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|fonse_treatment_closure=
|fonse_treatment_closure=
|top_motifs=CDC5L:2.32966715289;MYBL2:1.72285249396;ZNF148:1.62640083893;ZNF384:1.49390692413;DBP:1.47479386719;IKZF2:1.43315528708;CDX1,2,4:1.4269259998;GFI1:1.35207675702;T:1.31920241302;TOPORS:1.30084691057;HMGA1,2:1.19302555111;NKX3-1:1.107701292;HMX1:1.07108619978;SRF:1.05853644628;ADNP_IRX_SIX_ZHX:1.0279284195;SNAI1..3:0.957926833649;TLX2:0.951582290201;FOXP1:0.863871642516;TFCP2:0.832497551463;ZNF238:0.832304343541;TP53:0.775086014646;PAX4:0.772675600849;FOXM1:0.75265350466;MAZ:0.751256912731;ONECUT1,2:0.719484656992;FOX{I1,J2}:0.718793834816;HAND1,2:0.706377114616;RBPJ:0.704076694495;GTF2I:0.696241073982;HNF1A:0.684640829312;E2F1..5:0.684367592976;XCPE1{core}:0.683508164095;RXRA_VDR{dimer}:0.682734760599;TBX4,5:0.681818942256;RREB1:0.662308850422;NKX2-2,8:0.662203763785;EVI1:0.649287530794;FOXA2:0.644961231077;GZF1:0.642142864424;NANOG:0.632630760973;NFY{A,B,C}:0.611025056221;EBF1:0.599920642796;GATA4:0.595650634974;TEAD1:0.574386603289;ZBTB16:0.571721344997;NKX2-1,4:0.563924646866;SOX5:0.528538871196;TEF:0.525612647629;GLI1..3:0.520097543822;TLX1..3_NFIC{dimer}:0.519369387149;GATA6:0.510470117292;TBP:0.501024432742;KLF4:0.494381392876;ZNF423:0.48590889152;SP1:0.472970695038;ZIC1..3:0.459219529784;PRDM1:0.419459773194;FOX{D1,D2}:0.416098536671;HNF4A_NR2F1,2:0.409946712917;IKZF1:0.405434498075;PDX1:0.393454229363;POU1F1:0.386330448784;EP300:0.380136912774;POU6F1:0.365775168705;NKX6-1,2:0.364461337043;ZEB1:0.32913776608;FOS_FOS{B,L1}_JUN{B,D}:0.321260138598;CRX:0.3150774995;FOX{F1,F2,J1}:0.304627872528;PAX1,9:0.301835404754;PATZ1:0.297548067757;FOXD3:0.289010664463;STAT1,3:0.248211574936;NKX3-2:0.24351431474;TFDP1:0.237639146976;GCM1,2:0.235897824324;LEF1_TCF7_TCF7L1,2:0.222603127031;BACH2:0.211612505586;ZNF143:0.194621658625;SPZ1:0.193087898945;FOXO1,3,4:0.18789245739;SOX{8,9,10}:0.177586701689;HIC1:0.176164594203;HSF1,2:0.175549502536;GFI1B:0.169219491209;AR:0.164594096092;PAX5:0.163524534383;PRRX1,2:0.163301139167;BPTF:0.14148914539;PITX1..3:0.130570573525;UFEwm:0.129085724439;GTF2A1,2:0.121920841484;BREu{core}:0.112758993746;LHX3,4:0.108581587403;HIF1A:0.100994654602;FOXN1:0.0761705282668;SOX2:0.0698291834727;VSX1,2:0.0650369756314;