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Difference between revisions of "FF:12460-132E3"

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Line 100: Line 100:
 
|top_motifs=NKX3-1:2.82742501064;HAND1,2:2.31760427084;CDC5L:2.05421866551;GLI1..3:1.96313368836;ALX4:1.89536674788;TEF:1.81787023222;UFEwm:1.79591534373;FOXP3:1.49567291675;BACH2:1.36053696439;NFE2L1:1.35507925255;NFE2L2:1.33774671721;HMX1:1.26330264702;HES1:1.26257981667;YY1:1.21089780065;HSF1,2:1.17109202274;TP53:1.1685994567;IRF7:1.1445537979;NFE2:1.07259188108;SRF:1.05249921565;IKZF2:1.02574069079;CDX1,2,4:0.951576417241;GCM1,2:0.909993467112;TEAD1:0.892592285005;ZNF238:0.891266263761;POU1F1:0.8677684272;ELK1,4_GABP{A,B1}:0.844224549107;ZBTB16:0.827470138228;ALX1:0.817025491812;PDX1:0.793682550379;NR3C1:0.737254484954;ZNF384:0.73183158061;NKX6-1,2:0.724201308146;FOS_FOS{B,L1}_JUN{B,D}:0.720427104329;TLX1..3_NFIC{dimer}:0.717133219715;FOXL1:0.710194113322;RUNX1..3:0.664801544847;ATF4:0.615976611094;EVI1:0.561056100785;E2F1..5:0.542779663218;ZNF423:0.539661884383;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:0.536271348603;RXR{A,B,G}:0.5206905365;NKX2-2,8:0.514274022747;NANOG{mouse}:0.489155216789;HMGA1,2:0.478026249993;SOX17:0.474326062146;CEBPA,B_DDIT3:0.455285791481;FOXM1:0.453388381892;NFATC1..3:0.438421525848;HIF1A:0.42689898702;POU3F1..4:0.406126001667;SREBF1,2:0.401030561907;NKX2-3_NKX2-5:0.38914711909;MYBL2:0.374050949546;DMAP1_NCOR{1,2}_SMARC:0.331949784066;SOX5:0.29762760486;ONECUT1,2:0.289933675291;POU2F1..3:0.288328270236;MTE{core}:0.28646405669;EN1,2:0.273943096101;ESR1:0.272116811493;HOX{A4,D4}:0.270256045288;GFI1B:0.259939635629;MYB:0.25501788788;SMAD1..7,9:0.244657854238;HLF:0.235990670442;ATF6:0.233902810625;KLF4:0.232068984374;NR6A1:0.206663013826;NFIL3:0.198829798306;STAT1,3:0.188077371237;ELF1,2,4:0.176288159624;STAT2,4,6:0.163396839162;RXR{A,B,G}_{NR1H2,PPAR}dimers:0.16076635887;PAX8:0.137754847152;PAX4:0.126884025637;TFAP4:0.112905034764;ZNF143:0.083184451565;GZF1:0.0421942661623;TFCP2:0.0395015590759;IKZF1:0.00240688368382;FOSL2:-0.0200758157751;POU5F1:-0.0232714791782;NR1H4:-0.023854851057;NKX2-1,4:-0.0256045804538;IRF1,2:-0.0275546872924;EBF1:-0.0285161669102;RFX1:-0.0308035797699;RBPJ:-0.0320950504388;GATA4:-0.0415802678214;SPIB:-0.0504219955168;GFI1:-0.0525875