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|fonse_treatment_closure=
|fonse_treatment_closure=
|top_motifs=REST:2.79022320535;ZBTB6:2.75645727888;MTF1:2.74894616104;HAND1,2:2.32277866445;MYFfamily:2.32031364292;POU6F1:2.29606180865;KLF4:2.25762578795;MED-1{core}:2.21944248001;ZFP161:2.21666926598;EGR1..3:2.21451895639;TFAP2B:2.20430096889;LMO2:2.18571710212;ATF2:2.10676240667;UFEwm:2.0695335349;NHLH1,2:2.06370593284;HIC1:2.05095860891;EVI1:2.0403742895;PAX6:2.01853556764;ZIC1..3:2.00174665381;AHR_ARNT_ARNT2:1.8937151267;OCT4_SOX2{dimer}:1.8773812321;PAX5:1.79573110646;MTE{core}:1.79052308976;FOXD3:1.77966870518;BREu{core}:1.77672486205;MAFB:1.76901605366;RORA:1.75396445177;PBX1:1.74181576881;JUN:1.63717264758;CUX2:1.53926049272;NFIL3:1.5024092922;PRDM1:1.48743366239;GTF2I:1.44923012108;RBPJ:1.44307789959;GATA4:1.42835620173;FOXM1:1.4277457772;CREB1:1.42487178087;PRRX1,2:1.4124329799;TFDP1:1.37681131098;NRF1:1.37238823179;POU3F1..4:1.36475079093;DBP:1.36455857105;RFX1:1.34710776986;NKX2-2,8:1.32386146575;FOX{I1,J2}:1.31587711904;TGIF1:1.28858537837;PAX4:1.28797021898;HMGA1,2:1.22518637647;ARID5B:1.21564517332;ADNP_IRX_SIX_ZHX:1.20979932245;SMAD1..7,9:1.18152319326;GFI1B:1.16058915364;HBP1_HMGB_SSRP1_UBTF:1.15568278933;ZNF143:1.13713318309;TFAP2{A,C}:1.11796751805;FOXP3:1.0946073963;SREBF1,2:1.08142288008;MZF1:1.07275854763;CDC5L:1.06838699849;ATF5_CREB3:1.04007934151;IKZF1:1.03130694522;PATZ1:1.02993846774;MYOD1:1.01282423029;NANOG:0.944390457717;STAT1,3:0.925566733657;SOX2:0.920812193996;ONECUT1,2:0.87674883031;NR3C1:0.865104371231;HSF1,2:0.857146430424;NFE2L2:0.846606100671;FOXN1:0.842615003218;RFX2..5_RFXANK_RFXAP:0.814949000073;ZEB1:0.810664665142;NFE2:0.804644239691;AIRE:0.799659876876;RREB1:0.795852895267;GTF2A1,2:0.785374204558;HMX1:0.779734615971;PPARG:0.775872627253;NKX3-2:0.757829620713;SPZ1:0.743293078056;TEF:0.743084319188;ZNF423:0.736984814765;PAX2:0.657505660791;HES1:0.65646941833;ALX1:0.652088635435;FOXQ1:0.626517156611;MAZ:0.626149292956;HOXA9_MEIS1:0.590471554757;SOX5:0.583778199964;YY1:0.556766774784;SOX{8,9,10}:0.511580727538;TFAP4:0.498763209999;NR5A1,2:0.460331968944;EBF1:0.424132498663;POU5F1:0.403286957204;FOX{F1,F2,J1}:0.391491323821;LHX3,4:0.370451211221;GZF1:0.35270540034;PAX8:0.286247493653;TBX4,5:0.273034822777;VSX1,2:0.254513918796;NKX6-1,2:0.235218588654;ESRRA:0.22457802358;GLI1..3:0.214587357914;LEF1_TCF7_TCF7L1,2:0.13823443471;SP1:0.127139491025;SOX17:0.118940642933;NR1H4:0.115187433601;ZNF384:0.0319166707482;ATF4:0.0244382065985;NFE2L1:0.00272895393563;TFCP2:-0.00786608486715;MYBL2:-0.0117081071982;GCM1,2:-0.055567441221;bHLH_family:-0.130761251434;NKX2-3_NKX2-5:-0.161716816766;SNAI1..3:-0.167981663837;NKX2-1,4:-0.178194226766;POU1F1:-0.181953596611;PDX1:-0.211600598785;NFATC1..3:-0.227517612873;HIF1A:-0.232422320336;PAX1,9:-0.271179011314;CRX:-0.30016517695;BPTF:-0.31440006008;NKX3-1:-0.339761546168;TLX1..3_NFIC{dimer}:-0.343058766403;HLF:-0.348988101708;AR:-0.350744518873;XCPE1{core}:-0.357177