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{{f5samples
{{f5samples
|DRA_sample_Accession=CAGE@SAMD00004694
|DRA_sample_Accession=CAGE@SAMD00004694
|accession_numbers=CAGE;DRX009142;DRR010016;DRZ001441;DRZ002824
|accession_numbers=CAGE;DRX009142;DRR010016;DRZ001441;DRZ002824;DRZ012791;DRZ014174
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000922,UBERON:0000479,UBERON:0000061,UBERON:0000465,UBERON:0001062
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000922,UBERON:0000479,UBERON:0000061,UBERON:0000465,UBERON:0001062
|ancestors_in_cell_lineage_facet=
|ancestors_in_cell_lineage_facet=
Line 97: Line 97:
|top_motifs=ZNF384:2.68859382993;HSF1,2:2.57763485564;NFY{A,B,C}:2.47547758203;NANOG{mouse}:2.05055239599;GATA4:2.00956448808;LHX3,4:1.88220344794;SOX17:1.83038713821;VSX1,2:1.81428172522;SOX2:1.76466465706;MZF1:1.65126539476;UFEwm:1.63030321213;ZNF143:1.61121689062;TFDP1:1.537939566;OCT4_SOX2{dimer}:1.5143844128;NANOG:1.51382658564;E2F1..5:1.50225227862;IKZF2:1.49893856585;NRF1:1.49007559698;SOX{8,9,10}:1.40944066477;FOX{I1,J2}:1.38163379944;PBX1:1.37258339913;KLF4:1.367913181;ONECUT1,2:1.35245645762;FOXD3:1.34455159939;LEF1_TCF7_TCF7L1,2:1.32462296801;GFI1:1.31350131146;NKX6-1,2:1.29168406925;SOX5:1.27957131777;CDC5L:1.27162205054;EVI1:1.26989414801;BREu{core}:1.21222173055;POU5F1:1.15337160729;PAX6:1.10779644201;RREB1:1.07329521047;PAX1,9:1.07133975073;POU2F1..3:1.03524609816;PRRX1,2:1.02361279956;FOXL1:0.998359077079;NKX3-1:0.991781036873;GZF1:0.975135462106;ELK1,4_GABP{A,B1}:0.968928912473;FOXP3:0.966750321799;YY1:0.93984474753;RBPJ:0.92938587522;STAT5{A,B}:0.925799169716;DBP:0.853647511254;POU1F1:0.853112841879;PATZ1:0.834972003935;AHR_ARNT_ARNT2:0.815470974064;HOXA9_MEIS1:0.806292588538;TOPORS:0.793070468247;PDX1:0.776047637123;ZBTB16:0.773185407913;PRDM1:0.762480623053;HBP1_HMGB_SSRP1_UBTF:0.728563466558;NKX2-1,4:0.723658868873;HOX{A4,D4}:0.718600128697;MED-1{core}:0.70215672031;NFE2L1:0.674840745331;FOXQ1:0.665270026841;NKX3-2:0.583903908169;MYBL2:0.583739694409;RXR{A,B,G}_{NR1H2,PPAR}dimers:0.576195669967;POU6F1:0.544761698441;PAX8:0.542169581895;ADNP_IRX_SIX_ZHX:0.541632028518;NKX2-3_NKX2-5:0.523847991212;GFI1B:0.495572234644;RXR{A,B,G}:0.489133340118;MAZ:0.483713040409;GTF2I:0.482368858025;HOX{A5,B5}:0.474594466325;EN1,2:0.473408234337;MYB:0.460352997715;PITX1..3:0.460209498862;POU3F1..4:0.451611277372;STAT1,3:0.410028092278;ATF4:0.403582061812;RFX1:0.393942272414;RORA:0.376980829033;ZFP161:0.366736198905;HIC1:0.359855223587;RFX2..5_RFXANK_RFXAP:0.344576145867;NR3C1:0.333342704513;CUX2:0.302158350761;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:0.29598365003;HMGA1,2:0.291968439008;IKZF1:0.269600751012;CDX1,2,4:0.265021187422;ZIC1..3:0.234521501168;FOXM1:0.232217132946;FOXN1:0.217887463737;TEF:0.19415318334;DMAP1_NCOR{1,2}_SMARC:0.18430035591;SRF:0.184105534775;HES1:0.164233697803;CREB1:0.157075935707;ZNF423:0.130419577315;JUN:0.130167736098;HMX1:0.126004253123;ZNF238:0.123424108027;TFAP2B:0.120358209233;PAX4:0.10212266241;T:0.096743211805;AIRE:0.0896266430709;EGR1..3:0.0851266316266;TGIF1:0.0628128919872;GTF2A1,2:0.00202855832309;EP300:-0.00191025563389;ATF2:-0.0174085349314;TBX4,5:-0.0388459256719;MEF2{A