POU5F1:0.0641778586437;MZF1:0.0610008121577;DMAP1_NCOR{1,2}_SMARC:0.0524486337978;EN1,2:0.0455590174537;NKX2-3_NKX2-5:0.039613801482;FOXQ1:0.0347875975154;ALX4:0.0195389125833;ATF2:0.010353745352;MED-1{core}:0.00689463690284;NR6A1:0.0011137905023;SOX17:0.000669947466117;HOX{A5,B5}:-0.00721048286252;PBX1:-0.023955752162;REST:-0.0550023233596;AHR_ARNT_ARNT2:-0.0572755815491;HBP1_HMGB_SSRP1_UBTF:-0.0577450296944;TFAP2B:-0.0596017302439;PAX6:-0.0610702943652;ELF1,2,4:-0.0736372934768;ARID5B:-0.0769351483314;NFATC1..3:-0.0861728365091;LMO2:-0.0920247565946;OCT4_SOX2{dimer}:-0.127497495509;TAL1_TCF{3,4,12}:-0.128370891502;NFIX:-0.12953266931;TFAP2{A,C}:-0.149611654453;EGR1..3:-0.149824183831;NR3C1:-0.157262019813;TFAP4:-0.164740866712;CUX2:-0.178215408737;ETS1,2:-0.184483791108;NRF1:-0.186133217058;RFX2..5_RFXANK_RFXAP:-0.199235349386;FOSL2:-0.20512253432;AIRE:-0.205578685016;MYOD1:-0.211226231686;RXR{A,B,G}_{NR1H2,PPAR}dimers:-0.219841022734;ZFP161:-0.230697747328;HOXA9_MEIS1:-0.23168580156;SMAD1..7,9:-0.23248657026;ESRRA:-0.233330240555;TGIF1:-0.23583531737;MYFfamily:-0.236450169296;SPIB:-0.246662791871;FOXL1:-0.261834598824;ESR1:-0.27144895261;IRF1,2:-0.306977649124;MTE{core}:-0.325457685438;RFX1:-0.325661015345;ATF6:-0.328761433719;ELK1,4_GABP{A,B1}:-0.33979087242;MYB:-0.353266084689;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:-0.390195189794;POU3F1..4:-0.395360465543;STAT5{A,B}:-0.39712010989;POU2F1..3:-0.412074825901;NFE2:-0.418926921189;RXR{A,B,G}:-0.433972755594;ALX1:-0.467990689723;MTF1:-0.47174403444;MEF2{A,B,C,D}:-0.4733251431;PAX8:-0.486160203228;CEBPA,B_DDIT3:-0.487055007192;NFKB1_REL_RELA:-0.505949193669;RUNX1..3:-0.514962654578;IRF7:-0.533283623175;CREB1:-0.554849083721;ZBTB6:-0.558410991845;PPARG:-0.564863975408;SPI1:-0.576509860753;MAFB:-0.588887439698;YY1:-0.646470592574;NFE2L2:-0.653750779777;ATF5_CREB3:-0.657823837083;NANOG{mouse}:-0.68338991031;JUN:-0.686175097267;FOXP3:-0.739545406287;STAT2,4,6:-0.798175917685;ATF4:-0.808921926876;NHLH1,2:-0.857231453177;HLF:-0.870000798112;HES1:-0.885356743258;HOX{A4,D4}:-0.910177137576;NR5A1,2:-0.972654481671;bHLH_family:-0.978337922706;NR1H4:-1.04543668154;RORA:-1.18368144629;PAX2:-1.19092783471;SREBF1,2:-1.21527622098;NFE2L1:-1.26767875588;NFIL3:-1.26886913937
