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|fonse_treatment_closure=
|fonse_treatment_closure=
|top_motifs=SREBF1,2:2.52146445158;SPIB:2.29639066021;NFE2L1:2.10306704052;GLI1..3:2.09752499454;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:1.70768130277;EBF1:1.68589608104;SPZ1:1.60741903731;SPI1:1.603107981;HAND1,2:1.55859806481;TFCP2:1.45283430478;PAX2:1.44657281541;FOS_FOS{B,L1}_JUN{B,D}:1.38852221555;NFE2L2:1.27953572108;IRF1,2:1.24721404683;TP53:1.22965873999;RUNX1..3:1.22453135757;IRF7:1.22244354309;BACH2:1.12814027365;POU2F1..3:1.08769039786;UFEwm:1.05941101052;RXRA_VDR{dimer}:1.04614817977;DMAP1_NCOR{1,2}_SMARC:1.04039412416;ETS1,2:1.02803794376;ZNF423:0.992806635517;NFKB1_REL_RELA:0.984284890532;STAT2,4,6:0.981320620983;ATF6:0.941718654197;ESR1:0.902530553657;NR6A1:0.893429972665;IKZF1:0.849973911162;ALX1:0.804565211928;NR1H4:0.787491533941;FOXL1:0.76283276092;GTF2A1,2:0.729900258865;FOXM1:0.725394005191;HOXA9_MEIS1:0.668473347237;HLF:0.6604750903;TFAP2{A,C}:0.640856704244;CEBPA,B_DDIT3:0.627141683797;TFAP4:0.585789405718;ARID5B:0.577366598844;NFE2:0.576968006475;NFIL3:0.576538825741;NKX2-2,8:0.48679046885;ALX4:0.458887213253;EN1,2:0.446892278021;EP300:0.424464696558;bHLH_family:0.403099395033;NKX3-1:0.391993863429;SRF:0.3166541265;ZNF238:0.315806571796;HES1:0.267465229463;HOX{A4,D4}:0.21949884251;ATF4:0.209972564943;HOX{A5,B5}:0.188886919961;GATA4:0.184695463084;ESRRA:0.183647302423;MTF1:0.18080385065;SMAD1..7,9:0.174910681762;POU5F1:0.163653244402;FOX{F1,F2,J1}:0.145851953722;FOXP3:0.114176748568;ZNF148:0.0904542325844;FOXO1,3,4:0.0882516742021;NKX3-2:0.0695706509393;TEF:0.015902019609;ZBTB6:0.0135773627488;ELF1,2,4:0.00464116020936;KLF4:0.00109218410145;TBP:-0.0155377530995;NKX2-3_NKX2-5:-0.0208288905739;PAX4:-0.0475924165409;TLX1..3_NFIC{dimer}:-0.0636932454114;PRDM1:-0.0838388831546;GCM1,2:-0.085314004981;RXR{A,B,G}:-0.113418809896;JUN:-0.116605135931;ZIC1..3:-0.129467927907;VSX1,2:-0.141846354779;RREB1:-0.15298543602;MYB:-0.166409835368;TEAD1:-0.168533414873;IKZF2:-0.176761196506;REST:-0.204917584223;POU6F1:-0.258703768814;OCT4_SOX2{dimer}:-0.261974290502;HMX1:-0.288066037883;NFATC1..3:-0.296933666468;HNF4A_NR2F1,2:-0.301605237206;TAL1_TCF{3,4,12}:-0.322933951675;ZBTB16:-0.350269181854;FOSL2:-0.36061831304;STAT5{A,B}:-0.396480932483;MTE{core}:-0.398919916225;MYFfamily:-0.431801947171;RFX1:-0.436296436318;FOXQ1:-0.522874308971;HIC1:-0.563737928539;MEF2{A,B,C,D}:-0.567424147366;CDC5L:-0.58389699398;PATZ1:-0.598771007301;MAFB:-0.628316461427;XCPE1{core}:-0.636805961028;GTF2I:-0.643962890247;HNF1A:-0.661426523626;HIF1A:-0.661716929356;NR5A1,2:-0.664586480648;TOPORS:-0.68431494686;ZEB1:-0.690519901061;RORA:-0.69144968334;SP1:-0.693033057427;PAX8:-0.714286888718;MYOD1:-0.715554826806;ADNP_IRX_SIX_ZHX:-0.72966653099;LHX3,4:-0.73627141659;NHLH1,2:-0.745939099506;PPARG:-0.763541492553;ATF2:-0.765034026532;ZNF384:-0.775733256549;RXR{A,B,G}_{NR1H2,PPAR}dimers:-0.781768993184;GFI1B:-0.805389193342;POU3F1..4:-0.807502275783;SOX17:-0.82033053143;RFX2..