192639;HBP1_HMGB_SSRP1_UBTF:-0.0622026205819;HOX{A5,B5}:-0.0708494113828;HOXA9_MEIS1:-0.111178660693;GTF2I:-0.122826996263;GTF2A1,2:-0.152144184922;FOXD3:-0.155458861119;NKX3-2:-0.162344670794;NRF1:-0.179234178537;PAX5:-0.180588641759;NFY{A,B,C}:-0.232416031156;NFKB1_REL_RELA:-0.30122647292;NR5A1,2:-0.324601555257;FOX{F1,F2,J1}:-0.324873435261;SPI1:-0.334665542931;FOXQ1:-0.337155564917;HNF4A_NR2F1,2:-0.340258184164;AHR_ARNT_ARNT2:-0.341947515701;TBP:-0.362024342952;T:-0.400244290206;ADNP_IRX_SIX_ZHX:-0.40429916946;XCPE1{core}:-0.419742876377;HIC1:-0.437097531697;REST:-0.440657601037;CREB1:-0.443232908501;FOXP1:-0.444166410409;PITX1..3:-0.451578322108;MAFB:-0.471221345277;SOX{8,9,10}:-0.479047487883;TAL1_TCF{3,4,12}:-0.492980264766;TOPORS:-0.525091039336;ATF5_CREB3:-0.5322387754;ARID5B:-0.533184833971;ZBTB6:-0.545111187133;RREB1:-0.553895223241;MAZ:-0.560821803253;TFAP2{A,C}:-0.576338050461;PAX6:-0.584467261635;DBP:-0.58799453308;FOXO1,3,4:-0.589104399571;HNF1A:-0.593884355633;ZNF148:-0.600551058579;PPARG:-0.627743272788;RFX2..5_RFXANK_RFXAP:-0.629247495395;RXRA_VDR{dimer}:-0.630077377141;MEF2{A,B,C,D}:-0.633558698828;bHLH_family:-0.634519269162;JUN:-0.639635704469;PRDM1:-0.654537456284;OCT4_SOX2{dimer}:-0.661619705022;ETS1,2:-0.68102443022;PRRX1,2:-0.69031419515;TFDP1:-0.69164557233;EP300:-0.704218596378;RORA:-0.71079873302;MZF1:-0.715533341105;TFAP2B:-0.737282312154;LHX3,4:-0.759697345667;BPTF:-0.760565883801;AR:-0.766926296122;EGR1..3:-0.774860421629;FOXA2:-0.78823762283;FOXN1:-0.810536699715;PATZ1:-0.823099324167;ZFP161:-0.837388533986;AIRE:-0.845777275155;FOX{D1,D2}:-0.855142882616;BREu{core}:-0.895081641582;CRX:-0.972821077641;ATF2:-0.977805240046;MED-1{core}:-0.980251889473;MTF1:-0.981952282053;SP1:-0.989588878501;PAX2:-0.991937065323;FOX{I1,J2}:-0.994059450234;TBX4,5:-1.00518010282;ZIC1..3:-1.03528270747;POU6F1:-1.04834266575;SOX2:-1.05122469717;NFIX:-1.0795989536;PAX1,9:-1.08764761798;ESRRA:-1.08960193777;NHLH1,2:-1.11334012365;STAT5{A,B}:-1.17052007306;TLX2:-1.17451060849;NANOG:-1.25293730778;VSX1,2:-1.29252397023;MYFfamily:-1.31633383559;CUX2:-1.36675203991;GATA6:-1.37309713403;PBX1:-1.38209715814;TGIF1:-1.42689309361;LEF1_TCF7_TCF7L1,2:-1.51712338658;SPZ1:-1.64974369049;ZEB1:-1.83999719106;SNAI1..3:-2.01330055918;LMO2:-2.24617853197;MYOD1:-2.99143663937
 