|top_motifs=CDC5L:2.32966715289;MYBL2:1.72285249396;ZNF148:1.62640083893;ZNF384:1.49390692413;DBP:1.47479386719;IKZF2:1.43315528708;CDX1,2,4:1.4269259998;GFI1:1.35207675702;T:1.31920241302;TOPORS:1.30084691057;HMGA1,2:1.19302555111;NKX3-1:1.107701292;HMX1:1.07108619978;SRF:1.05853644628;ADNP_IRX_SIX_ZHX:1.0279284195;SNAI1..3:0.957926833649;TLX2:0.951582290201;FOXP1:0.863871642516;TFCP2:0.832497551463;ZNF238:0.832304343541;TP53:0.775086014646;PAX4:0.772675600849;FOXM1:0.75265350466;MAZ:0.751256912731;ONECUT1,2:0.719484656992;FOX{I1,J2}:0.718793834816;HAND1,2:0.706377114616;RBPJ:0.704076694495;GTF2I:0.696241073982;HNF1A:0.684640829312;E2F1..5:0.684367592976;XCPE1{core}:0.683508164095;RXRA_VDR{dimer}:0.682734760599;TBX4,5:0.681818942256;RREB1:0.662308850422;NKX2-2,8:0.662203763785;EVI1:0.649287530794;FOXA2:0.644961231077;GZF1:0.642142864424;NANOG:0.632630760973;NFY{A,B,C}:0.611025056221;EBF1:0.599920642796;GATA4:0.595650634974;TEAD1:0.574386603289;ZBTB16:0.571721344997;NKX2-1,4:0.563924646866;SOX5:0.528538871196;TEF:0.525612647629;GLI1..3:0.520097543822;TLX1..3_NFIC{dimer}:0.519369387149;GATA6:0.510470117292;TBP:0.501024432742;KLF4:0.494381392876;ZNF423:0.48590889152;SP1:0.472970695038;ZIC1..3:0.459219529784;PRDM1:0.419459773194;FOX{D1,D2}:0.416098536671;HNF4A_NR2F1,2:0.409946712917;IKZF1:0.405434498075;PDX1:0.393454229363;POU1F1:0.386330448784;EP300:0.380136912774;POU6F1:0.365775168705;NKX6-1,2:0.364461337043;ZEB1:0.32913776608;FOS_FOS{B,L1}_JUN{B,D}:0.321260138598;CRX:0.3150774995;FOX{F1,F2,J1}:0.304627872528;PAX1,9:0.301835404754;PATZ1:0.297548067757;FOXD3:0.289010664463;STAT1,3:0.248211574936;NKX3-2:0.24351431474;TFDP1:0.237639146976;GCM1,2:0.235897824324;LEF1_TCF7_TCF7L1,2:0.222603127031;BACH2:0.211612505586;ZNF143:0.194621658625;SPZ1:0.193087898945;FOXO1,3,4:0.18789245739;SOX{8,9,10}:0.177586701689;HIC1:0.176164594203;HSF1,2:0.175549502536;GFI1B:0.169219491209;AR:0.164594096092;PAX5:0.163524534383;PRRX1,2:0.163301139167;BPTF:0.14148914539;PITX1..3:0.130570573525;UFEwm:0.129085724439;GTF2A1,2:0.121920841484;BREu{core}:0.112758993746;LHX3,4:0.108581587403;HIF1A:0.100994654602;FOXN1:0.0761705282668;SOX2:0.0698291834727;VSX1,2:0.0650369756314;POU5F1:0.0641778586437;MZF1:0.0610008121577;DMAP1_NCOR{1,2}_SMARC:0.0524486337978;EN1,2:0.0455590174537;NKX2-3_NKX2-5:0.039613801