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|fonse_treatment_closure=
|fonse_treatment_closure=
|top_motifs=GFI1:1.58027977257;MYBL2:1.52383748888;ZNF238:1.45836648497;TOPORS:1.29207745914;RBPJ:1.27741801059;NANOG:1.2007086093;SRF:1.17203934436;NFY{A,B,C}:1.12434419814;DBP:1.09969424113;GZF1:1.07338411251;ADNP_IRX_SIX_ZHX:1.04566513289;ZNF148:1.03139123154;NKX3-1:1.01189875326;E2F1..5:0.99729525936;MAZ:0.994995279822;EP300:0.904631223877;RREB1:0.879373419036;XCPE1{core}:0.875437167035;ZNF143:0.865915851109;FOXA2:0.82653089485;IKZF1:0.826425018644;TFDP1:0.812311545612;CRX:0.80926983628;GTF2I:0.807697752746;ZNF384:0.790895032468;GATA6:0.787658017992;PAX1,9:0.769642496573;ONECUT1,2:0.752514505874;PATZ1:0.738179624969;PAX6:0.720473434472;HMGA1,2:0.713345620273;TP53:0.711856829559;FOX{I1,J2}:0.709948896622;SNAI1..3:0.700427363797;SOX{8,9,10}:0.699872186939;TLX2:0.696091831461;NKX2-1,4:0.687794098889;CDC5L:0.683400631558;IKZF2:0.669670345197;SP1:0.637260351487;TEAD1:0.630130598154;TFCP2:0.622082942409;T:0.61674744261;HBP1_HMGB_SSRP1_UBTF:0.615576360256;MZF1:0.584376719421;STAT1,3:0.577947580699;ZNF423:0.56312076542;PBX1:0.562618101795;GFI1B:0.557039049884;HMX1:0.53507698325;HNF1A:0.518821983547;PRRX1,2:0.514321865488;TBX4,5:0.508956299341;TLX1..3_NFIC{dimer}:0.498588313373;SOX2:0.480640116627;EN1,2:0.453958404582;TFAP2B:0.438322773231;SOX17:0.432980291948;VSX1,2:0.428260721604;FOX{D1,D2}:0.417245973468;BREu{core}:0.40237681434;NRF1:0.401367927912;HIC1:0.397985918957;TBP:0.396902412692;FOXM1:0.37606206469;GATA4:0.370935409455;FOX{F1,F2,J1}:0.367803971759;TFAP2{A,C}:0.365218026486;ZIC1..3:0.356330484187;AHR_ARNT_ARNT2:0.338415310587;SOX5:0.329014779663;NANOG{mouse}:0.319091139676;MED-1{core}:0.301901661033;GCM1,2:0.290989238752;PRDM1:0.288861013752;ZEB1:0.277159126643;SPZ1:0.272171123187;POU5F1:0.266677445552;CDX1,2,4:0.251840662558;ESR1:0.2481729687;ALX4:0.248067877619;LEF1_TCF7_TCF7L1,2:0.243924741892;TFAP4:0.240058835135;TGIF1:0.237635465163;RXRA_VDR{dimer}:0.237070150034;HIF1A:0.230074896758;EGR1..3:0.225147856522;EBF1:0.218122649122;KLF4:0.206701071566;FOXQ1:0.153179757313;GTF2A1,2:0.152785564897;RXR{A,B,G}:0.150591574225;LMO2:0.147791656326;TAL1_TCF{3,4,12}:0.117844870013;STAT5{A,B}:0.114036666028;CUX2:0.101437705951;TEF:0.101242125238;GLI1..3:0.0