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|fonse_treatment_closure=
|fonse_treatment_closure=
|top_motifs=SOX5:2.01860851737;SOX2:1.87573053007;EN1,2:1.55695236091;RXR{A,B,G}:1.53996643493;ONECUT1,2:1.46698165473;PDX1:1.3193724843;POU3F1..4:1.30639083314;JUN:1.27230155899;SOX17:1.2678678559;SREBF1,2:1.25552868681;TFDP1:1.23961244257;TP53:1.22360696421;ZFP161:1.20784218497;ZNF143:1.11272651826;TFAP2B:1.09799605076;AHR_ARNT_ARNT2:1.08095808178;FOXD3:1.05256597528;NANOG:1.03860190289;PRRX1,2:1.03681433058;MTE{core}:0.997773788667;MED-1{core}:0.992048630846;ZNF384:0.967597894161;NRF1:0.941836923107;ATF4:0.940661636905;FOSL2:0.922547230524;GZF1:0.911160034711;TFAP2{A,C}:0.900647349044;DBP:0.862045319397;MZF1:0.859925770734;LEF1_TCF7_TCF7L1,2:0.858258024774;EGR1..3:0.80958483641;CDC5L:0.790572909777;RORA:0.761372244421;HMX1:0.755426532989;NHLH1,2:0.713191558678;SOX{8,9,10}:0.712546261919;ADNP_IRX_SIX_ZHX:0.671220270986;BREu{core}:0.662627092204;PATZ1:0.6527459707;NKX2-1,4:0.625251948406;PAX5:0.623267765411;HIC1:0.570550043603;HBP1_HMGB_SSRP1_UBTF:0.561285360588;MAZ:0.554083014356;SP1:0.550885659786;VSX1,2:0.545000827121;FOS_FOS{B,L1}_JUN{B,D}:0.513728053849;ELK1,4_GABP{A,B1}:0.495113148213;GFI1:0.474340186148;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:0.473643207273;TFCP2:0.457884168407;GTF2I:0.453069398908;ATF2:0.422812035477;EP300:0.393920989635;ZNF423:0.381011798891;STAT1,3:0.351640868236;RFX2..5_RFXANK_RFXAP:0.347181040062;XCPE1{core}:0.343649996017;ZBTB16:0.333907423309;ATF5_CREB3:0.304185974127;GTF2A1,2:0.301728808331;CUX2:0.297666570967;MYFfamily:0.296623406213;NFE2:0.292845518988;FOX{D1,D2}:0.288259006837;BACH2:0.284261777984;LHX3,4:0.280826000334;HIF1A:0.27608891328;RREB1:0.274241290894;NR1H4:0.266412656238;ZNF148:0.264718841631;GATA4:0.26367934598;IKZF1:0.263076508683;HAND1,2:0.261873852279;TFAP4:0.25977699757;CREB1:0.258577870886;NKX3-1:0.250426236615;TEF:0.2383718995;ZBTB6:0.228840186577;NFY{A,B,C}:0.217679399584;PAX8:0.204976298195;RFX1:0.203293927476;E2F1..5:0.199565317483;REST:0.194103707624;TEAD1:0.149838155016;SMAD1..7,9:0.13728919572;NFIL3:0.130248066128;TLX2:0.129075011908;POU2F1..3:0.11805943835;ZIC1..3:0.116594698409;RBPJ:0.0933025813685;ATF6:0.0901206677359;ZNF238:0.0898386829198;HSF1,2:0.0771104822074;GFI1B:0.0594800087789;HES1:0.0501834600046;MTF1:0.0313811103731;NKX3-2:0.0301705230765;HOX{A4,D4}:0.0299551805536;MYB:0.0263026105799;PBX1:0.0254605595746;AR:0.0134790922837;OCT4_SOX2{dimer}:0.00921189141826;FOXP3:-0.0248726586937;FOX{I1,J2}:-0.06027748785;POU5F1:-0.0863516017785;EVI1:-0.0946018943765;NFE2L1:-0.111715849292;RXR{A,B,G}_{NR1H2,PPAR}dimers:-0.148221471577;CRX:-0.152827712667;YY1:-0.154574167892;EBF1:-0.159678971658;HMGA1,2:-0.164063360777;STAT5{A,B}:-0.170129248048;ESRRA:-0.174929603508;KLF4:-0.175130042345;PRDM1:-0.185874447881;PITX1..3:-0.201997149212;UFEwm:-0.218967573311;DMAP1_NCOR{1,2}_SMARC:-0.222585976806;GLI1..3:-0.237829164035;NFATC1..3:-0.273804696513;RUNX1..3:-0.275706489609;TLX1..3_NFIC{dimer}:-0.296410974246;FOXM1:-0.303115537626