482;FOXQ1:0.0347875975154;ALX4:0.0195389125833;ATF2:0.010353745352;MED-1{core}:0.00689463690284;NR6A1:0.0011137905023;SOX17:0.000669947466117;HOX{A5,B5}:-0.00721048286252;PBX1:-0.023955752162;REST:-0.0550023233596;AHR_ARNT_ARNT2:-0.0572755815491;HBP1_HMGB_SSRP1_UBTF:-0.0577450296944;TFAP2B:-0.0596017302439;PAX6:-0.0610702943652;ELF1,2,4:-0.0736372934768;ARID5B:-0.0769351483314;NFATC1..3:-0.0861728365091;LMO2:-0.0920247565946;OCT4_SOX2{dimer}:-0.127497495509;TAL1_TCF{3,4,12}:-0.128370891502;NFIX:-0.12953266931;TFAP2{A,C}:-0.149611654453;EGR1..3:-0.149824183831;NR3C1:-0.157262019813;TFAP4:-0.164740866712;CUX2:-0.178215408737;ETS1,2:-0.184483791108;NRF1:-0.186133217058;RFX2..5_RFXANK_RFXAP:-0.199235349386;FOSL2:-0.20512253432;AIRE:-0.205578685016;MYOD1:-0.211226231686;RXR{A,B,G}_{NR1H2,PPAR}dimers:-0.219841022734;ZFP161:-0.230697747328;HOXA9_MEIS1:-0.23168580156;SMAD1..7,9:-0.23248657026;ESRRA:-0.233330240555;TGIF1:-0.23583531737;MYFfamily:-0.236450169296;SPIB:-0.246662791871;FOXL1:-0.261834598824;ESR1:-0.27144895261;IRF1,2:-0.306977649124;MTE{core}:-0.325457685438;RFX1:-0.325661015345;ATF6:-0.328761433719;ELK1,4_GABP{A,B1}:-0.33979087242;MYB:-0.353266084689;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:-0.390195189794;POU3F1..4:-0.395360465543;STAT5{A,B}:-0.39712010989;POU2F1..3:-0.412074825901;NFE2:-0.418926921189;RXR{A,B,G}:-0.433972755594;ALX1:-0.467990689723;MTF1:-0.47174403444;MEF2{A,B,C,D}:-0.4733251431;PAX8:-0.486160203228;CEBPA,B_DDIT3:-0.487055007192;NFKB1_REL_RELA:-0.505949193669;RUNX1..3:-0.514962654578;IRF7:-0.533283623175;CREB1:-0.554849083721;ZBTB6:-0.558410991845;PPARG:-0.564863975408;SPI1:-0.576509860753;MAFB:-0.588887439698;YY1:-0.646470592574;NFE2L2:-0.653750779777;ATF5_CREB3:-0.657823837083;NANOG{mouse}:-0.68338991031;JUN:-0.686175097267;FOXP3:-0.739545406287;STAT2,4,6:-0.798175917685;ATF4:-0.808921926876;NHLH1,2:-0.857231453177;HLF:-0.870000798112;HES1:-0.885356743258;HOX{A4,D4}:-0.910177137576;NR5A1,2:-0.972654481671;bHLH_family:-0.978337922706;NR1H4:-1.04543668154;RORA:-1.18368144629;PAX2:-1.19092783471;SREBF1,2:-1.21527622098;NFE2L1:-1.26767875588;NFIL3:-1.26886913937
|comment=
|created_by=
|creation_date=
|def=
|has_quality=
|is_a=EFO:0002091;;FF:0000004;;FF:0000103;;FF:0011358
|namespace=FANTOM5
|part_of=
}}
}}