5_RFXANK_RFXAP:-0.846437301182;ELK1,4_GABP{A,B1}:-0.863215940895;TLX2:-0.866418964247;CRX:-0.887574826252;PRRX1,2:-0.892519974885;PAX5:-0.910690066214;PDX1:-0.914890385754;HSF1,2:-0.916496094361;SOX2:-0.924056480029;TBX4,5:-0.961130715978;NANOG{mouse}:-0.971245372901;NR3C1:-0.981102052657;NANOG:-0.998876884596;FOXN1:-1.0038149525;DBP:-1.00699548633;MZF1:-1.02834316532;TFAP2B:-1.040329213;HBP1_HMGB_SSRP1_UBTF:-1.0505847948;GZF1:-1.06110924797;GATA6:-1.0682370184;EGR1..3:-1.08406391322;E2F1..5:-1.09807839071;EVI1:-1.10842995521;FOX{I1,J2}:-1.11477189212;SNAI1..3:-1.15060576457;PAX1,9:-1.17032079153;FOX{D1,D2}:-1.173885189;RBPJ:-1.17873709959;MAZ:-1.1802873549;ZFP161:-1.18546987953;ATF5_CREB3:-1.18832189114;MED-1{core}:-1.1906675899;TFDP1:-1.20627285596;LMO2:-1.21809109991;HMGA1,2:-1.26764958447;ONECUT1,2:-1.28961208926;AIRE:-1.29559035093;AHR_ARNT_ARNT2:-1.3139600333;LEF1_TCF7_TCF7L1,2:-1.32635749927;SOX{8,9,10}:-1.35889999434;AR:-1.37353980275;YY1:-1.38189083835;GFI1:-1.39085177688;STAT1,3:-1.40665897428;TGIF1:-1.44679627547;PITX1..3:-1.4723678093;FOXA2:-1.47498864142;POU1F1:-1.47682737395;BREu{core}:-1.56197045092;CREB1:-1.56569911868;NRF1:-1.58140873708;SOX5:-1.60450552974;FOXP1:-1.70246972844;NKX6-1,2:-1.72796431045;BPTF:-1.86572002475;ZNF143:-1.9005961148;MYBL2:-1.9571233457;CUX2:-1.9688034727;T:-1.99222363555;PAX6:-2.1607139004;CDX1,2,4:-2.23325389994;PBX1:-2.25763568637;NFIX:-2.26168799694;FOXD3:-2.28178276202;NKX2-1,4:-2.30307738366;NFY{A,B,C}:-2.48260902074
|top_motifs=SREBF1,2:2.52146445158;SPIB:2.29639066021;NFE2L1:2.10306704052;GLI1..3:2.09752499454;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:1.70768130277;EBF1:1.68589608104;SPZ1:1.60741903731;SPI1:1.603107981;HAND1,2:1.55859806481;TFCP2:1.45283430478;PAX2:1.44657281541;FOS_FOS{B,L1}_JUN{B,D}:1.38852221555;NFE2L2:1.27953572108;IRF1,2:1.24721404683;TP53:1.22965873999;RUNX1..3:1.22453135757;IRF7:1.22244354309;BACH2:1.12814027365;POU2F1..3:1.08769039786;UFEwm:1.05941101052;RXRA_VDR{dimer}:1.04614817977;DMAP1_NCOR{1,2}_SMARC:1.04039412416;ETS1,2:1.02803794376;ZNF423:0.992806635517;NFKB1_REL_RELA:0.984284890532;STAT2,4,6:0.981320620983;ATF6:0.941718654197;ESR1:0.902530553657;NR6A1:0.893429972665;IKZF1:0.849973911162;ALX1:0.804565211928;NR1H4:0.787491533941;FOXL1:0.76283276092;GTF2A1,2:0.729900258865;FOXM1:0.725394005191;HOXA9_MEIS1:0.668473347237;HLF:0.6604750903;TFAP2{A,C}:0.640856704244;CEBPA,B_DDIT3:0.627141683797;TFAP4:0.585789405718;ARID5B:0.577366598844;NFE2:0.576968006475;NFIL3:0.576538825741;NKX2-2,8:0.48679046885;ALX4:0.458887213253;EN1,2:0.446892278021;EP300:0.424464696558;bHLH_family:0.403099395033;NKX3-1:0.391993863429;SRF:0.3166541265;ZNF238:0.315806571796;HES1:0.267465229463;HOX{A4,D4}:0.21949884251;ATF4:0.209972564943;HOX{A5,B5}:0.188886919961;GATA4:0.184695463084;ESRRA:0.183647302423;MTF1:0.18080385065;SMAD1..7,9:0.174910681762;POU5F1:0.163653244402;FOX{F1,F2,J1}:0.145851953722;FOXP3:0.114176748568;ZNF148:0.0904542325844;FOXO1,3,4:0.0882516742021;NKX3-2:0.0695706509393;TEF:0.015902019609