|top_motifs=NKX3-1:2.82742501064;HAND1,2:2.31760427084;CDC5L:2.05421866551;GLI1..3:1.96313368836;ALX4:1.89536674788;TEF:1.81787023222;UFEwm:1.79591534373;FOXP3:1.49567291675;BACH2:1.36053696439;NFE2L1:1.35507925255;NFE2L2:1.33774671721;HMX1:1.26330264702;HES1:1.26257981667;YY1:1.21089780065;HSF1,2:1.17109202274;TP53:1.1685994567;IRF7:1.1445537979;NFE2:1.07259188108;SRF:1.05249921565;IKZF2:1.02574069079;CDX1,2,4:0.951576417241;GCM1,2:0.909993467112;TEAD1:0.892592285005;ZNF238:0.891266263761;POU1F1:0.8677684272;ELK1,4_GABP{A,B1}:0.844224549107;ZBTB16:0.827470138228;ALX1:0.817025491812;PDX1:0.793682550379;NR3C1:0.737254484954;ZNF384:0.73183158061;NKX6-1,2:0.724201308146;FOS_FOS{B,L1}_JUN{B,D}:0.720427104329;TLX1..3_NFIC{dimer}:0.717133219715;FOXL1:0.710194113322;RUNX1..3:0.664801544847;ATF4:0.615976611094;EVI1:0.561056100785;E2F1..5:0.542779663218;ZNF423:0.539661884383;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:0.536271348603;RXR{A,B,G}:0.5206905365;NKX2-2,8:0.514274022747;NANOG{mouse}:0.489155216789;HMGA1,2:0.478026249993;SOX17:0.474326062146;CEBPA,B_DDIT3:0.455285791481;FOXM1:0.453388381892;NFATC1..3:0.438421525848;HIF1A:0.42689898702;POU3F1..4:0.406126001667;SREBF1,2:0.401030561907;NKX2-3_NKX2-5:0.38914711909;MYBL2:0.374050949546;DMAP1_NCOR{1,2}_SMARC:0.331949784066;SOX5:0.29762760486;ONECUT1,2:0.289933675291;POU2F1..3:0.288328270236;MTE{core}:0.28646405669;EN1,2:0.273943096101;ESR1:0.272116811493;HOX{A4,D4}:0.270256045288;GFI1B:0.259939635629;MYB:0.25501788788;SMAD1..7,9:0.244657854238;HLF:0.235990670442;ATF6:0.233902810625;KLF4:0.232068984374;NR6A1:0.206663013826;NFIL3:0.198829798306;STAT1,3:0.188077371237;ELF1,2,4:0.176288159624;STAT2,4,6:0.163396839162;RXR{A,B,G}_{NR1H2,PPAR}dimers:0.16076635887;PAX8:0.137754847152;PAX4:0.126884025637;TFAP4:0.112905034764;ZNF143:0.083184451565;GZF1:0.0421942661623;TFCP2:0.0395015590759;IKZF1:0.00240688368382;FOSL2:-0.0200758157751;POU5F1:-0.0232714791782;NR1H4:-0.023854851057;NKX2-1,4:-0.0256045804538;IRF1,2:-0.0275546872924;EBF1:-0.0285161669102;RFX1:-0.0308035797699;RBPJ:-0.0320950504388;GATA4:-0.0415802678214;SPIB:-0.0504219955168;GFI1:-0.0525875192639;HBP1_HMGB_SSRP1_UBTF:-0.0622026205819;HOX{A5,B5}:-0.0708494113828;HOXA9_MEIS1:-0.111178660693;GTF2I:-0.122826996263;GTF2A1,2:-0.152144184922;FOXD3:-0.155458861119;NKX3-2:-0.162344670794;NRF1:-0.179234178537;PAX5:-0.180588641759;NFY{A,B,C}:-0.232416031156;NFKB1_REL_RELA:-0.30122647292;NR5A1,2:-0.324601555257;FOX{F1,F2,J1}:-0.324873435261;SPI1:-0.334665542931;FOXQ1:-0.337155564917;HNF4A_NR2F1,2:-0.340258184164;AHR_ARNT_ARNT2:-0.341947515701;TBP:-0.362024342952;T:-0.400244290206;ADNP_IRX_SIX_ZHX:-0.40429916946;XCPE1{core}:-0.419742876377;HIC1:-0.437097531697;REST:-0.440657601037;CREB1:-0.443232908501;FOXP1:-0.444166410409;PITX1..3:-0.451578322108;MAFB:-0.471221345277;SOX{8,9,10}:-0.479047487883;TAL1_TCF{3,4,12}:-0.492980264766;TOPORS:-0.525091039336;ATF5_CREB3:-0.5322387754;ARID5B:-0.533184833971;ZBTB6:-0.545111187133;RREB1:-0.553895223241;MAZ:-0.560821803253;TFAP2{A,C}:-0.576338050461;PAX6:-0.584467261635;DBP:-0.58799453308;FOXO1,3,4:-0.589104399571;HNF1A:-0.593884355633;ZNF148:-0.600551058579;PPARG:-0.627743272788;RFX2..5_RFXANK_RFXAP:-0.629247495395;RXRA_VDR{dimer}:-0.630077377141;MEF2{A,B,C,D}:-0.633558698828;bHLH_family:-0.634519269162;JUN:-0.639635704469;PRDM1:-0.654537456284;OCT4_SOX2{dimer}:-0.661619705022;ETS1,2:-0.68102443022;PRRX1,2:-0.69031419515;TFDP1:-0.69164557233;EP300:-0.704218596378;RORA:-0.71079873302;MZF1:-0.715533341105;TFAP2B:-0.737282312154;LHX3,4:-0.759697345667;BPTF:-0.760565883801;AR:-0.766926296122;EGR1..3:-0.774860421629;FOXA2:-0.78823762283;FOXN1:-0.810536699715;PATZ1:-0.823099324167;ZFP161:-0.837388533986;AIRE:-0.845777275155;FOX{D1,D2}:-0.855142882616;BREu{core}:-0.895081641582;CRX:-0.972821077641;ATF2:-0.977805240046;MED-1{core}:-0.980251889473;MTF1:-0.981952282053;SP1:-0.989588878501;PAX2:-0.991937065323;FOX{I1,J2}:-0.994059450234;TBX4,5:-1.00518010282;ZIC1..3:-1.03528270747;POU6F1:-1.04834266575;SOX2:-1.05122469717;NFIX:-1.0795989536;PAX1,9:-1.08764761798;ESRRA:-1.08960193777;NHLH1,2:-1.11334012365;STAT5{A,B}:-1.17052007306;TLX2:-1.17451060849;NANOG:-1.25293730778;VSX1,2:-1.29252397023;MYFfamily:-1.31633383559;CUX2:-1.36675203991;GATA6:-1.37309713403;PBX1:-1.38209715814;TGIF1:-1.42689309361;LEF1_TCF7_TCF7L1,2:-1.51712338658;SPZ1:-1.64974369049;ZEB1:-1.83999719106;SNAI1..3:-2.01330055918;LMO2:-2.24617853197;MYOD1:-2.99143663937
 