281532;ZBTB16:-0.358621974091;FOXA2:-0.36168305884;HOX{A4,D4}:-0.413239964823;MEF2{A,B,C,D}:-0.416464785163;NANOG{mouse}:-0.419268958609;TAL1_TCF{3,4,12}:-0.421134606072;TP53:-0.440842451883;RXR{A,B,G}:-0.45469833697;CDX1,2,4:-0.461765507911;ZNF148:-0.482803485132;EN1,2:-0.493925052119;EP300:-0.50034431199;TOPORS:-0.566455996165;HOX{A5,B5}:-0.572847661609;NFY{A,B,C}:-0.58042288896;ATF6:-0.616632179789;SPI1:-0.633838841088;FOSL2:-0.638503418857;ELK1,4_GABP{A,B1}:-0.650234751703;IKZF2:-0.663885794705;STAT2,4,6:-0.665587989664;MYB:-0.684749019143;HNF4A_NR2F1,2:-0.721115981272;ZNF238:-0.748979775793;ESR1:-0.779377716784;T:-0.810646489123;BACH2:-0.814740146346;FOXL1:-0.829574298987;FOXO1,3,4:-0.837607408292;GATA6:-0.864886859083;POU2F1..3:-0.883769424351;HNF1A:-0.884905063385;RUNX1..3:-0.891122304635;CEBPA,B_DDIT3:-0.899739296262;NFIX:-1.01182383384;FOS_FOS{B,L1}_JUN{B,D}:-1.02619380628;STAT5{A,B}:-1.03206693599;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:-1.03968579883;ALX4:-1.07579175025;FOX{D1,D2}:-1.09672794316;IRF1,2:-1.1375587602;TEAD1:-1.13999972705;NFKB1_REL_RELA:-1.14679788271;DMAP1_NCOR{1,2}_SMARC:-1.15109395243;IRF7:-1.17043847159;ETS1,2:-1.24607715917;FOXP1:-1.28363796852;NR6A1:-1.30408059951;ELF1,2,4:-1.33619874211;RXR{A,B,G}_{NR1H2,PPAR}dimers:-1.58195605269;SPIB:-1.58649057779;TBP:-1.67558096402;RXRA_VDR{dimer}:-1.68658383462;E2F1..5:-1.71345062585;GFI1:-1.8321427635;SRF:-1.94066607851;TLX2:-1.96635238321;PITX1..3:-2.10611627389
|top_motifs=REST:2.79022320535;ZBTB6:2.75645727888;MTF1:2.74894616104;HAND1,2:2.32277866445;MYFfamily:2.32031364292;POU6F1:2.29606180865;KLF4:2.25762578795;MED-1{core}:2.21944248001;ZFP161:2.21666926598;EGR1..3:2.21451895639;TFAP2B:2.20430096889;LMO2:2.18571710212;ATF2:2.10676240667;UFEwm:2.0695335349;NHLH1,2:2.06370593284;HIC1:2.05095860891;EVI1:2.0403742895;PAX6:2.01853556764;ZIC1..3:2.00174665381;AHR_ARNT_ARNT2:1.8937151267;OCT4_SOX2{dimer}:1.8773812321;PAX5:1.79573110646;MTE{core}:1.79052308976;FOXD3:1.77966870518;BREu{core}:1.77672486205;MAFB:1.76901605366;RORA:1.75396445177;PBX1:1.74181576881;JUN:1.63717264758;CUX2:1.53926049272;NFIL3:1.5024092922;PRDM1:1.48743366239;GTF2I:1.44923012108;RBPJ:1.44307789959;GATA4:1.42835620173;FOXM1:1.4277457772;CREB1:1.42487178087;PRRX1,2:1.4124329799;TFDP1:1.37681131098;NRF1:1.37238823179;POU3F1..4:1.36475079093;DBP:1.36455857105;RFX1:1.34710776986;NKX2-2,8:1.32386146575;FOX{I1,J2}:1.31587711904;TGIF1:1.28858537837;PAX4:1.28797021898;HMGA1,2:1.22518637647;ARID5B:1.21564517332;ADNP_IRX_SIX_ZHX:1.20979932245;SMAD1..7,9:1.18152319326;GFI1B:1.16058915364;HBP1_HMGB_SSRP1_UBTF:1.15568278933;ZNF143:1.13713318309;TFAP2{A,C}:1.11796751805;FOXP3:1.0946073963;SREBF1,2:1.08142288008;MZF1:1.07275854763;CDC5L:1.06838699849;ATF5_CREB3:1.04007934151;IKZF1:1.03130694522;PATZ1:1.02993846774;MYOD1:1.01282423029;NANOG:0.944390457717;STAT1,3:0.925566733657;SOX2:0.920812193996;ONECUT1,2:0.87674883031;NR3C1:0.865104371231;HSF1,2:0.857146430424;NFE2L2:0.846606100671;FOXN1:0.842