;ZBTB6:0.0135773627488;ELF1,2,4:0.00464116020936;KLF4:0.00109218410145;TBP:-0.0155377530995;NKX2-3_NKX2-5:-0.0208288905739;PAX4:-0.0475924165409;TLX1..3_NFIC{dimer}:-0.0636932454114;PRDM1:-0.0838388831546;GCM1,2:-0.085314004981;RXR{A,B,G}:-0.113418809896;JUN:-0.116605135931;ZIC1..3:-0.129467927907;VSX1,2:-0.141846354779;RREB1:-0.15298543602;MYB:-0.166409835368;TEAD1:-0.168533414873;IKZF2:-0.176761196506;REST:-0.204917584223;POU6F1:-0.258703768814;OCT4_SOX2{dimer}:-0.261974290502;HMX1:-0.288066037883;NFATC1..3:-0.296933666468;HNF4A_NR2F1,2:-0.301605237206;TAL1_TCF{3,4,12}:-0.322933951675;ZBTB16:-0.350269181854;FOSL2:-0.36061831304;STAT5{A,B}:-0.396480932483;MTE{core}:-0.398919916225;MYFfamily:-0.431801947171;RFX1:-0.436296436318;FOXQ1:-0.522874308971;HIC1:-0.563737928539;MEF2{A,B,C,D}:-0.567424147366;CDC5L:-0.58389699398;PATZ1:-0.598771007301;MAFB:-0.628316461427;XCPE1{core}:-0.636805961028;GTF2I:-0.643962890247;HNF1A:-0.661426523626;HIF1A:-0.661716929356;NR5A1,2:-0.664586480648;TOPORS:-0.68431494686;ZEB1:-0.690519901061;RORA:-0.69144968334;SP1:-0.693033057427;PAX8:-0.714286888718;MYOD1:-0.715554826806;ADNP_IRX_SIX_ZHX:-0.72966653099;LHX3,4:-0.73627141659;NHLH1,2:-0.745939099506;PPARG:-0.763541492553;ATF2:-0.765034026532;ZNF384:-0.775733256549;RXR{A,B,G}_{NR1H2,PPAR}dimers:-0.781768993184;GFI1B:-0.805389193342;POU3F1..4:-0.807502275783;SOX17:-0.82033053143;RFX2..5_RFXANK_RFXAP:-0.846437301182;ELK1,4_GABP{A,B1}:-0.863215940895;TLX2:-0.866418964247;CRX:-0.887574826252;PRRX1,2:-0.892519974885;PAX5:-0.910690066214;PDX1:-0.914890385754;HSF1,2:-0.916496094361;SOX2:-0.924056480029;TBX4,5:-0.961130715978;NANOG{mouse}:-0.971245372901;NR3C1:-0.981102052657;NANOG:-0.998876884596;FOXN1:-1.0038149525;DBP:-1.00699548633;MZF1:-1.02834316532;TFAP2B:-1.040329213;HBP1_HMGB_SSRP1_UBTF:-1.0505847948;GZF1:-1.06110924797;GATA6:-1.0682370184;EGR1..3:-1.08406391322;E2F1..5:-1.09807839071;EVI1:-1.10842995521;FOX{I1,J2}:-1.11477189212;SNAI1..3:-1.15060576457;PAX1,9:-1.17032079153;FOX{D1,D2}:-1.173885189;RBPJ:-1.17873709959;MAZ:-1.1802873549;ZFP161:-1.18546987953;ATF5_CREB3:-1.18832189114;MED-1{core}:-1.1906675899;TFDP1:-1.20627285596;LMO2:-1.21809109991;HMGA1,2:-1.26764958447;ONECUT1,2:-1.28961208926;AIRE:-1.29559035093;AHR_ARNT_ARNT2:-1.3139600333;LEF1_TCF7_TCF7L1,2:-1.32635749927;SOX{8,9,10}:-1.35889999434;AR:-1.37353980275;YY1:-1.38189083835;GFI1:-1.39085177688;STAT1,3:-1.40665897428;TGIF1:-1.44679627547;PITX1..3:-1.4723678093;FOXA2:-1.47498864142;POU1F1:-1.47682737395;BREu{core}:-1.56197045092;CREB1:-1.56569911868;NRF1:-1.58140873708;SOX5:-1.60450552974;FOXP1:-1.70246972844;NKX6-1,2:-1.72796431045;BPTF:-1.86572002475;ZNF143:-1.9005961148;MYBL2:-1.9571233457;CUX2:-1.9688034727;T:-1.99222363555;PAX6:-2.1607139004;CDX1,2,4:-2.23325389994;PBX1:-2.25763568637;NFIX:-2.26168799694;FOXD3:-2.28178276202;NKX2-1,4:-2.30307738366;NFY{A,B,C}:-2.48260902074
|comment=
|created_by=
|creation_date=
|def=
|has_quality=
|is_a=EFO:0002091;;FF:0000002;;FF:0000103;;FF:0000112
|namespace=FANTOM5
|part_of=
}}
}}

