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{{f5samples
{{f5samples
|DRA_sample_Accession=CAGE@SAMD00005255
|DRA_sample_Accession=CAGE@SAMD00005255
|accession_numbers=CAGE;DRX008924;DRR009798;DRZ001223;DRZ002606
|accession_numbers=CAGE;DRX008924;DRR009798;DRZ001223;DRZ002606;DRZ012573;DRZ013956
|ancestors_in_anatomy_facet=UBERON:0000479,UBERON:0000061,UBERON:0000465,UBERON:0001062
|ancestors_in_anatomy_facet=UBERON:0000479,UBERON:0000061,UBERON:0000465,UBERON:0001062
|ancestors_in_cell_lineage_facet=
|ancestors_in_cell_lineage_facet=
Line 92: Line 92:
|top_motifs=HLF:4.02605674701;NR1H4:3.8059256142;TBP:3.13739641578;ESRRA:2.75336086294;FOXA2:2.70057190096;NR5A1,2:2.61877086395;FOX{F1,F2,J1}:2.53317881297;NR3C1:2.4873052594;PAX1,9:2.28733939418;ESR1:2.27200032969;HNF1A:2.26432285587;NFIL3:2.21409638017;HNF4A_NR2F1,2:1.89346664289;MYOD1:1.8625831093;AR:1.82742864942;NFE2L1:1.69117361571;NFIX:1.61083366982;MEF2{A,B,C,D}:1.5969480987;JUN:1.56546234168;NKX3-2:1.47493600696;RXRA_VDR{dimer}:1.37730136552;RXR{A,B,G}_{NR1H2,PPAR}dimers:1.30395686134;STAT2,4,6:1.23648071167;GCM1,2:1.16645722591;CEBPA,B_DDIT3:1.16125743438;TBX4,5:1.09762423316;TFCP2:1.05608635665;TFAP4:1.0197083406;MAFB:0.990851446115;SNAI1..3:0.964591584687;LMO2:0.944762050457;ZNF148:0.93002391563;ALX1:0.890165602388;MYB:0.864831426373;FOXL1:0.838446750267;FOX{D1,D2}:0.82055022497;ZEB1:0.816499822605;GATA6:0.811125283874;HOX{A4,D4}:0.806282404593;SOX17:0.794574486852;RFX1:0.771868346754;T:0.764351275706;NFE2L2:0.722483583978;PPARG:0.668400356755;TFAP2{A,C}:0.655161863447;bHLH_family:0.641191564787;TLX2:0.636738797513;PBX1:0.589377145307;ATF6:0.585319047375;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:0.57566439449;NFE2:0.540323371706;RBPJ:0.537441003529;HAND1,2:0.493261100967;SRF:0.48863236904;RFX2..5_RFXANK_RFXAP:0.468916552099;EBF1:0.446307850906;HSF1,2:0.427578666751;TLX1..3_NFIC{dimer}:0.427159697462;FOSL2:0.382481650656;FOXO1,3,4:0.322757679171;LEF1_TCF7_TCF7L1,2:0.299561055161;TGIF1:0.296660354908;GTF2A1,2:0.286471392747;FOS_FOS{B,L1}_JUN{B,D}:0.275710992464;ONECUT1,2:0.24796599635;GFI1:0.231845981755;DMAP1_NCOR{1,2}_SMARC:0.219814574561;ZBTB6:0.192931674274;NHLH1,2:0.186861841543;NR6A1:0.168171886424;ZIC1..3:0.14263131405;TP53:0.139463196846;MYBL2:0.129849706912;SMAD1..7,9:0.128520323248;NKX2-3_NKX2-5:0.111913262285;MYFfamily:0.0866833850713;REST:0.0789749029167;MTF1:0.0266667172261;PDX1:0.00799187014254;TEAD1:-0.00736722065162;SOX5:-0.105499880506;CUX2:-0.116025100805;ATF2:-0.130839524556;PATZ1:-0.131191935919;PAX5:-0.151475073206;GLI1..3:-0.15302164139;STAT5{A,B}:-0.156283795773;PAX6:-0.180116732074;NFY{A,B,C}:-0.188985413491;RUNX1..3:-0.241956610345;TOPORS:-0.259418612076;POU1F1:-0.266530645199;IRF1,2:-0.301155915815;XCPE1{core}:-0.312558854678;NFATC1..3:-0.320858957203;RXR{A,B,G}:-0.329145219206;HIC1:-0.333307322737;HMX1:-0.343425305281;GTF2I:-0.354586607566;ATF5_CREB3:-0.364034759396;OCT4_SOX2{dimer}:-0.38603855084;POU2F1..3:-0.401014668964;ZNF423:-0.403944944078;SP1:-0.425923040919;GFI1B:-0.443138719544;ZNF238:-0.44321880747;ETS1,2:-0.447904303574;SPI1:-0.451647408932;HES1:-0.461939285392;IRF7:-0.469151194252;ALX4:-0.469887794