945251455921;ATF2:0.0927899261263;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:0.0902310048823;HSF1,2:0.0880221733131;OCT4_SOX2{dimer}:0.0660268615759;PDX1:0.054653368704;FOXD3:0.0380528894681;NFATC1..3:0.0358424478409;ZFP161:0.0297735263334;MTE{core}:0.029765331564;ZBTB16:0.0226404779918;ELF1,2,4:0.0178169448856;HAND1,2:0.0125294181344;FOSL2:0.00598929023409;PAX5:0.00375895245457;ELK1,4_GABP{A,B1}:-0.000447870247568;FOXN1:-0.0141309689517;POU6F1:-0.0327398037919;NKX3-2:-0.0381452964848;MTF1:-0.0411680124363;BPTF:-0.0574807876432;SMAD1..7,9:-0.0580178498396;MYFfamily:-0.0631218345144;NKX2-3_NKX2-5:-0.0700652777427;FOXP1:-0.07174491524;REST:-0.0805532642396;RFX1:-0.08529599881;PITX1..3:-0.0867094353703;ETS1,2:-0.093631513801;NFIX:-0.0974848117485;HNF4A_NR2F1,2:-0.110823772853;RFX2..5_RFXANK_RFXAP:-0.120885049263;NR3C1:-0.127958060093;YY1:-0.138770126358;MYB:-0.141910727795;BACH2:-0.151791833559;NHLH1,2:-0.1568720894;FOXO1,3,4:-0.165628202726;bHLH_family:-0.18590739218;FOS_FOS{B,L1}_JUN{B,D}:-0.196303649082;RXR{A,B,G}_{NR1H2,PPAR}dimers:-0.199888432307;JUN:-0.215724165366;ARID5B:-0.224566495965;POU2F1..3:-0.230723604561;SPIB:-0.245578388246;NKX2-2,8:-0.249343478418;ESRRA:-0.252103379427;EVI1:-0.279048366861;MEF2{A,B,C,D}:-0.283031507161;PAX4:-0.283920434051;ATF6:-0.294469035783;NFKB1_REL_RELA:-0.299122354206;ZBTB6:-0.302078771209;HOXA9_MEIS1:-0.30356840942;MYOD1:-0.324353420063;HES1:-0.347380749563;ALX1:-0.352187347128;POU3F1..4:-0.403692022926;HOX{A5,B5}:-0.408664898028;CREB1:-0.416266648005;AR:-0.421582930297;RUNX1..3:-0.431697667566;SPI1:-0.439596422165;HLF:-0.465636912407;UFEwm:-0.493297470324;IRF7:-0.497688034071;NR6A1:-0.507232934878;ATF5_CREB3:-0.520771684166;AIRE:-0.538398127368;DMAP1_NCOR{1,2}_SMARC:-0.543285793353;NFE2:-0.550016586349;FOXL1:-0.558314937877;IRF1,2:-0.590266455235;POU1F1:-0.612052918561;NFE2L2:-0.654238796867;LHX3,4:-0.665244681042;MAFB:-0.725463073224;NR5A1,2:-0.733770297428;NR1H4:-0.805069861996;CEBPA,B_DDIT3:-0.809021365857;STAT2,4,6:-0.853301101109;HOX{A4,D4}:-0.856707293554;NKX6-1,2:-0.861679787759;PAX8:-0.899686927149;ATF4:-0.935275596383;RORA:-0.955062650627;NFIL3:-1.01256219611;NFE2L1:-1.07632359166;PAX2:-1.19284567714;SREBF1,2:-1.22635110715;PPARG:-1.22746937943;FOXP3:-1.36407110994
