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|fonse_treatment_closure=
|fonse_treatment_closure=
|top_motifs=LHX3,4:2.18946212618;SOX{8,9,10}:1.5451957894;FOXD3:1.53615137703;CDC5L:1.3243749878;RXR{A,B,G}:1.32285893998;SOX5:1.30242493609;FOXP1:1.27953813251;PAX1,9:1.27630011345;EP300:1.25725387249;SOX2:1.23802490781;ZNF384:1.18393309703;NFY{A,B,C}:1.09594253084;PATZ1:1.0708489498;NKX3-1:1.06453278805;PAX6:1.03121911841;MZF1:1.02968792268;RFX1:1.01328479542;ZNF143:1.0069920174;VSX1,2:1.00491830809;NRF1:0.982388887607;MAZ:0.946187672754;ZIC1..3:0.895534253181;MYBL2:0.874804001021;NANOG:0.84345511684;TOPORS:0.838810391396;OCT4_SOX2{dimer}:0.807003362921;RREB1:0.790611345969;GFI1:0.786615620565;LEF1_TCF7_TCF7L1,2:0.782028108761;PAX4:0.776966927867;FOXM1:0.762814847548;HOXA9_MEIS1:0.761290519088;FOXP3:0.719634462145;IKZF2:0.715508615902;GTF2I:0.701510537692;ADNP_IRX_SIX_ZHX:0.696733852105;HMGA1,2:0.691682447781;EN1,2:0.688058095359;FOXN1:0.68788818524;HIF1A:0.680992083555;SP1:0.674342308481;HMX1:0.654269179027;TFDP1:0.644264947107;KLF4:0.643972639391;MED-1{core}:0.639060280062;NKX2-1,4:0.633758909363;PRRX1,2:0.629982303496;XCPE1{core}:0.613016648282;HSF1,2:0.602277197681;BREu{core}:0.593254662406;ZFP161:0.593146303642;GATA4:0.592093583729;RFX2..5_RFXANK_RFXAP:0.585139788415;ELK1,4_GABP{A,B1}:0.576948431339;HIC1:0.532034511167;NANOG{mouse}:0.506317953005;ARID5B:0.487840605576;POU6F1:0.476810103557;TFAP2B:0.473215008499;GTF2A1,2:0.470773318915;ALX1:0.470675573524;LMO2:0.458311907422;CDX1,2,4:0.454477710238;SPZ1:0.439685647986;HES1:0.392728643174;AHR_ARNT_ARNT2:0.383113856674;SOX17:0.373623634557;TFAP2{A,C}:0.361141140111;REST:0.348560306789;ESR1:0.344618552293;SNAI1..3:0.337810395072;ZNF238:0.332186385654;PAX5:0.330602119387;ONECUT1,2:0.328865786567;HBP1_HMGB_SSRP1_UBTF:0.323386054132;MTE{core}:0.311149537979;IKZF1:0.306682436987;ATF2:0.30615061349;EGR1..3:0.303918457901;ZNF423:0.292212944837;ZBTB16:0.285045326299;GLI1..3:0.277547324714;POU5F1:0.2614342649;EVI1:0.259704575282;TFAP4:0.256633525538;MYOD1:0.238557521397;DBP:0.227091049001;NKX2-3_NKX2-5:0.225728722936;E2F1..5:0.219805921431;PRDM1:0.219678345596;ATF6:0.216469030421;CUX2:0.216414857116;POU2F1..3:0.205887824325;TEF:0.201284214436;GCM1,2:0.187871614907;HOX{A5,B5}:0.178569926486;NKX6-1,2:0.175151948618;CREB1:0.155477956359;EBF1:0.151988900554;CRX:0.143375808095;STAT1,3:0.135871958257;FOXL1:0.133986219269;POU3F1..4:0.131860815183;UFEwm:0.119125230565;TLX1..3_NFIC{dimer}:0.117485445434;GFI1B:0.101590501506;GZF1:0.100861135651;TFCP2:0.0654267874678;ZBTB6:0.0627594037942;TAL1_TCF{3,4,12}:0.0496723110068;HAND1,2:0.0447779203528;TEAD1:0.0371307563697;MTF1:0.0203854482184;BPTF:0.00576290669664;RBPJ:0.00480186535601;ZEB1:0.00186237818151;PAX8:-0.0122655491573;JUN:-0.0392676769646;YY1:-0.0557405188814;SPIB:-0.056542909532;MYB:-0.0583918256631;TBX4,5:-0.0634713365619;POU1F1:-0.0688084205349;ELF1,2,4:-0.0937351955774;FOX{I1,J2}:-0.104507012443;NR3C1:-0.130016901584;TGIF1:-0.131245468569;DMAP1_NCOR{1,2}_SMARC:-0.132345890385;NHLH1,2:-0.141290839875;AIRE:-0.158097574182;FOXQ1:-0.162855754433;PITX1..3:-0.178284152181;NKX3-2:-0.200468702274;SPI1:-0.2188773188;FOSL2:-0.227383380857;T:-0.234100487731;MYFfamily:-0.245806419237;RORA:-0.251277252178;PAX2:-0.273802068809;TBP:-0.27468243323;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:-0.34803419529;NFIL3:-0.376113231557;ATF4:-0.380321436744;bHLH_family:-0.382062213701;RUNX1..3:-0.388164144271;SMAD1..7,9:-0.391591401906;ETS1,2:-0.397209403219;SREBF1,2:-0.41730751516;ZNF148:-0.422279294322;STAT5{A,B}:-0.434702307183;RXRA_VDR{dimer}:-0.464004429791;FOX{D1,D2}:-0.466893203553;FOXO1,3,4:-0.468886711308;HOX{A4,D4}:-0.479634566906;NR6A1:-0.482833184603;ATF5_CREB3:-0.49742773489;TLX2:-0.50318427296;MAFB:-0.510000678135;MEF2{A,B,C,D}:-0.5280074103;RXR{A,B,G}_{NR1H2,PPAR}dimers:-0.537121149118;GATA6:-0.57792295445;NKX2-2,8:-0.580210240683;PDX1:-0.595369101786;HNF4A_NR2F1,2:-0.604764416328;PBX1:-0.616389361749;HLF:-0.626602804361;SRF:-0.62748227001;NFATC1..3:-0.638341080184;NFIX:-0.647947001493;HNF1A:-0.673962163415;NFKB1_REL_RELA:-0.6823768;NR5A1,2:-0.726584983846;NFE2L2:-0.741302629463;IRF1,2:-0.756735844843;ESRRA:-0.763063702294;FOXA2:-0.786728918332;FOX{F1,F2,J1}:-0.786892906645;ALX4:-0.800232989403;AR:-0.804346095027;NR1H4:-0.835578037319;TP53:-0.861634013444;PPARG:-0.930553740405;IRF7:-0.934191420927;FOS_FOS{B,L1}_JUN{B,D}:-0.954503447259;NFE2L1:-0.964907029205;STAT2,4,6:-1.00321543376;BACH2:-1.13322196899;CEBPA,B_DDIT3:-1.26345431922;NFE2:-1.38767316875
|top_motifs=LHX3,4:2.18946212618;SOX{8,9,10}:1.5451957894;FOXD3:1.53615137703;CDC5L:1.3243749878;RXR{A,B,G}:1.32285893998;SOX5:1.30242493609;FOXP1:1.27953813251;PAX1,9:1.27630011345;EP300:1.25725387249;SOX2:1.23802490781;ZNF384:1.18393309703;NFY{A,B,C}:1.09594253084;PATZ1:1.0708489498;NKX3-1:1.06453278805;PAX6:1.03121911841;MZF1:1.02968792268;RFX1:1.01328479542;ZNF143:1.0069920174;VSX1,2:1.00491830809;NRF1:0.982388887607;MAZ:0.946187672754;ZIC1..3:0.895534253181;MYBL2:0.874804001021;NANOG:0.84345511684;TOPORS:0.838810391396;OCT4_SOX2{dimer}:0.807003362921;RREB1:0.790611345969;GFI1:0.786615620565;LEF1_TCF7_TCF7L1,2:0.782028108761;PAX4:0.776966927867;FOXM1:0.762814847548;HOXA9_MEIS1:0.761290519088;FOXP3:0.719634462145;IKZF2:0.715508615902;GTF2I:0.701510537692;ADNP_IRX_SIX_ZHX:0.696733852105;HMGA1,2:0.691682447781;EN1,2:0.688058095359;FOXN1:0.68788818524;HIF1A:0.680992083555;SP1:0.674342308481;HMX1:0.654269179027;TFDP1:0.644264947107;KLF4:0.643972639391;MED-1{core}:0.639060280062;NKX2-1,4:0.633758909363;PRRX1,2:0.629982303496;XCPE1{core}:0.613016648282;HSF1,2:0.602277197681;BREu{core}:0.593254662406;ZFP161:0.593146303642;GATA4:0.592093583729;RFX2..5_RFXANK_RFXAP:0.585139788415;ELK1,4_GABP{A,B1}:0.576948431339;HIC1:0.532034511167;NANOG{mouse}:0.506317953005;ARID5B:0.487840605576;POU6F1:0.476810103557;TFAP2B:0.473215008499;GTF2A1,2:0.470773318915;ALX1:0.470675573524;LMO2:0.458311907422;CDX1,2,4:0.454477710238;SPZ1:0.439685647986;HES1:0.392728643174;AHR_ARNT_ARNT2:0.383113856674;SOX17:0.373623634557;TFAP2{A,C}:0.361141140