087;KLF4:-0.484393852053;BACH2:-0.509891071281;HBP1_HMGB_SSRP1_UBTF:-0.515890459242;HOX{A5,B5}:-0.583686003703;YY1:-0.6035355563;SREBF1,2:-0.608748142261;MAZ:-0.617939789594;MED-1{core}:-0.624657349234;SOX{8,9,10}:-0.631171533736;NFKB1_REL_RELA:-0.637760247901;STAT1,3:-0.6574087723;POU6F1:-0.659673109714;HMGA1,2:-0.690038443995;EVI1:-0.692687935036;FOXM1:-0.721658014349;ADNP_IRX_SIX_ZHX:-0.755341259233;SPZ1:-0.76864603183;TFAP2B:-0.794351179;ATF4:-0.794984967542;RORA:-0.797908476965;NKX2-2,8:-0.803470115419;ARID5B:-0.809476291691;FOXN1:-0.907684035719;UFEwm:-0.952541884158;HOXA9_MEIS1:-0.966252982908;EN1,2:-0.966832723447;LHX3,4:-1.00304844011;E2F1..5:-1.0260727667;PAX8:-1.03709769101;BREu{core}:-1.04655920771;NRF1:-1.05740178182;FOXQ1:-1.06148893133;HIF1A:-1.07579959956;FOXP3:-1.07715059047;ELF1,2,4:-1.10012069094;PRRX1,2:-1.10767679972;ZFP161:-1.11379554429;SPIB:-1.12997400254;MZF1:-1.19254939433;AHR_ARNT_ARNT2:-1.24292555066;GATA4:-1.28183570258;GZF1:-1.28373630079;IKZF1:-1.29793935108;TAL1_TCF{3,4,12}:-1.29802035373;EGR1..3:-1.31864566529;RREB1:-1.32140043889;CREB1:-1.357154689;MTE{core}:-1.36391488095;POU3F1..4:-1.36806228364;PRDM1:-1.37452249749;POU5F1:-1.39724355254;CRX:-1.41214533151;IKZF2:-1.46416945517;ZNF143:-1.49300432952;PAX2:-1.49371710428;VSX1,2:-1.51555326335;NANOG{mouse}:-1.52866117786;FOXD3:-1.54271728356;TEF:-1.59731812064;CDC5L:-1.66023265463;NKX2-1,4:-1.69901034668;SOX2:-1.77392376821;EP300:-1.81987950773;FOX{I1,J2}:-1.90331199109;ELK1,4_GABP{A,B1}:-1.96348666771;DBP:-1.96700647987;TFDP1:-2.02008794255;NKX6-1,2:-2.07480541708;NANOG:-2.09000557994;PITX1..3:-2.20755624232;BPTF:-2.23879617299;NKX3-1:-2.41570857831;ZNF384:-2.51285613124;CDX1,2,4:-2.96685840274;PAX4:-2.98453096572;ZBTB16:-3.1306197203;FOXP1:-3.2066641176;AIRE:-3.53918376021
|top_motifs=HLF:4.02605674701;NR1H4:3.8059256142;TBP:3.13739641578;ESRRA:2.75336086294;FOXA2:2.70057190096;NR5A1,2:2.61877086395;FOX{F1,F2,J1}:2.53317881297;NR3C1:2.4873052594;PAX1,9:2.28733939418;ESR1:2.27200032969;HNF1A:2.26432285587;NFIL3:2.21409638017;HNF4A_NR2F1,2:1.89346664289;MYOD1:1.8625831093;AR:1.82742864942;NFE2L1:1.69117361571;NFIX:1.61083366982;MEF2{A,B,C,D}:1.5969480987;JUN:1.56546234168;NKX3-2:1.47493600696;RXRA_VDR{dimer}:1.37730136552;RXR{A,B,G}_{NR1H2,PPAR}dimers:1.30395686134;STAT2,4,6:1.23648071167;GCM1,2:1.16645722591;CEBPA,B_DDIT3:1.16125743438;TBX4,5:1.09762423316;TFCP2:1.05608635665;TFAP4:1.0197083406;MAFB:0.990851446115;SNAI1..3:0.964591584687;LMO2:0.944762050457;ZNF148:0.93002391563;ALX1:0.890165602388;MYB:0.864831426373;FOXL1:0.838446750267;FOX{D1,D2}:0.82055022497;ZEB1:0.816499822605;GATA6:0.811125283874;HOX{A4,D4}:0.806282404593;SOX17:0.794574486852;RFX1:0.771868346754;T:0.764351275706;NFE2L2:0.722483583978;PPARG:0.668400356755;TFAP2{A,C}:0.655161863447;bHLH_family:0.641191564787;TLX2:0.636738797513;PBX1:0.589377145307;ATF6:0.585319047375;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:0.57566439449;NFE2:0.540323371706;RBPJ:0.537441003529;HAND1,2:0.493261100967;SRF:0.48863236904;RFX2..5_RFXANK_RFXAP:0.468916552099;EBF1:0.446307850906;HSF1,2:0.427578666751;TLX1..3_NFIC{dimer}:0.427159697462;FOSL2:0.382481650656;FOXO1,3,4:0.322757