|xref=
 
|xref=
 +
|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_mouse;search_select_hide=table111:12460-132E3;search_select_hide=table117:12460-132E3
 
}}
 
}}

Latest revision as of 09:39, 4 June 2020


Name:ST2 (Mesenchymal stem cells) cells, medium change (without induction)
Species:Mouse (Mus musculus)
Library ID:CNhs13275
Sample type:time courses
Genomic View: UCSC
CAGEd-oPOSSUM:link
ZENBU report :link
Additional information
Sample information
strainNA
tissuebone marrow
dev stageNA
sexNA
ageNA
cell typemesenchymal stem cell
cell lineST2
companyNA
collaborationYasushi Okazaki (Saitama medical college)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberNA
sample typeNA
extraction protocol (Details)NA

CAGE Accession numbers
MethodSample accession id
CAGE  SAMD00005712
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs13275 CAGE DRX008906 DRR009780
Accession ID Mm9

Library idBAMCTSS
CNhs13275 DRZ001205 DRZ002588
Accession ID Mm10

Library idBAMCTSS
CNhs13275 DRZ012555 DRZ013938
Download raw sequence, BAM & CTSS
Mm9
FastaBAMCTSS
downloaddownloaddonwload
Mm10
BAMCTSS
downloaddonwload


Relative expression to median (log10)


Transcription factors with enriched expression in this sampleRanked list of transcription factor promoter expression in this sample relative to the median expression in the FANTOM5 collection is shown. Value is log10 transformed.



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

CNhs13275

00
10
100
1000
10000.236
1001-0.0631
1002-0.0655
10030.173
10040
10050
1006-0.142
1007-0.0401
10080
10090.653
101-0.024
10100
1011-0.237
10120
10130.0697
1014-0.0851
10150.171
10160.113
10170
10180
10190
1020
10200.1
10210.182
1022-0.124
10230
1024-0.307
10250
10260
1027-0.048
10280.1
1029-0.176
1030.45
10300
1031-0.446
1032-0.167
10330.1
10340
10350
10360.179
10370
10380.0302
1039-0.0646
1040
10400.31
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