111;REST:0.348560306789;ESR1:0.344618552293;SNAI1..3:0.337810395072;ZNF238:0.332186385654;PAX5:0.330602119387;ONECUT1,2:0.328865786567;HBP1_HMGB_SSRP1_UBTF:0.323386054132;MTE{core}:0.311149537979;IKZF1:0.306682436987;ATF2:0.30615061349;EGR1..3:0.303918457901;ZNF423:0.292212944837;ZBTB16:0.285045326299;GLI1..3:0.277547324714;POU5F1:0.2614342649;EVI1:0.259704575282;TFAP4:0.256633525538;MYOD1:0.238557521397;DBP:0.227091049001;NKX2-3_NKX2-5:0.225728722936;E2F1..5:0.219805921431;PRDM1:0.219678345596;ATF6:0.216469030421;CUX2:0.216414857116;POU2F1..3:0.205887824325;TEF:0.201284214436;GCM1,2:0.187871614907;HOX{A5,B5}:0.178569926486;NKX6-1,2:0.175151948618;CREB1:0.155477956359;EBF1:0.151988900554;CRX:0.143375808095;STAT1,3:0.135871958257;FOXL1:0.133986219269;POU3F1..4:0.131860815183;UFEwm:0.119125230565;TLX1..3_NFIC{dimer}:0.117485445434;GFI1B:0.101590501506;GZF1:0.100861135651;TFCP2:0.0654267874678;ZBTB6:0.0627594037942;TAL1_TCF{3,4,12}:0.0496723110068;HAND1,2:0.0447779203528;TEAD1:0.0371307563697;MTF1:0.0203854482184;BPTF:0.00576290669664;RBPJ:0.00480186535601;ZEB1:0.00186237818151;PAX8:-0.0122655491573;JUN:-0.0392676769646;YY1:-0.0557405188814;SPIB:-0.056542909532;MYB:-0.0583918256631;TBX4,5:-0.0634713365619;POU1F1:-0.0688084205349;ELF1,2,4:-0.0937351955774;FOX{I1,J2}:-0.104507012443;NR3C1:-0.130016901584;TGIF1:-0.131245468569;DMAP1_NCOR{1,2}_SMARC:-0.132345890385;NHLH1,2:-0.141290839875;AIRE:-0.158097574182;FOXQ1:-0.162855754433;PITX1..3:-0.178284152181;NKX3-2:-0.200468702274;SPI1:-0.2188773188;FOSL2:-0.227383380857;T:-0.234100487731;MYFfamily:-0.245806419237;RORA:-0.251277252178;PAX2:-0.273802068809;TBP:-0.27468243323;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:-0.34803419529;NFIL3:-0.376113231557;ATF4:-0.380321436744;bHLH_family:-0.382062213701;RUNX1..3:-0.388164144271;SMAD1..7,9:-0.391591401906;ETS1,2:-0.397209403219;SREBF1,2:-0.41730751516;ZNF148:-0.422279294322;STAT5{A,B}:-0.434702307183;RXRA_VDR{dimer}:-0.464004429791;FOX{D1,D2}:-0.466893203553;FOXO1,3,4:-0.468886711308;HOX{A4,D4}:-0.479634566906;NR6A1:-0.482833184603;ATF5_CREB3:-0.49742773489;TLX2:-0.50318427296;MAFB:-0.510000678135;MEF2{A,B,C,D}:-0.5280074103;RXR{A,B,G}_{NR1H2,PPAR}dimers:-0.537121149118;GATA6:-0.57792295445;NKX2-2,8:-0.580210240683;PDX1:-0.595369101786;HNF4A_NR2F1,2:-0.604764416328;PBX1:-0.616389361749;HLF:-0.626602804361;SRF:-0.62748227001;NFATC1..3:-0.638341080184;NFIX:-0.647947001493;HNF1A:-0.673962163415;NFKB1_REL_RELA:-0.6823768;NR5A1,2:-0.726584983846;NFE2L2:-0.741302629463;IRF1,2:-0.756735844843;ESRRA:-0.763063702294;FOXA2:-0.786728918332;FOX{F1,F2,J1}:-0.786892906645;ALX4:-0.800232989403;AR:-0.804346095027;NR1H4:-0.835578037319;TP53:-0.861634013444;PPARG:-0.930553740405;IRF7:-0.934191420927;FOS_FOS{B,L1}_JUN{B,D}:-0.954503447259;NFE2L1:-0.964907029205;STAT2,4,6:-1.00321543376;BACH2:-1.13322196899;CEBPA,B_DDIT3:-1.26345431922;NFE2:-1.38767316875
|comment=
|created_by=
|creation_date=
|def=
|has_quality=
|is_a=EFO:0002091;;FF:0000004;;FF:0000103;;FF:0011334
|namespace=FANTOM5
|part_of=
}}
}}