679171;LEF1_TCF7_TCF7L1,2:0.299561055161;TGIF1:0.296660354908;GTF2A1,2:0.286471392747;FOS_FOS{B,L1}_JUN{B,D}:0.275710992464;ONECUT1,2:0.24796599635;GFI1:0.231845981755;DMAP1_NCOR{1,2}_SMARC:0.219814574561;ZBTB6:0.192931674274;NHLH1,2:0.186861841543;NR6A1:0.168171886424;ZIC1..3:0.14263131405;TP53:0.139463196846;MYBL2:0.129849706912;SMAD1..7,9:0.128520323248;NKX2-3_NKX2-5:0.111913262285;MYFfamily:0.0866833850713;REST:0.0789749029167;MTF1:0.0266667172261;PDX1:0.00799187014254;TEAD1:-0.00736722065162;SOX5:-0.105499880506;CUX2:-0.116025100805;ATF2:-0.130839524556;PATZ1:-0.131191935919;PAX5:-0.151475073206;GLI1..3:-0.15302164139;STAT5{A,B}:-0.156283795773;PAX6:-0.180116732074;NFY{A,B,C}:-0.188985413491;RUNX1..3:-0.241956610345;TOPORS:-0.259418612076;POU1F1:-0.266530645199;IRF1,2:-0.301155915815;XCPE1{core}:-0.312558854678;NFATC1..3:-0.320858957203;RXR{A,B,G}:-0.329145219206;HIC1:-0.333307322737;HMX1:-0.343425305281;GTF2I:-0.354586607566;ATF5_CREB3:-0.364034759396;OCT4_SOX2{dimer}:-0.38603855084;POU2F1..3:-0.401014668964;ZNF423:-0.403944944078;SP1:-0.425923040919;GFI1B:-0.443138719544;ZNF238:-0.44321880747;ETS1,2:-0.447904303574;SPI1:-0.451647408932;HES1:-0.461939285392;IRF7:-0.469151194252;ALX4:-0.469887794087;KLF4:-0.484393852053;BACH2:-0.509891071281;HBP1_HMGB_SSRP1_UBTF:-0.515890459242;HOX{A5,B5}:-0.583686003703;YY1:-0.6035355563;SREBF1,2:-0.608748142261;MAZ:-0.617939789594;MED-1{core}:-0.624657349234;SOX{8,9,10}:-0.631171533736;NFKB1_REL_RELA:-0.637760247901;STAT1,3:-0.6574087723;POU6F1:-0.659673109714;HMGA1,2:-0.690038443995;EVI1:-0.692687935036;FOXM1:-0.721658014349;ADNP_IRX_SIX_ZHX:-0.755341259233;SPZ1:-0.76864603183;TFAP2B:-0.794351179;ATF4:-0.794984967542;RORA:-0.797908476965;NKX2-2,8:-0.803470115419;ARID5B:-0.809476291691;FOXN1:-0.907684035719;UFEwm:-0.952541884158;HOXA9_MEIS1:-0.966252982908;EN1,2:-0.966832723447;LHX3,4:-1.00304844011;E2F1..5:-1.0260727667;PAX8:-1.03709769101;BREu{core}:-1.04655920771;NRF1:-1.05740178182;FOXQ1:-1.06148893133;HIF1A:-1.07579959956;FOXP3:-1.07715059047;ELF1,2,4:-1.10012069094;PRRX1,2:-1.10767679972;ZFP161:-1.11379554429;SPIB:-1.12997400254;MZF1:-1.19254939433;AHR_ARNT_ARNT2:-1.24292555066;GATA4:-1.28183570258;GZF1:-1.28373630079;IKZF1:-1.29793935108;TAL1_TCF{3,4,12}:-1.29802035373;EGR1..3:-1.31864566529;RREB1:-1.32140043889;CREB1:-1.357154689;MTE{core}:-1.36391488095;POU3F1..4:-1.36806228364;PRDM1:-1.37452249749;POU5F1:-1.39724355254;CRX:-1.41214533151;IKZF2:-1.46416945517;ZNF143:-1.49300432952;PAX2:-1.49371710428;VSX1,2:-1.51555326335;NANOG{mouse}:-1.52866117786;FOXD3:-1.54271728356;TEF:-1.59731812064;CDC5L:-1.66023265463;NKX2-1,4:-1.69901034668;SOX2:-1.77392376821;EP300:-1.81987950773;FOX{I1,J2}:-1.90331199109;ELK1,4_GABP{A,B1}:-1.96348666771;DBP:-1.96700647987;TFDP1:-2.02008794255;NKX6-1,2:-2.07480541708;NANOG:-2.09000557994;PITX1..3:-2.20755624232;BPTF:-2.23879617299;NKX3-1:-2.41570857831;ZNF384:-2.51285613124;CDX1,2,4:-2.96685840274;PAX4:-2.98453096572;ZBTB16:-3.1306197203;FOXP1:-3.2066641176;AIRE:-3.53918376021
|xref=
|xref=
|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_mouse;search_select_hide=table111:10003-101A7;search_select_hide=table117:10003-101A7
}}
}}