615003218;RFX2..5_RFXANK_RFXAP:0.814949000073;ZEB1:0.810664665142;NFE2:0.804644239691;AIRE:0.799659876876;RREB1:0.795852895267;GTF2A1,2:0.785374204558;HMX1:0.779734615971;PPARG:0.775872627253;NKX3-2:0.757829620713;SPZ1:0.743293078056;TEF:0.743084319188;ZNF423:0.736984814765;PAX2:0.657505660791;HES1:0.65646941833;ALX1:0.652088635435;FOXQ1:0.626517156611;MAZ:0.626149292956;HOXA9_MEIS1:0.590471554757;SOX5:0.583778199964;YY1:0.556766774784;SOX{8,9,10}:0.511580727538;TFAP4:0.498763209999;NR5A1,2:0.460331968944;EBF1:0.424132498663;POU5F1:0.403286957204;FOX{F1,F2,J1}:0.391491323821;LHX3,4:0.370451211221;GZF1:0.35270540034;PAX8:0.286247493653;TBX4,5:0.273034822777;VSX1,2:0.254513918796;NKX6-1,2:0.235218588654;ESRRA:0.22457802358;GLI1..3:0.214587357914;LEF1_TCF7_TCF7L1,2:0.13823443471;SP1:0.127139491025;SOX17:0.118940642933;NR1H4:0.115187433601;ZNF384:0.0319166707482;ATF4:0.0244382065985;NFE2L1:0.00272895393563;TFCP2:-0.00786608486715;MYBL2:-0.0117081071982;GCM1,2:-0.055567441221;bHLH_family:-0.130761251434;NKX2-3_NKX2-5:-0.161716816766;SNAI1..3:-0.167981663837;NKX2-1,4:-0.178194226766;POU1F1:-0.181953596611;PDX1:-0.211600598785;NFATC1..3:-0.227517612873;HIF1A:-0.232422320336;PAX1,9:-0.271179011314;CRX:-0.30016517695;BPTF:-0.31440006008;NKX3-1:-0.339761546168;TLX1..3_NFIC{dimer}:-0.343058766403;HLF:-0.348988101708;AR:-0.350744518873;XCPE1{core}:-0.357177281532;ZBTB16:-0.358621974091;FOXA2:-0.36168305884;HOX{A4,D4}:-0.413239964823;MEF2{A,B,C,D}:-0.416464785163;NANOG{mouse}:-0.419268958609;TAL1_TCF{3,4,12}:-0.421134606072;TP53:-0.440842451883;RXR{A,B,G}:-0.45469833697;CDX1,2,4:-0.461765507911;ZNF148:-0.482803485132;EN1,2:-0.493925052119;EP300:-0.50034431199;TOPORS:-0.566455996165;HOX{A5,B5}:-0.572847661609;NFY{A,B,C}:-0.58042288896;ATF6:-0.616632179789;SPI1:-0.633838841088;FOSL2:-0.638503418857;ELK1,4_GABP{A,B1}:-0.650234751703;IKZF2:-0.663885794705;STAT2,4,6:-0.665587989664;MYB:-0.684749019143;HNF4A_NR2F1,2:-0.721115981272;ZNF238:-0.748979775793;ESR1:-0.779377716784;T:-0.810646489123;BACH2:-0.814740146346;FOXL1:-0.829574298987;FOXO1,3,4:-0.837607408292;GATA6:-0.864886859083;POU2F1..3:-0.883769424351;HNF1A:-0.884905063385;RUNX1..3:-0.891122304635;CEBPA,B_DDIT3:-0.899739296262;NFIX:-1.01182383384;FOS_FOS{B,L1}_JUN{B,D}:-1.02619380628;STAT5{A,B}:-1.03206693599;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:-1.03968579883;ALX4:-1.07579175025;FOX{D1,D2}:-1.09672794316;IRF1,2:-1.1375587602;TEAD1:-1.13999972705;NFKB1_REL_RELA:-1.14679788271;DMAP1_NCOR{1,2}_SMARC:-1.15109395243;IRF7:-1.17043847159;ETS1,2:-1.24607715917;FOXP1:-1.28363796852;NR6A1:-1.30408059951;ELF1,2,4:-1.33619874211;RXR{A,B,G}_{NR1H2,PPAR}dimers:-1.58195605269;SPIB:-1.58649057779;TBP:-1.67558096402;RXRA_VDR{dimer}:-1.68658383462;E2F1..5:-1.71345062585;GFI1:-1.8321427635;SRF:-1.94066607851;TLX2:-1.96635238321;PITX1..3:-2.10611627389
|comment=
|created_by=
|creation_date=
|def=
|has_quality=
|is_a=EFO:0002091;;FF:0000002;;FF:0000103;;FF:0000205
|namespace=FANTOM5
|part_of=
}}
}}