Revision as of 16:01, 7 March 2012


Name:pituitary gland, embryo E14
Species:Mouse (Mus musculus)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissuepituitary gland
dev stage14 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

CNhs11037

00
10.0843
100
1000.0843
10000.0489
10010
10020.249
1003-0.0633
10040.314
1005-0.0389
10060.0123
10070.025
10080
1009-0.0572
101-0.0221
10100
10110.0381
10120
1013-0.0891
10140.311
10150.211
10160.2
10170
10180
10190
1020
10200
10210
1022-0.0704
10230
10240.0416
10250.0232
10260
10270.155
10280
1029-0.0916
1030.176
10300
10310.337
1032-0.0922
10330.052
10340
10350
1036-0.0279
10370
10380.0519
1039-0.104
1040
10400
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: CNhs11037

Jaspar motifP-value
MA0002.21.50294e-4
MA0003.10.257
MA0004.10.779
MA0006.10.409
MA0007.10.666
MA0009.10.485
MA0014.10.541
MA0017.14.98527e-7
MA0018.20.121
MA0019.10.587
MA0024.10.0426
MA0025.10.227
MA0027.10.328
MA0028.10.36
MA0029.10.255
MA0030.10.204
MA0031.10.103
MA0035.20.00277
MA0038.10.0623
MA0039.20.25
MA0040.10.28
MA0041.10.261
MA0042.10.566
MA0043.10.0316
MA0046.13.02551e-24
MA0047.29.08795e-4
MA0048.10.72
MA0050.10.00115
MA0051.10.00508
MA0052.11.95773e-6
MA0055.10.197
MA0057.10.0915
MA0058.10.794
MA0059.10.718
MA0060.13.90768e-11
MA0061.10.0224
MA0062.20.741
MA0065.26.97524e-5
MA0066.10.0148
MA0067.10.369
MA0068.10.0668
MA0069.10.282
MA0070.10.803
MA0071.10.113
MA0072.10.0555
MA0073.10.806
MA0074.10.724
MA0076.10.145
MA0077.10.0324
MA0078.10.967
MA0079.20.303
MA0080.28.73642e-10
MA0081.10.286
MA0083.10.0345
MA0084.10.377
MA0087.10.16
MA0088.10.296
MA0090.10.236
MA0091.10.472
MA0092.10.523
MA0093.10.86
MA0099.23.73742e-5
MA0100.10.927
MA0101.10.138
MA0102.20.27
MA0103.10.325
MA0104.20.81
MA0105.10.00174
MA0106.10.0741
MA0107.10.0508
MA0108.20.475
MA0111.10.834
MA0112.24.35109e-7
MA0113.10.58
MA0114.15.30766e-6
MA0115.14.79412e-5
MA0116.10.0184
MA0117.10.511
MA0119.10.0239
MA0122.10.597
MA0124.10.532
MA0125.10.0161
MA0131.10.391
MA0135.10.769
MA0136.12.28705e-5
MA0137.20.0589
MA0138.20.0334
MA0139.10.144
MA0140.10.00695
MA0141.10.00184
MA0142.10.523
MA0143.10.061
MA0144.10.108
MA0145.10.0552
MA0146.10.517
MA0147.10.908
MA0148.11.53852e-4
MA0149.10.0144
MA0150.15.51819e-4
MA0152.10.92
MA0153.12.52776e-16
MA0154.10.0031
MA0155.10.904
MA0156.10.0421
MA0157.10.334
MA0159.10.00275
MA0160.10.00679
MA0162.10.53
MA0163.10.00784
MA0164.10.984
MA0258.11.4885e-4
MA0259.10.858