,B,C,D}:-0.107959961876;ELF1,2,4:-0.121842916497;BPTF:-0.130407524934;ZBTB6:-0.138472267493;GATA6:-0.142945176125;SMAD1..7,9:-0.143130628457;RUNX1..3:-0.156413505576;NFIX:-0.161441827363;TEAD1:-0.164681829383;TFAP2{A,C}:-0.173302535097;NHLH1,2:-0.185142164812;ALX4:-0.200676374653;ATF5_CREB3:-0.206252885652;REST:-0.221906864048;HAND1,2:-0.229116239284;TBP:-0.245600621078;MTE{core}:-0.265335174177;FOXO1,3,4:-0.288045658168;HIF1A:-0.303018794894;AR:-0.314676291315;IRF7:-0.339667301704;SPI1:-0.342231826803;HNF4A_NR2F1,2:-0.366263781308;GCM1,2:-0.377549128144;PAX2:-0.386316004255;bHLH_family:-0.391123220433;FOXP1:-0.398638916584;PAX5:-0.405336389023;ALX1:-0.44171886882;NR5A1,2:-0.450271253298;PPARG:-0.471922183479;HNF1A:-0.489778339466;HLF:-0.496080458951;FOX{F1,F2,J1}:-0.50956462333;TP53:-0.514009225166;SPIB:-0.520549054686;ESRRA:-0.543449454205;CRX:-0.560670120411;MTF1:-0.631560138573;XCPE1{core}:-0.634641531206;NFE2:-0.639245270324;SREBF1,2:-0.652668869073;TFAP4:-0.653305609106;FOXA2:-0.668341167072;BACH2:-0.671667958849;NR1H4:-0.692727952569;NFKB1_REL_RELA:-0.698922958864;NFATC1..3:-0.706224140153;EBF1:-0.725797345775;MYFfamily:-0.733223136217;TLX2:-0.737271041931;NFIL3:-0.737868542732;NKX2-2,8:-0.757940299879;ARID5B:-0.773799667957;TFCP2:-0.786479705165;SNAI1..3:-0.789374761908;ESR1:-0.792792003379;ETS1,2:-0.801078906936;SP1:-0.84399494666;TLX1..3_NFIC{dimer}:-0.844648422638;ZEB1:-0.87780500458;GLI1..3:-0.917584585834;MAFB:-0.928318942298;FOS_FOS{B,L1}_JUN{B,D}:-0.943592333709;NR6A1:-0.952498356082;IRF1,2:-0.954069468178;TAL1_TCF{3,4,12}:-0.966431913664;ATF6:-0.975714347988;ZNF148:-0.985805010386;CEBPA,B_DDIT3:-1.08383494795;FOSL2:-1.10527420436;RXRA_VDR{dimer}:-1.16313031027;FOX{D1,D2}:-1.20481442043;NFE2L2:-1.27493249169;MYOD1:-1.28631065839;LMO2:-1.31477755988;STAT2,4,6:-1.43667732436;SPZ1:-1.47992267216
|top_motifs=ZNF384:2.68859382993;HSF1,2:2.57763485564;NFY{A,B,C}:2.47547758203;NANOG{mouse}:2.05055239599;GATA4:2.00956448808;LHX3,4:1.88220344794;SOX17:1.83038713821;VSX1,2:1.81428172522;SOX2:1.76466465706;MZF1:1.65126539476;UFEwm:1.63030321213;ZNF143:1.61121689062;TFDP1:1.537939566;OCT4_SOX2{dimer}:1.5143844128;NANOG:1.51382658564;E2F1..5:1.50225227862;IKZF2:1.49893856585;NRF1:1.49007559698;SOX{8,9,10}:1.40944066477;FOX{I1,J2}:1.38163379944;PBX1:1.37258339913;KLF4:1.367913181;ONECUT1,2:1.35245645762;FOXD3:1.34455159939;LEF1_TCF7_TCF7L1,2:1.32462296801;GFI1:1.31350131146;NKX6-1,2:1.29168406925;SOX5:1.27957131777;CDC5L:1.27162205054;EVI1:1.26989414801;BREu{core}:1.21222173055;POU5F1:1.15337160729;PAX6:1.10779644201;RREB1:1.07329521047;PAX1,9:1.07133975073;POU2F1..3:1.03524609816;PRRX1,2:1.02361279956;FOXL1:0.998359077079;NKX3-1:0.991781036873;GZF1:0.975135462106;ELK1,4_GABP{A,B1}:0.968928912473;FOXP3:0.966750321799;YY1:0.93984474753;RBPJ:0.92938587522;STAT5{A,B}:0.925799169716;DBP:0.853647511254;POU1F1:0.853112841879;PATZ1:0.834972003935;AHR_ARNT_ARNT2:0.815470974064;HOXA9_MEIS1:0.806292588538;TOPORS:0.793070468247;PDX1:0.776047637123;ZBTB16:0.773185407913;PRDM1:0.762480623053;HBP1_HMGB_SSRP1_UBTF:0.728563466558;NKX2-1,4:0.723658868873;HOX{A4,D4}:0.718600128697;MED-1{core}:0.70215672031;NFE2L1:0.674840745331;FOXQ1:0.665270026841;NKX3-2:0.583