Revision as of 15:38, 7 March 2012


Name:Mouse Mesenchymal stem cells - bone marrow derived, donor2
Species:Mouse (Mus musculus)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuebone marrow
dev stageNA
sexNA
ageNA
cell typemesenchymal stem cell
cell lineNA
companySciencell/3H
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberRNAMCS2
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

CNhs12633

00
10
100
1000
10000.0777
1001-0.0631
10020.00981
1003-0.102
10040
10050
10060.145
1007-0.406
10080
1009-0.19
101-0.472
10100
10110.119
10120
10130.187
1014-0.0874
1015-0.0653
1016-0.321
10170
10180
10190
1020
10200.695
10210
1022-0.124
10230
1024-0.14
1025-0.0611
10260
10270
10280
1029-0.176
1030
10300
1031-0.111
1032-0.177
10330
10340
10350
1036-0.0393
10370
1038-0.298
1039-0.0323
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: CNhs12633

Jaspar motifP-value
MA0002.24.88808e-6
MA0003.10.125
MA0004.10.426
MA0006.10.493
MA0007.10.639
MA0009.10.669
MA0014.10.816
MA0017.10.234
MA0018.20.0802
MA0019.10.965
MA0024.10.0051
MA0025.10.765
MA0027.10.539
MA0028.10.485
MA0029.10.728
MA0030.10.204
MA0031.10.771
MA0035.20.244
MA0038.14.23469e-5
MA0039.20.995
MA0040.10.589
MA0041.10.541
MA0042.10.712
MA0043.10.0782
MA0046.16.88112e-6
MA0047.20.715
MA0048.10.723
MA0050.12.07149e-5
MA0051.14.77704e-4
MA0052.10.0562
MA0055.10.912
MA0057.10.314
MA0058.10.255
MA0059.10.156
MA0060.11.20161e-12
MA0061.10.0274
MA0062.20.537
MA0065.20.00696
MA0066.10.0124
MA0067.10.658
MA0068.10.285
MA0069.10.912
MA0070.10.172
MA0071.10.149
MA0072.10.43
MA0073.10.643
MA0074.10.029
MA0076.10.23
MA0077.10.728
MA0078.10.66
MA0079.20.461
MA0080.29.69998e-14
MA0081.10.00374
MA0083.10.384
MA0084.10.76
MA0087.10.942
MA0088.10.294
MA0090.10.665
MA0091.10.226
MA0092.10.392
MA0093.10.457
MA0099.20.00109
MA0100.10.928
MA0101.10.172
MA0102.20.513
MA0103.10.6
MA0104.20.841
MA0105.10.00166
MA0106.10.23
MA0107.10.164
MA0108.20.0922
MA0111.10.324
MA0112.27.3374e-5
MA0113.10.313
MA0114.10.321
MA0115.10.519
MA0116.10.00101
MA0117.10.777
MA0119.10.206
MA0122.10.718
MA0124.10.222
MA0125.10.0659
MA0131.10.12
MA0135.10.232
MA0136.15.07696e-10
MA0137.20.879
MA0138.20.526
MA0139.10.0593
MA0140.10.32
MA0141.10.0299
MA0142.10.318
MA0143.10.39
MA0144.10.405
MA0145.10.0392
MA0146.10.0121
MA0147.10.83
MA0148.10.777
MA0149.10.159
MA0150.10.01
MA0152.10.305
MA0153.15.91161e-4
MA0154.10.00461
MA0155.10.378
MA0156.10.00275
MA0157.10.538
MA0159.10.00245
MA0160.10.148
MA0162.10.184
MA0163.16.16997e-5
MA0164.10.943
MA0258.10.00576
MA0259.10.541