Revision as of 16:02, 7 March 2012


Name:stomach, embryo E16
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 stage16 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

CNhs11022

00
10.00282
100
1000
10000.0479
10010.00312
10020.47
10030.086
10040
10050.0849
1006-0.114
10070.0605
10080
10090.15
1010.074
10100.122
1011-0.063
10120.0445
1013-0.0608
10140.649
10150.125
10160.149
10170.799
10180.418
10190
1020
10200
1021-0.00415
1022-0.0704
10230
1024-0.0177
10250.821
10260.0151
10270.0666
10280
10290.285
1030.257
10300
10310.367
10320.0745
10330.0232
10340.101
10350
10360.135
10370
10380.0166
1039-0.074
1040
10400.0604
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: CNhs11022

Jaspar motifP-value
MA0002.20.00757
MA0003.10.69
MA0004.10.233
MA0006.10.285
MA0007.10.84
MA0009.10.245
MA0014.10.912
MA0017.10.715
MA0018.21.91569e-4
MA0019.10.443
MA0024.19.8003e-7
MA0025.11.85249e-4
MA0027.10.015
MA0028.10.00957
MA0029.10.855
MA0030.10.899
MA0031.10.227
MA0035.20.876
MA0038.10.45
MA0039.20.0889
MA0040.10.741
MA0041.10.154
MA0042.10.273
MA0043.15.35077e-4
MA0046.11.80805e-20
MA0047.20.00782
MA0048.10.015
MA0050.10.0154
MA0051.14.36365e-4
MA0052.11.28973e-6
MA0055.10.239
MA0057.10.343
MA0058.10.0239
MA0059.10.338
MA0060.10.00334
MA0061.10.287
MA0062.21.37405e-6
MA0065.20.0308
MA0066.10.511
MA0067.10.016
MA0068.10.279
MA0069.10.0703
MA0070.10.424
MA0071.10.00176
MA0072.10.0218
MA0073.10.432
MA0074.10.89
MA0076.10.00137
MA0077.10.748
MA0078.10.259
MA0079.20.886
MA0080.21.74044e-4
MA0081.10.00844
MA0083.16.81589e-7
MA0084.10.557
MA0087.10.502
MA0088.10.405
MA0090.10.36
MA0091.10.968
MA0092.10.442
MA0093.10.176
MA0099.20.461
MA0100.10.00575
MA0101.10.077
MA0102.20.825
MA0103.10.0164
MA0104.20.166
MA0105.10.535
MA0106.10.489
MA0107.10.0348
MA0108.20.253
MA0111.10.685
MA0112.20.949
MA0113.10.621
MA0114.10.77
MA0115.10.365
MA0116.10.362
MA0117.10.00281
MA0119.10.842
MA0122.10.103
MA0124.10.734
MA0125.10.983
MA0131.10.771
MA0135.10.714
MA0136.13.38478e-6
MA0137.20.105
MA0138.20.0417
MA0139.10.29
MA0140.10.79
MA0141.11.32523e-4
MA0142.10.233
MA0143.10.658
MA0144.10.485
MA0145.10.288
MA0146.10.527
MA0147.10.11
MA0148.10.00623
MA0149.10.88
MA0150.10.00176
MA0152.10.31
MA0153.12.10491e-14
MA0154.10.228
MA0155.10.159
MA0156.10.00149
MA0157.10.368
MA0159.10.163
MA0160.15.57235e-4
MA0162.10.222
MA0163.10.0777
MA0164.10.971
MA0258.10.0597
MA0259.10.401



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: CNhs11022

Novel motifP-value
10.423
100.877
1000.637
1010.49
1020.504
1030.696
1040.725
1050.891
1060.183
1070.0903
1080.931
1090.582
110.173
1100.932
1110.141
1120.929
1130.119
1140.0124
1150.619
1160.441
1170.19
1180.174
1190.459
120.443
1200.423
1210.138
1220.798
1230.247
1240.429
1250.419
1260.31
1270.613
1280.883
1290.487
130.0235
1300.211
1310.326
1320.687
1330.644
1340.428
1350.927
1360.922
1370.72
1380.00316
1390.379
140.465
1400.2
1410.955
1420.909
1430.206
1440.472
1450.388
1460.567
1470.411
1480.597
1490.86
150.0398
1500.414
1510.0992
1520.358
1530.216
1540.982
1550.541
1560.017
1570.434
1580.432
1590.0834
1600.0168
1610.387
1620.924
1630.638
1640.513
1650.735
1660.0613
1670.772
1680.271
1690.565
170.626
180.0681
190.103
20.936
200.292
210.605
220.594
230.619
240.585
250.0437
260.0525
270.68
280.235
290.711
30.608
300.37
310.488
320.691
330.861
340.991
350.0662
360.682
370.858
380.572
390.248
40.275
400.945
410.0575
420.968
430.498
440.296
450.77
460.795
470.653
480.322
490.17
50.515
500.361
510.945
520.0792
530.506
540.999
550.485
560.577
570.591
580.44
590.541
60.39
600.383
610.612
620.0531
630.5
640.507
650.496
660.508
670.385
680.0923
690.0499
70.721
700.0192
710.574
720.948
730.501
740.483
750.375
760.413
770.149
780.987
790.813
80.225
800.184
810.544
820.134
830.402
840.393
850.142
860.997
870.00533
880.181
890.672
90.499
900.25
910.566
920.881
930.696
940.229
950.335
960.736
970.662
980.082
990.128



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: CNhs11022


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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