903908169;MYBL2:0.583739694409;RXR{A,B,G}_{NR1H2,PPAR}dimers:0.576195669967;POU6F1:0.544761698441;PAX8:0.542169581895;ADNP_IRX_SIX_ZHX:0.541632028518;NKX2-3_NKX2-5:0.523847991212;GFI1B:0.495572234644;RXR{A,B,G}:0.489133340118;MAZ:0.483713040409;GTF2I:0.482368858025;HOX{A5,B5}:0.474594466325;EN1,2:0.473408234337;MYB:0.460352997715;PITX1..3:0.460209498862;POU3F1..4:0.451611277372;STAT1,3:0.410028092278;ATF4:0.403582061812;RFX1:0.393942272414;RORA:0.376980829033;ZFP161:0.366736198905;HIC1:0.359855223587;RFX2..5_RFXANK_RFXAP:0.344576145867;NR3C1:0.333342704513;CUX2:0.302158350761;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:0.29598365003;HMGA1,2:0.291968439008;IKZF1:0.269600751012;CDX1,2,4:0.265021187422;ZIC1..3:0.234521501168;FOXM1:0.232217132946;FOXN1:0.217887463737;TEF:0.19415318334;DMAP1_NCOR{1,2}_SMARC:0.18430035591;SRF:0.184105534775;HES1:0.164233697803;CREB1:0.157075935707;ZNF423:0.130419577315;JUN:0.130167736098;HMX1:0.126004253123;ZNF238:0.123424108027;TFAP2B:0.120358209233;PAX4:0.10212266241;T:0.096743211805;AIRE:0.0896266430709;EGR1..3:0.0851266316266;TGIF1:0.0628128919872;GTF2A1,2:0.00202855832309;EP300:-0.00191025563389;ATF2:-0.0174085349314;TBX4,5:-0.0388459256719;MEF2{A,B,C,D}:-0.107959961876;ELF1,2,4:-0.121842916497;BPTF:-0.130407524934;ZBTB6:-0.138472267493;GATA6:-0.142945176125;SMAD1..7,9:-0.143130628457;RUNX1..3:-0.156413505576;NFIX:-0.161441827363;TEAD1:-0.164681829383;TFAP2{A,C}:-0.173302535097;NHLH1,2:-0.185142164812;ALX4:-0.200676374653;ATF5_CREB3:-0.206252885652;REST:-0.221906864048;HAND1,2:-0.229116239284;TBP:-0.245600621078;MTE{core}:-0.265335174177;FOXO1,3,4:-0.288045658168;HIF1A:-0.303018794894;AR:-0.314676291315;IRF7:-0.339667301704;SPI1:-0.342231826803;HNF4A_NR2F1,2:-0.366263781308;GCM1,2:-0.377549128144;PAX2:-0.386316004255;bHLH_family:-0.391123220433;FOXP1:-0.398638916584;PAX5:-0.405336389023;ALX1:-0.44171886882;NR5A1,2:-0.450271253298;PPARG:-0.471922183479;HNF1A:-0.489778339466;HLF:-0.496080458951;FOX{F1,F2,J1}:-0.50956462333;TP53:-0.514009225166;SPIB:-0.520549054686;ESRRA:-0.543449454205;CRX:-0.560670120411;MTF1:-0.631560138573;XCPE1{core}:-0.634641531206;NFE2:-0.639245270324;SREBF1,2:-0.652668869073;TFAP4:-0.653305609106;FOXA2:-0.668341167072;BACH2:-0.671667958849;NR1H4:-0.692727952569;NFKB1_REL_RELA:-0.698922958864;NFATC1..3:-0.706224140153;EBF1:-0.725797345775;MYFfamily:-0.733223136217;TLX2:-0.737271041931;NFIL3:-0.737868542732;NKX2-2,8:-0.757940299879;ARID5B:-0.773799667957;TFCP2:-0.786479705165;SNAI1..3:-0.789374761908;ESR1:-0.792792003379;ETS1,2:-0.801078906936;SP1:-0.84399494666;TLX1..3_NFIC{dimer}:-0.844648422638;ZEB1:-0.87780500458;GLI1..3:-0.917584585834;MAFB:-0.928318942298;FOS_FOS{B,L1}_JUN{B,D}:-0.943592333709;NR6A1:-0.952498356082;IRF1,2:-0.954069468178;TAL1_TCF{3,4,12}:-0.966431913664;ATF6:-0.975714347988;ZNF148:-0.985805010386;CEBPA,B_DDIT3:-1.08383494795;FOSL2:-1.10527420436;RXRA_VDR{dimer}:-1.16313031027;FOX{D1,D2}:-1.20481442043;NFE2L2:-1.27493249169;MYOD1:-1.28631065839;LMO2:-1.31477755988;STAT2,4,6:-1.43667732436;SPZ1:-1.47992267216
|xref=
|xref=
|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_mouse;search_select_hide=table111:324-5I8;search_select_hide=table117:324-5I8
}}
}}