|top_motifs=GFI1:1.58027977257;MYBL2:1.52383748888;ZNF238:1.45836648497;TOPORS:1.29207745914;RBPJ:1.27741801059;NANOG:1.2007086093;SRF:1.17203934436;NFY{A,B,C}:1.12434419814;DBP:1.09969424113;GZF1:1.07338411251;ADNP_IRX_SIX_ZHX:1.04566513289;ZNF148:1.03139123154;NKX3-1:1.01189875326;E2F1..5:0.99729525936;MAZ:0.994995279822;EP300:0.904631223877;RREB1:0.879373419036;XCPE1{core}:0.875437167035;ZNF143:0.865915851109;FOXA2:0.82653089485;IKZF1:0.826425018644;TFDP1:0.812311545612;CRX:0.80926983628;GTF2I:0.807697752746;ZNF384:0.790895032468;GATA6:0.787658017992;PAX1,9:0.769642496573;ONECUT1,2:0.752514505874;PATZ1:0.738179624969;PAX6:0.720473434472;HMGA1,2:0.713345620273;TP53:0.711856829559;FOX{I1,J2}:0.709948896622;SNAI1..3:0.700427363797;SOX{8,9,10}:0.699872186939;TLX2:0.696091831461;NKX2-1,4:0.687794098889;CDC5L:0.683400631558;IKZF2:0.669670345197;SP1:0.637260351487;TEAD1:0.630130598154;TFCP2:0.622082942409;T:0.61674744261;HBP1_HMGB_SSRP1_UBTF:0.615576360256;MZF1:0.584376719421;STAT1,3:0.577947580699;ZNF423:0.56312076542;PBX1:0.562618101795;GFI1B:0.557039049884;HMX1:0.53507698325;HNF1A:0.518821983547;PRRX1,2:0.514321865488;TBX4,5:0.508956299341;TLX1..3_NFIC{dimer}:0.498588313373;SOX2:0.480640116627;EN1,2:0.453958404582;TFAP2B:0.438322773231;SOX17:0.432980291948;VSX1,2:0.428260721604;FOX{D1,D2}:0.417245973468;BREu{core}:0.40237681434;NRF1:0.401367927912;HIC1:0.397985918957;TBP:0.396902412692;FOXM1:0.37606206469;GATA4:0.370935409455;FOX{F1,F2,J1}:0.367803971759;TFAP2{A,C}:0.365218026486;ZIC1..3:0.356330484187;AHR_ARNT_ARNT2:0.338415310587;SOX5:0.329014779663;NANOG{mouse}:0.319091139676;MED-1{core}:0.301901661033;GCM1,2:0.290989238752;PRDM1:0.288861013752;ZEB1:0.277159126643;SPZ1:0.272171123187;POU5F1:0.266677445552;CDX1,2,4:0.251840662558;ESR1:0.2481729687;ALX4:0.248067877619;LEF1_TCF7_TCF7L1,2:0.243924741892;TFAP4:0.240058835135;TGIF1:0.237635465163;RXRA_VDR{dimer}:0.237070150034;HIF1A:0.230074896758;EGR1..3:0.225147856522;EBF1:0.218122649122;KLF4:0.206701071566;FOXQ1:0.153179757313;GTF2A1,2:0.152785564897;RXR{A,B,G}:0.150591574225;LMO2:0.147791656326;TAL1_TCF{3,4,12}:0.117844870013;STAT5{A,B}:0.114036666028;CUX2:0.101437705951;TEF:0.101242125238;GLI1..3:0.0945251455921;ATF2:0.0927899261263;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:0.0902310048823;HSF1,2:0.0880221733131;OCT4_SOX2{dimer}:0.0660268615759;PDX1:0.054653368704;FOXD3:0.0380528894681;NFATC1..3:0.0358424478409;ZFP161:0.0297735263334;MTE{core}:0.029765331564;ZBTB16:0.0226404779918;ELF1,2,4:0.0178169448856;HAND1,2:0.0125294181344;FOSL2:0.00598929023409;PAX5:0.00375895245457;ELK1,4_GABP{A,B1}:-0.000447870247568;FOXN1:-0.0141309689517;POU6F1:-0.0327398037919;NKX3-2:-0.0381452964848;MTF1:-0.0411680124363;BPTF:-0.0574807876432;SMAD1..7,9:-0.0580178498396;MYFfamily:-0.0631218345144;NKX2-3_NKX2-5:-0.0700652777427;FOXP1:-0.07174491524;REST:-0.0805532642396;RFX1:-0.08529599881;PITX1..3:-0.0867094353703;ETS1,2:-0.093631513801;NFIX:-0.0974848117485;HNF4A_NR2F1,2:-0.110823772853;RFX2..5_RFXANK_RFXAP:-0.120885049263;NR3C1:-0.127958060093;YY1:-0.138770126358;MYB:-0.141910727795;BACH2:-0.151791833559;NHLH1,2:-0.1568720894;FOXO1,3,4:-0.165628202726;bHLH_family:-0.18590739218;FOS_FOS{B,L1}_JUN{B,D}:-0.196303649082;RXR{A,B,G}_{NR1H2,PPAR}dimers:-0.199888432307;JUN:-0.215724165366;ARID5B:-0.224566495965;POU2F1..3:-0.230723604561;SPIB:-0.245578388246;NKX2-2,8:-0.249343478418;ESRRA:-0.252103379427;EVI1:-0.279048366861;MEF2{A,B,C,D}:-0.283031507161;PAX4:-0.283920434051;ATF6:-0.294469035783;NFKB1_REL_RELA:-0.299122354206;ZBTB6:-0.302078771209;HOXA9_MEIS1:-0.30356840942;MYOD1:-0.324353420063;HES1:-0.347380749563;ALX1:-0.352187347128;POU3F1..4:-0.403692022926;HOX{A5,B5}:-0.408664898028;CREB1:-0.416266648005;AR:-0.421582930297;RUNX1..3:-0.431697667566;SPI1:-0.439596422165;HLF:-0.465636912407;UFEwm:-0.493297470324;IRF7:-0.497688034071;NR6A1:-0.507232934878;ATF5_CREB3:-0.520771684166;AIRE:-0.538398127368;DMAP1_NCOR{1,2}_SMARC:-0.543285793353;NFE2:-0.550016586349;FOXL1:-0.558314937877;IRF1,2:-0.590266455235;POU1F1:-0.612052918561;NFE2L2:-0.654238796867;LHX3,4:-0.665244681042;MAFB:-0.725463073224;NR5A1,2:-0.733770297428;NR1H4:-0.805069861996;CEBPA,B_DDIT3:-0.809021365857;STAT2,4,6:-0.853301101109;HOX{A4,D4}:-0.856707293554;NKX6-1,2:-0.861679787759;PAX8:-0.899686927149;ATF4:-0.935275596383;RORA:-0.955062650627;NFIL3:-1.01256219611;NFE2L1:-1.07632359166;PAX2:-1.19284567714;SREBF1,2:-1.22635110715;PPARG:-1.22746937943;FOXP3:-1.36407110994
|comment=fantom:1252-16G8
|created_by=
|creation_date=
|def=
|has_quality=
|is_a=EFO:0002091;;FF:0000004;;FF:0000103;;FF:0011523
|namespace=FANTOM5
|part_of=
}}
}}