Latest revision as of 12:13, 3 June 2020


Name:SABiosciences XpressRef Mouse Universal Total RNA, pool1
Species:Mouse (Mus musculus)
Library ID:CNhs10611
Sample type:tissues
Genomic View: UCSC
CAGEd-oPOSSUM:link
ZENBU report :link
Additional information
Sample information
strainNA
tissuewhole body
dev stageUNDEFINED
sexmixed
ageNA
cell typeCELL MIXTURE - tissue sample
cell lineNA
companySABiosciences
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberA705103
catalog numberCat:GA-005
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-TRIzol-isopropanol-v1.0

CAGE Accession numbers
MethodSample accession id
CAGE  SAMD00005255
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs10611 CAGE DRX008924 DRR009798
Accession ID Mm9

Library idBAMCTSS
CNhs10611 DRZ001223 DRZ002606
Accession ID Mm10

Library idBAMCTSS
CNhs10611 DRZ012573 DRZ013956
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

CNhs10611

00.153
10.0571
100.0571
1000
10000.744
10010.11
1002-0.0334
10030.131
10040
10050.131
10060.596
1007-0.145
10081.177
10090.0974
101-0.0481
10100
10110.206
10120
10130.22
1014-0.0874
1015-0.193
1016-0.272
10170
10180.194
10190.297
1020
10200
10210
10220.741
10230
10240.144
10250.236
10260.194
10270
10280
1029-0.0685
1030.123
10300.108
1031-0.3
10320.174
1033-0.0737
10340.269
10350
1036-0.367
10370.108
1038-0.11
10390.502
1040
1040-0.158
10410.451