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: CNhs12633

Novel motifP-value
10.126
100.0714
1000.78
1010.936
1020.63
1030.0842
1040.949
1050.756
1060.0244
1070.201
1080.5
1090.0281
110.059
1100.0881
1110.0105
1120.061
1130.891
1140.0248
1150.267
1160.141
1170.0914
1180.297
1190.192
120.779
1200.0301
1210.503
1220.868
1230.848
1240.663
1250.115
1260.417
1270.379
1280.0332
1290.118
130.109
1300.994
1310.0348
1320.563
1330.068
1340.655
1350.928
1360.846
1370.275
1380.393
1390.0821
140.599
1400.313
1410.187
1420.672
1430.00713
1440.971
1450.248
1460.7
1470.827
1480.0845
1490.0129
150.0913
1500.179
1510.223
1520.182
1530.809
1540.72
1550.411
1560.422
1570.505
1580.599
1590.923
1600.478
1610.0706
1620.842
1630.892
1640.159
1650.0588
1660.835
1670.42
1680.711
1690.00484
170.0371
180.0877
190.135
20.521
200.526
210.442
220.141
230.0929
240.142
250.752
260.0134
270.357
280.674
290.0968
30.0361
300.78
310.297
320.117
330.409
340.388
350.516
360.00894
370.0533
380.193
390.549
40.281
400.0735
410.292
420.295
430.0508
440.0521
450.486
460.0725
470.178
480.2
490.07
50.185
500.491
510.702
520.38
530.888
540.671
550.397
560.18
570.54
580.346
590.00906
60.667
600.134
610.484
620.117
630.117
640.251
650.0494
660.734
670.271
680.105
690.273
70.462
703.23278e-4
710.0341
720.186
730.0726
740.827
750.0681
760.401
770.139
780.0862
790.593
80.0691
800.678
810.168
820.093
830.802
840.608
850.0856
860.471
870.325
880.836
890.0523
90.448
900.286
910.174
920.0958
930.118
940.664
950.0721
960.669
970.832
980.0962
990.59



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: CNhs12633


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)
0000034 (stem cell)
0000048 (multi fate stem cell)
0000134 (mesenchymal cell)
0000219 (motile cell)
0000255 (eukaryotic cell)
0000548 (animal cell)
0000723 (somatic stem cell)
0002092 (bone marrow cell)
0002320 (connective tissue cell)
0002371 (somatic cell)
0002540 (mesenchymal stem cell of the bone marrow)

UBERON: Anatomy
0000061 (anatomical structure)
0000062 (organ)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000479 (tissue)
0000480 (anatomical group)
0000922 (embryo)
0000923 (germ layer)
0000926 (mesoderm)
0001062 (anatomical entity)
0001434 (skeletal system)
0001474 (bone element)
0002050 (embryonic structure)
0002193 (hemolymphoid system)
0002204 (musculoskeletal system)
0002371 (bone marrow)
0002384 (connective tissue)
0002390 (hematopoietic system)
0002405 (immune system)
0002532 (epiblast (generic))
0004120 (mesoderm-derived structure)
0004765 (skeletal element)
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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