;PAX4:-0.304101500309;ESR1:-0.3062410856;ALX4:-0.319796601118;CEBPA,B_DDIT3:-0.31985946145;ELF1,2,4:-0.324808366307;SPIB:-0.330927578282;MYBL2:-0.337738427014;HOXA9_MEIS1:-0.338037469855;AIRE:-0.350649390901;IRF7:-0.357203945627;HNF4A_NR2F1,2:-0.373435006411;HNF1A:-0.373913442389;PAX6:-0.376431527961;TGIF1:-0.379798534532;SPZ1:-0.397585796432;POU6F1:-0.403194429823;FOXA2:-0.40339286416;IKZF2:-0.403537304671;FOX{F1,F2,J1}:-0.405590162655;FOXL1:-0.442996554353;PAX2:-0.449615692913;NFKB1_REL_RELA:-0.453712996955;LMO2:-0.466444985845;FOXQ1:-0.472115221985;NKX2-3_NKX2-5:-0.482624661315;bHLH_family:-0.484159391469;MEF2{A,B,C,D}:-0.492151752763;PAX1,9:-0.496122148688;ALX1:-0.497004852118;SPI1:-0.503541994623;SRF:-0.509244921883;FOXP1:-0.517664634367;IRF1,2:-0.522746689515;RXRA_VDR{dimer}:-0.524597870619;HLF:-0.534239107979;T:-0.543346584001;FOXO1,3,4:-0.582002176341;TAL1_TCF{3,4,12}:-0.588797296461;NR3C1:-0.59486978866;NFE2L2:-0.59639527706;STAT2,4,6:-0.600924920305;NFIX:-0.626586999111;TOPORS:-0.631660442421;GCM1,2:-0.638881226307;TBP:-0.665867163577;POU1F1:-0.708361773852;ETS1,2:-0.710653162799;BPTF:-0.748454652956;NR5A1,2:-0.793185619556;NKX2-2,8:-0.816706473395;NKX6-1,2:-0.86966344405;FOXN1:-0.889690204332;GATA6:-0.90729815333;HOX{A5,B5}:-0.926950926789;MAFB:-0.98527718265;NR6A1:-0.990904550195;MYOD1:-1.00653766602;NANOG{mouse}:-1.12377574763;PPARG:-1.12396974314;CDX1,2,4:-1.16256037607;SNAI1..3:-1.27727379011;ZEB1:-1.41378104584;ARID5B:-1.57281827799;TBX4,5:-1.92632159807
|top_motifs=SOX5:2.01860851737;SOX2:1.87573053007;EN1,2:1.55695236091;RXR{A,B,G}:1.53996643493;ONECUT1,2:1.46698165473;PDX1:1.3193724843;POU3F1..4:1.30639083314;JUN:1.27230155899;SOX17:1.2678678559;SREBF1,2:1.25552868681;TFDP1:1.23961244257;TP53:1.22360696421;ZFP161:1.20784218497;ZNF143:1.11272651826;TFAP2B:1.09799605076;AHR_ARNT_ARNT2:1.08095808178;FOXD3:1.05256597528;NANOG:1.03860190289;PRRX1,2:1.03681433058;MTE{core}:0.997773788667;MED-1{core}:0.992048630846;ZNF384:0.967597894161;NRF1:0.941836923107;ATF4:0.940661636905;FOSL2:0.922547230524;GZF1:0.911160034711;TFAP2{A,C}:0.900647349044;DBP:0.862045319397;MZF1:0.859925770734;LEF1_TCF7_TCF7L1,2:0.858258024774;EGR1..3:0.80958483641;CDC5L:0.790572909777;RORA:0.761372244421;HMX1:0.755426532989;NHLH1,2:0.713191558678;SOX{8,9,10}:0.712546261919;ADNP_IRX_SIX_ZHX:0.671220270986;BREu{core}:0.662627092204;PATZ1:0.6527459707;NKX2-1,4:0.625251948406;PAX5:0.623267765411;HIC1:0.570550043603;HBP1_HMGB_SSRP1_UBTF:0.561285360588;MAZ:0.554083014356;SP1:0.550885659786;VSX1,2:0.545000827121;FOS_FOS{B,L1}_JUN{B,D}:0.513728053849;ELK1,4_GABP{A,B1}:0.495113148213;GFI1:0.474340186148;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:0.473643207273;TFCP2:0.457884168407;GTF2I:0.453069398908;ATF2:0.422812035477;EP300:0.393920989635;ZNF423:0.381011798891;STAT1,3:0.351640868236;RFX2..5_RFXANK_RFXAP:0.347181040062;XCPE1{core}:0.343649996017;ZBTB16:0.333907423309;ATF5_CREB3:0.304185974127;GTF2A1,2:0.301728808331;CUX2:0.297666570967;MYFfamily:0.296623406213;NFE2:0.292845518988;FOX{D1,D2}:0.288259006