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: CNhs10611

Jaspar motifP-value
MA0002.20.0556
MA0003.10.00892
MA0004.10.852
MA0006.10.279
MA0007.10.523
MA0009.10.162
MA0014.10.866
MA0017.12.24196e-10
MA0018.20.978
MA0019.10.903
MA0024.10.0125
MA0025.10.00948
MA0027.10.532
MA0028.10.0337
MA0029.10.446
MA0030.10.0262
MA0031.10.0268
MA0035.25.46371e-4
MA0038.10.901
MA0039.20.121
MA0040.10.0885
MA0041.10.264
MA0042.10.565
MA0043.10.378
MA0046.11.99647e-57
MA0047.26.87632e-4
MA0048.10.332
MA0050.10.344
MA0051.10.911
MA0052.14.35728e-7
MA0055.10.382
MA0057.10.255
MA0058.10.728
MA0059.10.795
MA0060.10.533
MA0061.10.806
MA0062.21.50984e-4
MA0065.22.17268e-10
MA0066.10.0906
MA0067.10.353
MA0068.10.683
MA0069.10.461
MA0070.10.966
MA0071.10.0398
MA0072.10.268
MA0073.10.848
MA0074.10.564
MA0076.10.00812
MA0077.10.832
MA0078.10.0537
MA0079.20.572
MA0080.20.165
MA0081.10.103
MA0083.10.217
MA0084.10.735
MA0087.10.922
MA0088.10.398
MA0090.10.112
MA0091.10.83
MA0092.10.338
MA0093.10.742
MA0099.20.509
MA0100.10.0415
MA0101.10.296
MA0102.20.955
MA0103.10.0203
MA0104.20.96
MA0105.10.157
MA0106.10.863
MA0107.10.228
MA0108.28.75735e-18
MA0111.10.413
MA0112.23.11231e-6
MA0113.10.393
MA0114.13.83557e-10
MA0115.16.07712e-7
MA0116.10.0351
MA0117.10.883
MA0119.10.0557
MA0122.10.636
MA0124.10.488
MA0125.10.433
MA0131.10.429
MA0135.10.624
MA0136.10.0191
MA0137.20.334
MA0138.21.7811e-4
MA0139.10.153
MA0140.10.0411
MA0141.12.92985e-4
MA0142.10.525
MA0143.10.0883
MA0144.10.638
MA0145.10.0186
MA0146.10.121
MA0147.10.871
MA0148.10.00108
MA0149.10.182
MA0150.10.0598
MA0152.10.138
MA0153.11.08698e-33
MA0154.10.0101
MA0155.10.206
MA0156.10.00361
MA0157.10.13
MA0159.10.00464
MA0160.11.75553e-5
MA0162.10.117
MA0163.10.001
MA0164.10.746
MA0258.11.009e-4
MA0259.10.304



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: CNhs10611

Novel motifP-value
10.177
100.534
1000.724
1010.138
1020.797
1030.27
1040.368
1050.475
1060.0836
1070.147
1080.989
1090.0937
110.128
1100.228
1110.255
1120.0753
1130.598
1140.08
1150.628
1160.0657
1170.76
1180.708
1190.0623
120.599
1200.611
1210.0711
1220.447
1230.743
1240.78
1250.741
1260.437
1270.865
1280.167
1290.681
130.14
1300.639
1310.217
1320.588
1330.556
1340.916
1350.507
1360.211
1370.784
1380.989
1390.0577
140.314
1400.966
1410.43
1420.991
1430.926
1440.847
1450.276
1460.16
1470.874
1480.96
1490.268
150.318
1500.448
1510.303
1520.12
1530.596
1540.647
1550.873
1561.16178e-4
1570.607
1580.351
1590.476
1600.405
1610.717
1620.441
1630.842
1640.606
1650.199
1660.477
1670.303
1680.239
1690.00211
170.129
180.98
190.0768
20.34
200.547
210.66
220.147
230.153
240.0518
250.427
260.308
270.53
280.389
290.521
30.213
300.32
310.27
320.0213
330.64
340.302
350.527
360.436
370.133
380.41
390.388
40.601
400.0997
410.0295
420.512
430.206
440.0191
450.248
460.234
470.148
480.186
490.27
50.481
500.624
510.553
520.2
530.662
540.401
550.951
560.495
570.975
580.237
590.0169
60.663
600.15
610.853
620.115
630.105
640.437
650.22
660.604
670.589
680.478
690.514
70.271
700.0449
710.205
720.273
730.178
740.409
750.251
760.369
770.0615
780.558
790.366
80.018
800.265
810.435
820.045
830.232
840.104
850.0185
860.31
870.0196
880.36
890.0467
90.541
900.401
910.249
920.283
930.689
940.855
950.211
960.404
970.121
980.421
990.101



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: CNhs10611


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
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)
0000004 (tissue sample)
0000343 (control treatment 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
NA

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