Latest revision as of 19:09, 4 June 2020


Name:whole body, embryo E11
Species:Mouse (Mus musculus)
Library ID:CNhs11014
Sample type:developmental
Genomic View: UCSC
CAGEd-oPOSSUM:link
ZENBU report :link
Additional information
Sample information
strainC57BL/6J
tissuewhole body
dev stage11 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

CAGE Accession numbers
MethodSample accession id
CAGE  SAMD00004694
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11014 CAGE DRX009142 DRR010016
Accession ID Mm9

Library idBAMCTSS
CNhs11014 DRZ001441 DRZ002824
Accession ID Mm10

Library idBAMCTSS
CNhs11014 DRZ012791 DRZ014174
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

CNhs11014

00
10.00413
100
1000.227
1000-0.0157
1001-0.0239
10020.156
1003-0.121
10040.116
1005-0.223
1006-0.105
10070.231
10080
1009-0.108
1010.194
10100
1011-0.117
10120
1013-0.4
10140.193
10150.4
10160.105
10170
10180.0429
10190
1020
10200
10210.0019
1022-0.252
10230
1024-0.0576
10250.21
10260
10270.3
10280
1029-0.115
103-0.0802
10300
1031-0.0459
1032-0.396
10330.0344
10340
10350
10360.0745
10370
1038-0.0517
1039-0.062
1040
1040-0.00315
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: CNhs11014