837;BACH2:0.284261777984;LHX3,4:0.280826000334;HIF1A:0.27608891328;RREB1:0.274241290894;NR1H4:0.266412656238;ZNF148:0.264718841631;GATA4:0.26367934598;IKZF1:0.263076508683;HAND1,2:0.261873852279;TFAP4:0.25977699757;CREB1:0.258577870886;NKX3-1:0.250426236615;TEF:0.2383718995;ZBTB6:0.228840186577;NFY{A,B,C}:0.217679399584;PAX8:0.204976298195;RFX1:0.203293927476;E2F1..5:0.199565317483;REST:0.194103707624;TEAD1:0.149838155016;SMAD1..7,9:0.13728919572;NFIL3:0.130248066128;TLX2:0.129075011908;POU2F1..3:0.11805943835;ZIC1..3:0.116594698409;RBPJ:0.0933025813685;ATF6:0.0901206677359;ZNF238:0.0898386829198;HSF1,2:0.0771104822074;GFI1B:0.0594800087789;HES1:0.0501834600046;MTF1:0.0313811103731;NKX3-2:0.0301705230765;HOX{A4,D4}:0.0299551805536;MYB:0.0263026105799;PBX1:0.0254605595746;AR:0.0134790922837;OCT4_SOX2{dimer}:0.00921189141826;FOXP3:-0.0248726586937;FOX{I1,J2}:-0.06027748785;POU5F1:-0.0863516017785;EVI1:-0.0946018943765;NFE2L1:-0.111715849292;RXR{A,B,G}_{NR1H2,PPAR}dimers:-0.148221471577;CRX:-0.152827712667;YY1:-0.154574167892;EBF1:-0.159678971658;HMGA1,2:-0.164063360777;STAT5{A,B}:-0.170129248048;ESRRA:-0.174929603508;KLF4:-0.175130042345;PRDM1:-0.185874447881;PITX1..3:-0.201997149212;UFEwm:-0.218967573311;DMAP1_NCOR{1,2}_SMARC:-0.222585976806;GLI1..3:-0.237829164035;NFATC1..3:-0.273804696513;RUNX1..3:-0.275706489609;TLX1..3_NFIC{dimer}:-0.296410974246;FOXM1:-0.303115537626;PAX4:-0.304101500309;ESR1:-0.3062410856;ALX4:-0.319796601118;CEBPA,B_DDIT3:-0.31985946145;ELF1,2,4:-0.324808366307;SPIB:-0.330927578282;MYBL2:-0.337738427014;HOXA9_MEIS1:-0.338037469855;AIRE:-0.350649390901;IRF7:-0.357203945627;HNF4A_NR2F1,2:-0.373435006411;HNF1A:-0.373913442389;PAX6:-0.376431527961;TGIF1:-0.379798534532;SPZ1:-0.397585796432;POU6F1:-0.403194429823;FOXA2:-0.40339286416;IKZF2:-0.403537304671;FOX{F1,F2,J1}:-0.405590162655;FOXL1:-0.442996554353;PAX2:-0.449615692913;NFKB1_REL_RELA:-0.453712996955;LMO2:-0.466444985845;FOXQ1:-0.472115221985;NKX2-3_NKX2-5:-0.482624661315;bHLH_family:-0.484159391469;MEF2{A,B,C,D}:-0.492151752763;PAX1,9:-0.496122148688;ALX1:-0.497004852118;SPI1:-0.503541994623;SRF:-0.509244921883;FOXP1:-0.517664634367;IRF1,2:-0.522746689515;RXRA_VDR{dimer}:-0.524597870619;HLF:-0.534239107979;T:-0.543346584001;FOXO1,3,4:-0.582002176341;TAL1_TCF{3,4,12}:-0.588797296461;NR3C1:-0.59486978866;NFE2L2:-0.59639527706;STAT2,4,6:-0.600924920305;NFIX:-0.626586999111;TOPORS:-0.631660442421;GCM1,2:-0.638881226307;TBP:-0.665867163577;POU1F1:-0.708361773852;ETS1,2:-0.710653162799;BPTF:-0.748454652956;NR5A1,2:-0.793185619556;NKX2-2,8:-0.816706473395;NKX6-1,2:-0.86966344405;FOXN1:-0.889690204332;GATA6:-0.90729815333;HOX{A5,B5}:-0.926950926789;MAFB:-0.98527718265;NR6A1:-0.990904550195;MYOD1:-1.00653766602;NANOG{mouse}:-1.12377574763;PPARG:-1.12396974314;CDX1,2,4:-1.16256037607;SNAI1..3:-1.27727379011;ZEB1:-1.41378104584;ARID5B:-1.57281827799;TBX4,5:-1.92632159807
|comment=
|created_by=
|creation_date=
|def=
|has_quality=
|is_a=EFO:0002091;;FF:0000002;;FF:0000103;;FF:0011143
|namespace=
|part_of=UBERON:0000011
}}
}}

