460.503
1470.561
1480.224
1490.206
150.0932
1500.47
1510.143
1520.21
1530.132
1540.367
1550.907
1560.0158
1570.846
1580.35
1590.0806
1600.519
1610.667
1620.612
1630.213
1640.445
1650.144
1660.679
1670.936
1680.315
1690.00487
170.044
180.334
190.21
20.629
200.781
210.962
220.312
230.0503
240.677
250.335
260.352
270.324
280.291
290.544
30.233
300.88
310.291
320.304
330.809
340.865
350.257
360.489
370.0915
380.435
390.882
40.613
400.659
410.601
420.538
430.14
440.101
450.634
460.231
470.138
480.195
490.108
50.144
500.894
510.54
520.329
530.598
540.43
550.969
560.36
570.436
580.248
590.0583
60.513
600.143
610.978
620.0785
630.135
640.544
650.157
660.404
670.519
680.192
690.278
70.319
700.0011
710.298
720.562
730.206
740.223
750.267
760.77
770.228
780.258
790.287
80.149
800.251
810.298
820.0957
830.142
840.882
850.00325
860.56
870.663
880.838
890.177
90.498
900.0465
910.175
920.083
930.981
940.166
950.316
960.209
970.908
980.264
990.77



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: CNhs10588


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)
0000062 (organ)
0000077 (mixed endoderm/mesoderm-derived structure)
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)
0000926 (mesoderm)
0000945 (stomach)
0001007 (digestive system)
0001041 (foregut)
0001062 (anatomical entity)
0001555 (digestive tract)
0002050 (embryonic structure)
0002532 (epiblast (generic))
0003104 (mesenchyme)
0004119 (endoderm-derived structure)
0004120 (mesoderm-derived structure)
0004185 (endodermal part of digestive tract)
0004921 (subdivision of digestive tract)
0005409 (gastrointestinal system)
0005423 (developing anatomical structure)
0007026 (primitive gut)
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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