Jaspar motifP-value
MA0002.21.52861e-4
MA0003.10.0789
MA0004.10.963
MA0006.10.238
MA0007.10.199
MA0009.10.537
MA0014.10.241
MA0017.18.41182e-4
MA0018.20.0472
MA0019.10.605
MA0024.16.95345e-6
MA0025.10.0661
MA0027.10.236
MA0028.10.0474
MA0029.10.701
MA0030.10.0688
MA0031.10.0085
MA0035.20.0366
MA0038.11.06987e-4
MA0039.24.70676e-4
MA0040.10.412
MA0041.10.762
MA0042.10.328
MA0043.10.00391
MA0046.15.63481e-13
MA0047.20.0131
MA0048.10.0675
MA0050.14.28676e-7
MA0051.18.05779e-6
MA0052.10.00354
MA0055.10.0665
MA0057.10.0285
MA0058.10.678
MA0059.10.478
MA0060.11.88308e-20
MA0061.10.116
MA0062.20.168
MA0065.20.00283
MA0066.10.244
MA0067.10.715
MA0068.10.183
MA0069.10.708
MA0070.10.729
MA0071.10.138
MA0072.10.17
MA0073.10.869
MA0074.10.48
MA0076.10.036
MA0077.10.00727
MA0078.10.0211
MA0079.20.124
MA0080.21.2062e-9
MA0081.10.353
MA0083.10.919
MA0084.10.857
MA0087.10.222
MA0088.10.717
MA0090.10.196
MA0091.10.927
MA0092.10.268
MA0093.10.948
MA0099.25.43705e-6
MA0100.10.295
MA0101.10.53
MA0102.20.545
MA0103.10.00411
MA0104.20.22
MA0105.10.354
MA0106.10.204
MA0107.10.261
MA0108.20.255
MA0111.10.665
MA0112.22.04525e-4
MA0113.10.339
MA0114.10.00514
MA0115.10.535
MA0116.10.0466
MA0117.10.804
MA0119.10.0318
MA0122.10.737
MA0124.10.847
MA0125.10.245
MA0131.10.173
MA0135.10.847
MA0136.15.42465e-4
MA0137.20.252
MA0138.20.00573
MA0139.10.0477
MA0140.10.167
MA0141.10.0199
MA0142.10.0172
MA0143.19.66636e-5
MA0144.10.158
MA0145.10.0102
MA0146.10.278
MA0147.10.268
MA0148.10.00101
MA0149.10.00404
MA0150.10.0264
MA0152.10.221
MA0153.12.82423e-8
MA0154.10.00558
MA0155.10.574
MA0156.10.0396
MA0157.10.0248
MA0159.10.047
MA0160.10.103
MA0162.10.701
MA0163.10.0752
MA0164.10.241
MA0258.10.0129
MA0259.10.269



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: CNhs11014

Novel motifP-value
10.131
100.505
1000.774
1010.553
1020.767
1030.056
1040.697
1050.0727
1060.00537
1070.0819
1080.98
1090.0308
110.155
1100.486
1110.0387
1120.0466
1130.422
1140.0784
1150.257
1160.848
1170.848
1180.968
1190.00719
120.591
1200.544
1210.684
1220.77
1230.199
1240.14
1250.999
1260.66
1270.0979
1280.0226
1290.263
130.158
1300.976
1310.113
1320.207
1330.198
1340.995
1350.292
1360.391
1370.552
1380.645
1390.00658
140.17
1400.0188
1410.0689
1420.938
1430.697
1440.953
1450.513
1460.351
1470.516
1480.246
1490.0728
150.092
1500.543
1510.119
1520.0294
1530.186
1540.741
1550.631
1563.6311e-7
1570.924
1580.511
1590.0182
1600.58
1610.647
1620.695
1630.115
1640.128
1650.676
1660.617
1670.797
1680.804
1690.00853
170.0677
180.94
190.0625
20.312
200.482
210.594
220.152
230.0686
240.233
250.648
260.158
270.361
280.381
290.939
30.326
300.482
310.47
320.0502
330.497
340.535
350.978
360.439
370.134
380.109
390.362
40.478
400.17
410.621
420.653
430.153
440.866
450.314
460.31
470.151
480.149
490.137
50.241
500.589
510.582
520.166
530.325
540.587
550.79
560.317
570.717
580.193
590.0538
60.555
600.054
610.714
620.146
630.0702
640.48
650.0754
660.229
670.914
680.218
690.235
70.248
704.32794e-4
710.373
720.303
730.0866
740.544
750.384
760.863
770.212
780.381
790.337
80.373
800.588
810.323
820.094
830.793
840.99
850.0151
860.457
870.662
880.924
890.148
90.398
900.321
910.555
920.086
930.296
940.714
950.0996
960.339
970.391
980.146
990.444



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: CNhs11014


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
0000468 (multi-cellular organism)
0000922 (embryo)
0000479 (tissue)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0001062 (anatomical entity)

FF: FANTOM5
0000102 (sample by type)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000999 (fetal tissue sample)
0000292 (embryonic day sample - mouse)
0000004 (tissue sample)
0000294 (mouse embryonic day 11 sample)
0011311 (mouse whole body- embryo E11 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
FF:0000294 (mouse embryonic day 11 sample)

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