Revision as of 15:39, 7 March 2012


Name:neurospheres - parasympathetic neuron derived, biol_rep3
Species:Mouse (Mus musculus)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueANATOMICAL SYSTEM
dev stageNA
sexNA
ageNA
cell typeNA
cell lineNA
companyNA
collaborationHideki Enomoto (RIKEN CDB)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberpara3
catalog numberNA
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-miRNeasy_Mini-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

CNhs13086

00
10
100
1000
10000
1001-0.0749
1002-0.116
1003-0.118
10040
1005-0.101
1006-0.0376
10070.121
10080
10090.00729
101-0.0159
10100
1011-0.108
10120
1013-0.123
1014-0.0851
10150.213
10160.442
10170
10180
10190
1020
10200.431
10210.198
1022-0.14
10230
1024-0.0313
1025-0.0525
10260
10270.267
10280
1029-0.115
103-0.0848
10300
10310.383
10320.0944
10330.148
10340
10350
1036-0.0746
10370
10380.0604
1039-0.17
1040
10400.103
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: CNhs13086

Jaspar motifP-value
MA0002.20.00263
MA0003.10.053
MA0004.10.982
MA0006.10.347
MA0007.10.617
MA0009.10.0363
MA0014.10.761
MA0017.17.01846e-4
MA0018.26.51267e-5
MA0019.10.944
MA0024.10.0374
MA0025.10.634
MA0027.10.961
MA0028.10.611
MA0029.10.572
MA0030.10.608
MA0031.10.579
MA0035.20.006
MA0038.10.441
MA0039.20.386
MA0040.10.943
MA0041.10.124
MA0042.10.509
MA0043.10.0101
MA0046.11.03915e-6
MA0047.20.0452
MA0048.10.883
MA0050.10.00316
MA0051.10.00936
MA0052.10.0712
MA0055.10.75
MA0057.10.263
MA0058.10.737
MA0059.10.172
MA0060.13.74419e-4
MA0061.10.0486
MA0062.20.767
MA0065.22.67924e-4
MA0066.10.213
MA0067.10.257
MA0068.10.338
MA0069.10.448
MA0070.10.0269
MA0071.10.279
MA0072.10.6
MA0073.10.941
MA0074.10.625
MA0076.10.244
MA0077.10.0264
MA0078.10.059
MA0079.20.244
MA0080.21.4951e-7
MA0081.10.747
MA0083.10.4
MA0084.10.72
MA0087.10.579
MA0088.10.837
MA0090.10.728
MA0091.10.911
MA0092.10.749
MA0093.10.936
MA0099.20.351
MA0100.10.554
MA0101.10.326
MA0102.20.759
MA0103.13.05695e-4
MA0104.20.834
MA0105.13.2462e-5
MA0106.10.671
MA0107.10.136
MA0108.20.116
MA0111.10.985
MA0112.24.1254e-5
MA0113.10.443
MA0114.14.37954e-4
MA0115.10.27
MA0116.17.7378e-4
MA0117.10.831
MA0119.10.11
MA0122.10.866
MA0124.10.877
MA0125.10.0803
MA0131.10.587
MA0135.10.332
MA0136.13.39243e-5
MA0137.20.467
MA0138.20.0827
MA0139.10.0245
MA0140.10.00695
MA0141.10.00632
MA0142.10.19
MA0143.10.0316
MA0144.10.667
MA0145.10.123
MA0146.10.641
MA0147.10.608
MA0148.10.0558
MA0149.10.741
MA0150.10.276
MA0152.10.796
MA0153.14.01314e-5
MA0154.10.00529
MA0155.10.554
MA0156.10.00762
MA0157.10.0657