Revision as of 15:37, 7 March 2012


Name:Mouse Neurons - raphe, donor3
Species:Mouse (Mus musculus)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueraphe nuclei
dev stageNA
sexNA
ageNA
cell typeneuron
cell lineNA
companySciencell/3H
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberRNARAP1
catalog numbercustom
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-TRIzol-ethanol-v1.0
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

CNhs12619

00
10.772
100
1000
10000
10010.161
1002-0.0851
10030.0905
10040
10050
10060.728
1007-0.116
10080
1009-0.0737
101-0.129
10100
10110.346
10120.15
10130.181
1014-0.0309
1015-0.135
10160.0128
10170
10180
10190
1020
10200.558
10210
10220.00628
10230
1024-0.0232
1025-0.0611
10260
10270.337
10280
1029-0.0596
103-0.0861
10300
1031-0.505
10320.504
10330.0498
10340
10350.0621
1036-0.172
10370
1038-0.0146
10390.0952
1040
1040-0.121
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: CNhs12619

Jaspar motifP-value
MA0002.20.00175
MA0003.10.301
MA0004.10.511
MA0006.10.182
MA0007.10.293
MA0009.10.747
MA0014.10.804
MA0017.13.35748e-6
MA0018.20.00896
MA0019.10.626
MA0024.10.0754
MA0025.10.0017
MA0027.10.109
MA0028.10.0878
MA0029.10.949
MA0030.10.863
MA0031.10.232
MA0035.20.0374
MA0038.10.929
MA0039.20.0215
MA0040.10.656
MA0041.10.167
MA0042.10.292
MA0043.10.0692
MA0046.14.86825e-8
MA0047.20.00102
MA0048.10.0421
MA0050.11.82302e-6
MA0051.11.27452e-4
MA0052.10.77
MA0055.10.009
MA0057.10.341
MA0058.10.529
MA0059.10.211
MA0060.10.876
MA0061.10.0257
MA0062.20.00153
MA0065.26.99742e-6
MA0066.10.107
MA0067.10.315
MA0068.10.145
MA0069.10.0982
MA0070.10.457
MA0071.10.194
MA0072.10.719
MA0073.10.873
MA0074.10.123
MA0076.10.219
MA0077.10.272
MA0078.10.951
MA0079.20.39
MA0080.22.82048e-10
MA0081.10.236
MA0083.10.00264
MA0084.10.578
MA0087.10.131
MA0088.10.339
MA0090.10.071
MA0091.10.202
MA0092.10.198
MA0093.10.572
MA0099.20.00379
MA0100.10.207
MA0101.10.0115
MA0102.20.664
MA0103.10.244
MA0104.20.901
MA0105.10.00727
MA0106.10.0839
MA0107.10.0257
MA0108.23.76214e-4
MA0111.10.999
MA0112.20.00101
MA0113.10.426
MA0114.11.55402e-5
MA0115.12.58548e-4
MA0116.10.0869
MA0117.10.973
MA0119.10.125
MA0122.10.998
MA0124.10.59
MA0125.10.1
MA0131.10.633
MA0135.10.511
MA0136.11.77123e-11
MA0137.20.164
MA0138.21.62955e-4
MA0139.10.572
MA0140.14.51848e-4
MA0141.10.0331
MA0142.10.299
MA0143.10.796
MA0144.10.0778
MA0145.10.115
MA0146.10.0344
MA0147.10.773
MA0148.10.00106
MA0149.10.184
MA0150.10.254
MA0152.10.0407
MA0153.15.16326e-9
MA0154.10.0577
MA0155.10.446
MA0156.15.86633e-9
MA0157.10.134
MA0159.10.011
MA0160.10.0534
MA0162.10.225
MA0163.10.00112
MA0164.10.894
MA0258.10.0176
MA0259.10.892