Revision as of 15:45, 7 March 2012


Name:stomach, embryo E15
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 stage15 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

CNhs10603

00
10
100
1000
10000.00779
10010.0474
10020.429
10030.0564
10040
10050
1006-0.0434
10070.076
10080
10090.091
1010.101
10100.482
10110.00686
10120
1013-0.0891
10140.357
10150.263
10160.256
10170.0804
10180.305
10190
1020
10200
10210
10220.00999
10230
10240.00862
10250.773
10260
10270.146
10280
10290.269
1030.157
10300
10310.435
10320.0163
10330
10340
10350
10360.119
10370
10380.0684
1039-0.141
1040
10400.0799
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: CNhs10603

Jaspar motifP-value
MA0002.20.00111
MA0003.10.643
MA0004.10.572
MA0006.10.974
MA0007.10.287
MA0009.10.433
MA0014.10.467
MA0017.16.92823e-5
MA0018.20.511
MA0019.10.746
MA0024.13.77252e-7
MA0025.10.0389
MA0027.10.0139
MA0028.10.496
MA0029.10.345
MA0030.10.248
MA0031.10.87
MA0035.20.612
MA0038.10.00192
MA0039.20.416
MA0040.10.909
MA0041.10.64
MA0042.10.668
MA0043.10.945
MA0046.11.83716e-17
MA0047.20.00146
MA0048.10.732
MA0050.12.01891e-5
MA0051.14.26164e-4
MA0052.10.00951
MA0055.10.531
MA0057.10.534
MA0058.10.354
MA0059.10.15
MA0060.11.13476e-13
MA0061.10.211
MA0062.20.108
MA0065.22.71669e-4
MA0066.10.0525
MA0067.10.127
MA0068.10.171
MA0069.10.526
MA0070.10.271
MA0071.10.00605
MA0072.10.0236
MA0073.10.847
MA0074.10.834
MA0076.10.657
MA0077.10.206
MA0078.10.603
MA0079.20.119
MA0080.21.39501e-4
MA0081.10.152
MA0083.11.03307e-6
MA0084.10.99
MA0087.10.397
MA0088.10.889
MA0090.10.289
MA0091.10.853
MA0092.10.789
MA0093.10.592
MA0099.20.228
MA0100.10.204
MA0101.10.612
MA0102.20.905
MA0103.10.684
MA0104.20.573
MA0105.10.0272
MA0106.10.719
MA0107.10.485
MA0108.20.0185
MA0111.10.313
MA0112.28.61779e-5
MA0113.10.66
MA0114.18.48374e-4
MA0115.10.00347
MA0116.10.0186
MA0117.10.0218
MA0119.10.225
MA0122.10.443
MA0124.10.801
MA0125.10.195
MA0131.10.463
MA0135.10.0235
MA0136.11.97159e-4
MA0137.20.34
MA0138.20.0404
MA0139.10.659
MA0140.10.792
MA0141.11.32011e-5
MA0142.10.755
MA0143.10.382
MA0144.10.587
MA0145.10.526
MA0146.10.267
MA0147.10.392
MA0148.10.00914
MA0149.10.0287
MA0150.10.0015
MA0152.10.393
MA0153.11.86046e-11
MA0154.10.0531
MA0155.10.527
MA0156.10.171
MA0157.10.666
MA0159.10.00544
MA0160.10.00154
MA0162.10.948
MA0163.10.187
MA0164.10.687
MA0258.18.97642e-5
MA0259.10.725



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: CNhs10603

Novel motifP-value
10.0464
100.123
1000.7
1010.577
1020.606
1030.0858
1040.93
1050.829
1060.248
1070.715
1080.913
1090.171
110.0556
1100.161
1110.00479
1120.0701
1130.692
1142.86038e-5
1150.846
1160.738
1170.0335
1180.202
1190.0834
120.622
1200.33
1210.618
1220.93
1230.374
1240.508
1250.157
1260.658
1270.197
1280.149
1290.141
130.578
1300.15
1310.699
1320.937
1330.507
1340.548
1350.928
1360.563
1370.826
1380.0233
1390.0224
140.577
1400.778
1410.754
1420.472
1430.0143
1440.524
1450.734
1460.685
1470.408
1480.139
1490.68
150.0282
1500.536
1510.0748
1520.822
1530.194
1540.446
1550.195
1560.076
1570.82
1580.227
1590.122
1600.977
1610.505
1620.548
1630.359
1640.145
1650.473
1660.229
1670.48
1680.326
1690.0321
170.148
180.0987
190.67
20.855
200.351
210.726
220.555
230.174
240.885
250.115
260.788
270.658
280.266
290.27
30.0767
300.625
310.379
320.202
330.824
340.877
350.027
360.128
370.0896
380.46
390.781
40.891
400.73
410.16
420.433
430.123
440.0724
450.985
460.224
470.156
480.0884
490.0706
50.0955
500.617
510.538
520.638
530.758
540.548
550.47
560.468
570.227
580.309
590.142
60.897
600.578
610.815
620.0279
630.208
640.36
650.285
660.655
670.357
680.0373
690.0571
70.453
705.39113e-4
710.169
720.786
730.136
740.824
750.0283
760.32
770.312
780.267
790.271
80.0534
800.394
810.28
820.0535
830.176
840.901
850.00693
860.68
870.364
880.627
890.466
90.938
900.0162
910.429
920.159
930.525
940.0286
950.085
960.18
970.707
980.286
990.724



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: CNhs10603


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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