MA0159.10.193
MA0160.10.158
MA0162.10.172
MA0163.10.00127
MA0164.10.886
MA0258.10.0292
MA0259.10.992



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: CNhs13086

Novel motifP-value
10.103
100.0603
1000.911
1010.709
1020.836
1030.0161
1040.859
1050.307
1060.0392
1070.114
1080.744
1090.0254
110.0643
1100.149
1110.00398
1120.0567
1130.647
1140.0424
1150.324
1160.484
1170.239
1180.522
1190.0343
120.704
1200.437
1210.177
1220.328
1230.617
1240.774
1250.907
1260.35
1270.5
1280.0701
1290.0866
130.0306
1300.65
1310.975
1320.378
1330.673
1340.598
1350.585
1360.793
1370.415
1380.71
1390.17
140.536
1400.0402
1410.112
1420.589
1430.867
1440.645
1450.233
1460.582
1470.753
1480.536
1490.118
150.0851
1500.489
1510.441
1520.127
1530.605
1540.711
1550.716
1560.00188
1570.254
1580.676
1590.0549
1600.164
1610.412
1620.898
1630.404
1640.118
1650.173
1660.642
1670.892
1680.716
1690.0131
170.0401
180.745
190.117
20.506
200.828
210.489
220.416
230.325
240.257
250.365
260.0447
270.245
280.582
290.274
30.0723
300.763
310.854
320.104
330.382
340.495
350.551
360.196
370.0706
380.253
390.457
40.739
400.341
410.912
420.246
430.173
440.11
450.521
460.158
470.118
480.161
490.164
50.174
500.739
510.465
520.319
530.489
540.545
550.554
560.517
570.251
580.0951
590.0461
60.799
600.12
610.329
620.0275
630.164
640.368
650.141
660.352
670.957
680.484
690.915
70.103
700.00924
710.0751
720.474
730.153
740.177
750.118
760.96
770.213
780.0536
790.108
80.097
800.703
810.451
820.0313
830.236
840.901
850.0246
860.345
870.408
880.519
890.0625
90.509
900.183
910.222
920.0568
930.292
940.218
950.124
960.33
970.939
980.163
990.157



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: CNhs13086


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)
0000107 (autonomic neuron)
0000133 (neurectodermal cell)
0000211 (electrically active cell)
0000221 (ectodermal cell)
0000255 (eukaryotic cell)
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)

UBERON: Anatomy
0000010 (peripheral nervous system)
0000011 (parasympathetic nervous system)
0000061 (anatomical structure)
0000073 (regional part of nervous system)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000480 (anatomical group)
0000922 (embryo)
0000923 (germ layer)
0000924 (ectoderm)
0001016 (nervous system)
0001017 (central nervous system)
0001062 (anatomical entity)
0002050 (embryonic structure)
0002410 (autonomic nervous system)
0002532 (epiblast (generic))
0004121 (ectoderm-derived structure)
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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