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: CNhs11037

Novel motifP-value
10.061
100.128
1000.893
1010.54
1020.89
1030.134
1040.883
1050.232
1060.0066
1070.0265
1080.652
1090.244
110.175
1100.148
1110.0277
1120.0233
1130.547
1140.0289
1150.897
1160.566
1170.142
1180.756
1190.126
120.806
1200.718
1210.626
1220.787
1230.196
1240.889
1250.3
1260.658
1270.0326
1280.0448
1290.205
130.114
1300.266
1310.335
1320.477
1330.575
1340.445
1350.0688
1360.532
1370.772
1380.421
1390.0452
140.406
1400.0836
1410.145
1420.194
1430.632
1440.912
1450.271
1460.421
1470.506
1480.385
1490.253
150.0551
1500.383
1510.112
1520.164
1530.737
1540.571
1550.466
1561.52968e-6
1570.41
1580.145
1590.0666
1600.469
1610.86
1620.636
1630.27
1640.0458
1650.108
1660.841
1670.355
1680.44
1690.00167
170.142
180.23
190.214
20.671
200.685
210.728
220.253
230.0968
240.684
250.241
260.152
270.565
280.388
290.217
30.22
300.747
310.553
320.178
330.425
340.818
350.309
360.287
370.0481
380.377
390.761
40.537
400.441
410.252
420.604
430.14
440.133
450.488
460.14
470.225
480.133
490.123
50.0698
500.875
510.524
520.267
530.595
540.412
550.472
560.512
570.388
580.249
590.0923
60.777
600.0503
610.591
620.0518
630.113
640.626
650.164
660.252
670.71
680.273
690.859
70.114
700.00301
710.083
720.562
730.0988
740.658
750.105
760.62
770.208
780.0715
790.369
80.164
800.183
810.318
820.0945
830.334
840.168
850.0121
860.413
870.791
880.478
890.147
90.395
900.268
910.34
920.142
930.12
940.271
950.234
960.224
970.785
980.453
990.657



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: CNhs11037


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
0000007 (pituitary gland)
0000025 (tube)
0000033 (head)
0000061 (anatomical structure)
0000062 (organ)
0000073 (regional part of nervous system)
0000153 (anterior region of body)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000475 (organism subdivision)
0000479 (tissue)
0000480 (anatomical group)
0000481 (multi-tissue structure)
0000922 (embryo)
0000923 (germ layer)
0000924 (ectoderm)
0000949 (endocrine system)
0000955 (brain)
0001016 (nervous system)
0001017 (central nervous system)
0001049 (neural tube)
0001062 (anatomical entity)
0001890 (forebrain)
0001894 (diencephalon)
0002050 (embryonic structure)
0002346 (neurectoderm)
0002368 (endocrine gland)
0002530 (gland)
0002532 (epiblast (generic))
0002616 (regional part of brain)
0002780 (regional part of forebrain)
0003056 (pre-chordal neural plate)
0003075 (neural plate)
0003080 (anterior neural tube)
0003296 (gland of diencephalon)
0004121 (ectoderm-derived structure)
0005068 (neural rod)
0005291 (embryonic tissue)
0005423 (developing anatomical structure)
0006598 (presumptive structure)
0007135 (neural keel)
0007284 (presumptive neural plate)

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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