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: CNhs13275

Jaspar motifP-value
MA0002.20.187
MA0003.10.713
MA0004.10.432
MA0006.10.567
MA0007.10.698
MA0009.10.779
MA0014.10.242
MA0017.10.482
MA0018.20.1
MA0019.10.885
MA0024.10.288
MA0025.10.763
MA0027.10.35
MA0028.10.00164
MA0029.10.52
MA0030.10.267
MA0031.10.376
MA0035.20.00311
MA0038.10.737
MA0039.20.924
MA0040.10.263
MA0041.10.706
MA0042.10.236
MA0043.10.672
MA0046.16.82727e-8
MA0047.20.24
MA0048.18.77558e-4
MA0050.10.752
MA0051.10.992
MA0052.12.9933e-4
MA0055.16.42822e-5
MA0057.10.204
MA0058.10.155
MA0059.10.165
MA0060.10.0236
MA0061.10.264
MA0062.24.92563e-4
MA0065.20.109
MA0066.10.242
MA0067.10.997
MA0068.10.749
MA0069.10.522
MA0070.10.17
MA0071.10.55
MA0072.10.879
MA0073.10.576
MA0074.10.897
MA0076.10.00316
MA0077.10.521
MA0078.10.17
MA0079.20.0834
MA0080.20.0674
MA0081.10.482
MA0083.10.00283
MA0084.10.458
MA0087.10.75
MA0088.10.00398
MA0090.10.101
MA0091.10.412
MA0092.10.204
MA0093.10.431
MA0099.25.68978e-5
MA0100.10.149
MA0101.10.456
MA0102.20.401
MA0103.11.92649e-4
MA0104.20.988
MA0105.10.0171
MA0106.10.00156
MA0107.10.892
MA0108.20.0194
MA0111.10.335
MA0112.20.00476
MA0113.10.983
MA0114.10.938
MA0115.10.461
MA0116.10.0288
MA0117.10.556
MA0119.10.307
MA0122.10.68
MA0124.10.454
MA0125.10.00295
MA0131.10.576
MA0135.10.0307
MA0136.10.92
MA0137.20.0518
MA0138.20.00141
MA0139.10.479
MA0140.12.04701e-4
MA0141.10.166
MA0142.10.178
MA0143.10.783
MA0144.10.0887
MA0145.10.379
MA0146.10.0113
MA0147.10.88
MA0148.10.553
MA0149.10.0481
MA0150.10.231
MA0152.10.04
MA0153.12.50664e-5
MA0154.10.212
MA0155.10.952
MA0156.10.999
MA0157.10.774
MA0159.10.266
MA0160.10.673
MA0162.10.0601
MA0163.10.0184
MA0164.10.335
MA0258.10.232
MA0259.10.346



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: CNhs13275

Novel motifP-value
10.206
100.0123
1000.63
1010.235
1020.188
1030.0729
1040.708
1050.886
1060.542
1070.74
1080.543
1090.0248
110.0774
1100.0194
1110.501
1120.427
1130.118
1140.444
1150.689
1160.0351
1178.12752e-4
1180.843
1190.242
120.66
1200.211
1210.778
1220.147
1230.312
1240.145
1250.195
1260.34
1270.137
1280.657
1290.701
130.00555
1300.779
1310.527
1320.35
1330.163
1340.516
1350.188
1360.563
1370.538
1380.81
1390.349
140.503
1400.922
1410.797
1420.814
1430.0897
1440.159
1450.102
1460.443
1470.907
1480.543
1490.199
150.864
1500.0358
1510.973
1520.126
1530.921
1540.411
1550.206
1564.29054e-38
1570.823
1580.415
1590.124
1600.595
1610.376
1620.901
1630.598
1640.00508
1650.962
1660.764
1670.301
1680.411
1690.00264
170.15
180.228
190.316
20.421
200.0373
210.0336
220.32
230.129
240.706
250.868
260.0228
270.39
280.691
290.00394
30.0826
300.451
310.625
320.344
330.17
340.657
350.683
360.0261
370.0118
380.715
390.489
40.757
400.36
410.4
420.366
430.514
440.176
450.574
460.341
470.138
480.265
490.869
50.185
500.72
510.935
520.689
530.379
540.57
550.378
560.773
570.107
580.902
590.242
60.933
600.358
610.627
620.399
630.549
640.584
650.925
660.636
670.966
680.691
690.487
70.315
700.00285
710.00104
720.954
730.0189
740.735
750.0383
760.204
770.38
780.025
790.732
80.0824
800.0473
810.698
820.518
830.502
840.927
850.653
860.572
870.0823
880.711
890.783
90.959
900.0226
910.337
920.678
930.205
940.835
950.0439
960.415
970.661
980.402
990.748



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: CNhs13275


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)
0000723 (somatic stem cell)
0000048 (multi fate stem cell)
0000548 (animal cell)
0002320 (connective tissue cell)
0002371 (somatic cell)
0000219 (motile cell)
0000134 (mesenchymal cell)
0000255 (eukaryotic cell)
0000034 (stem cell)

UBERON: Anatomy
0002384 (connective tissue)
0000479 (tissue)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0001062 (anatomical entity)

FF: FANTOM5
0000102 (sample by type)
0000003 (cell line sample)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000350 (experimentally modified sample)
0000404 (mouse mesenchymal stem cell line: ST2 sample)
0000333 (medium change sample)
0000357 (0 hr sample)
0000488 (mouse ST2 Mesenchymal stem cells, cells 0hr after medium change , without induction sample)

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
CL:0000134 (mesenchymal cell)