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: CNhs12619

Novel motifP-value
10.24
100.0464
1000.287
1010.89
1020.877
1030.0902
1040.91
1050.446
1060.034
1070.115
1080.496
1090.00809
110.108
1100.0536
1110.311
1120.0139
1130.607
1140.608
1150.904
1160.396
1170.00546
1180.587
1190.159
120.863
1200.63
1210.415
1220.988
1231.22443e-4
1240.0994
1250.168
1260.0484
1270.438
1280.04
1290.28
131.15308e-7
1300.122
1310.314
1320.729
1330.756
1340.0832
1350.199
1360.168
1370.706
1380.59
1390.297
140.873
1400.269
1410.828
1420.695
1430.349
1440.635
1451.64637e-4
1460.248
1470.282
1480.933
1490.909
150.199
1500.0661
1510.836
1520.118
1530.463
1540.633
1550.458
1560.00432
1570.0917
1580.173
1590.702
1600.281
1610.225
1620.762
1630.806
1640.0402
1650.255
1660.514
1670.528
1680.553
1690.00265
170.0697
180.752
190.0988
20.62
200.0295
210.184
220.13
230.646
240.057
250.817
262.06561e-8
270.377
280.83
290.0439
30.0792
300.805
310.7
320.655
330.094
340.743
350.659
360.131
370.04
380.425
390.381
40.304
400.0717
410.585
420.165
430.119
440.812
450.648
460.0493
470.401
480.315
490.135
50.169
500.234
510.782
520.272
530.562
540.97
550.996
560.459
570.54
580.299
590.183
60.928
600.0385
610.0501
620.206
630.142
640.721
650.374
660.726
670.716
680.973
690.506
70.0143
700.0896
710.00281
720.582
730.0506
740.912
750.0593
760.31
770.573
780.00267
790.0712
80.0674
800.738
810.739
820.283
830.163
840.593
850.196
860.147
870.398
880.862
890.584
90.376
900.145
910.089
920.387
930.0598
940.713
950.0612
960.275
970.764
980.743
990.409



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: CNhs12619


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

CL: Cell type
0000000 (cell), 0000000 (cell)
0000003 (native cell)
0000031 (neuroblast)
0000034 (stem cell)
0000047 (neuronal stem cell)
0000048 (multi fate stem cell)
0000055 (non-terminally differentiated cell)
0000117 (CNS neuron (sensu Vertebrata))
0000133 (neurectodermal cell)
0000211 (electrically active cell)
0000221 (ectodermal cell)
0000255 (eukaryotic cell)
0000337 (neuroblast (sensu Vertebrata))
0000393 (electrically responsive cell)
0000404 (electrically signaling cell)
0000540 (neuron)
0000548 (animal cell)
0000723 (somatic stem cell)
0002319 (neural cell)
0002321 (embryonic cell)
0002371 (somatic cell)
0002610 (raphe nuclei neuron)

UBERON: Anatomy
0000033 (head)
0000061 (anatomical structure)
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)
0000480 (anatomical group)
0000481 (multi-tissue structure)
0000922 (embryo)
0000923 (germ layer)
0000924 (ectoderm)
0000955 (brain)
0001016 (nervous system)
0001017 (central nervous system)
0001062 (anatomical entity)
0002050 (embryonic structure)
0002275 (reticular formation)
0002532 (epiblast (generic))
0002616 (regional part of brain)
0004121 (ectoderm-derived structure)
0004684 (raphe nuclei)
0005423 (developing anatomical structure)

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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