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{{f5samples
{{f5samples
|DRA_sample_Accession=CAGE@SAMD00005965
|DRA_sample_Accession=CAGE@SAMD00005965
|accession_numbers=CAGE;DRX009143;DRR010017;DRZ001442;DRZ002825
|accession_numbers=CAGE;DRX009143;DRR010017;DRZ001442;DRZ002825;DRZ012792;DRZ014175
|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=SOX2:2.35028826135;VSX1,2:2.26436560215;MZF1:2.15172554045;SOX5:2.00388378697;TFDP1:1.98704448322;PRRX1,2:1.86848715597;NFY{A,B,C}:1.80914405071;RREB1:1.80884139896;SOX{8,9,10}:1.78907252152;STAT5{A,B}:1.57810825623;NANOG:1.57096179571;SOX17:1.55203349387;GFI1:1.54741528305;PATZ1:1.54707072956;ZNF143:1.54208254253;LEF1_TCF7_TCF7L1,2:1.52383517818;BREu{core}:1.48021672573;ZNF384:1.41440298035;PBX1:1.40868300032;MED-1{core}:1.35814975129;GFI1B:1.30599393945;MAZ:1.29058052263;FOXD3:1.24628905516;EP300:1.2030761263;ZNF238:1.18357721394;SMAD1..7,9:1.1683047046;AHR_ARNT_ARNT2:1.15457893164;NKX2-1,4:1.14950448401;PRDM1:1.13625109458;PAX6:1.12880604729;NKX2-3_NKX2-5:1.12227264879;GZF1:1.12173937012;NANOG{mouse}:1.10898861519;TOPORS:1.10440989557;OCT4_SOX2{dimer}:1.09097675228;TFAP2B:1.04978645019;NHLH1,2:1.04179934417;HIC1:0.978096717173;GTF2I:0.972758249008;GATA6:0.963990783075;ZBTB6:0.938795211974;LHX3,4:0.929033140535;MTE{core}:0.92494299914;NRF1:0.911262454636;GATA4:0.898656865488;POU5F1:0.883017101707;DBP:0.851010170161;EN1,2:0.848772378411;ONECUT1,2:0.847169664743;FOX{I1,J2}:0.840244320669;CUX2:0.837862147609;PITX1..3:0.829555916657;HBP1_HMGB_SSRP1_UBTF:0.814862212076;TGIF1:0.809735070677;E2F1..5:0.803801161052;RBPJ:0.785351553409;EGR1..3:0.755466453255;ZFP161:0.742699031179;HSF1,2:0.726401002236;KLF4:0.724953530196;TFAP2{A,C}:0.690865716855;TFAP4:0.682904582991;HMX1:0.656056859061;ATF2:0.63235385513;REST:0.557348005675;HOX{A4,D4}:0.557124816547;POU6F1:0.553745143528;ZNF423:0.525268063944;UFEwm:0.516852048378;PAX5:0.513793404362;IKZF2:0.509032455867;XCPE1{core}:0.495878711709;GTF2A1,2:0.494867011036;NKX3-2:0.471028503403;RXR{A,B,G}:0.45893568242;NKX3-1:0.458372476703;HOXA9_MEIS1:0.448308517775;POU1F1:0.447796133462;FOXN1:0.434187449908;MTF1:0.423837587281;MYBL2:0.420511368793;JUN:0.399624878255;RFX1:0.387041676283;POU3F1..4:0.372384808527;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:0.363878400066;MYFfamily:0.361972964295;HMGA1,2:0.353039598792;ZIC1..3:0.32292410946;SP1:0.316885986003;TLX2:0.304172673464;ZNF148:0.282941030614;CRX:0.27717796619;TEAD1:0.275187468777;ELK1,4_GABP{A,B1}:0.269495131497;PAX1,9:0.242839460053;YY1:0.24232735943;PDX1:0.241769509207;ADNP_IRX_SIX_ZHX:0.233840419879;TBX4,5:0.227459260483;IKZF1:0.143390905176;RFX2..5_RFXANK_RFXAP:0.138592430216;HIF1A:0.102201702305;MAFB:0.0822781937148;POU2F1..3:0.0787554512506;ZBTB16:0.066234763749;MYB:0.065057096686;PAX2:0.0562380181026;CREB1:0.0485470604921;TAL1_TCF{3,4,12}:0.040686755135;RXR{A,B,G}_{NR1H2,PPAR}dimers:0.0334415339362;SRF:0.012273380424;HOX{A5,B5}:-0.0154646722239;FOX{F1,F2,J1}:-0.019825317589;NKX6-1,2:-0.0287652089737;CDC5L:-0.0369355293345;TFCP2:-0.0411572357347;NR6A1:-0.0788020833359;ATF5_CREB3:-0.0864720922886;FOXP3:-0.0898535931626;ATF6:-0.0923034528293;T:-0.101727388649;bHLH_family:-0.11515642323;GCM1,2:-0.126989364245;RORA:-0.135735437952;NFIX:-0.140077156422;FOXM1:-0.144859669785;NR3C1:-0.148295662703;PAX8:-0.150567095547;AIRE:-0.176487728148;TBP:-0.188050155814;MEF2{A,B,C,D}:-0.206591651668;STAT1,3:-0.21384824949;ATF4:-0.226262642808;NR1H4:-0.230721810345;BPTF:-0.243545277494;FOXA2:-0.261970034204;SPIB:-0.27153925859;LMO2:-0.277734987799;HNF1A:-0.288496180656;RUNX1..3:-0.291638175706;SPI1:-0.305139972704;ELF1,2,4:-0.318849083563;SNAI1..3:-0.32581541097;TLX1..3_NFIC{dimer}:-0.354937385136;ESR1:-0.362049198415;HES1:-0.3800192242;FOXQ1:-0.387342495372;EVI1:-0.393571539208;NFE2L1:-0.394073888588;CDX1,2,4:-0.394197213413;GLI1..3:-0.394955544456;NFATC1..3:-0.412209584955;MYOD1:-0.418921182059;HNF4A_NR2F1,2:-0.439130214824;FOXP1:-0.445586811672;PAX4:-0.513573484667;DMAP1_NCOR{1,2}_SMARC:-0.515339401212;ARID5B:-0.553197698276;AR:-0.587892223997;FOXL1:-0.594296991408;SREBF1,2:-0.618658725962;NFKB1_REL_RELA:-0.618661118549;HLF:-0.684150309695;ETS1,2:-0.691997673333;NR5A1,2:-0.695447877329;TP53:-0.700955939406;NFE2:-0.710755267568;NFIL3:-0.750800784101;IRF7:-0.765611374702;EBF1:-0.776865481805;ZEB1:-0.805493200162;SPZ1:-0.805525949269;RXRA_VDR{dimer}:-0.846329831579;ALX1:-0.863467592596;FOS_FOS{B,L1}_JUN{B,D}:-0.876585680567;NFE2L2:-0.927305456141;FOX{D1,D2}:-1.01807471943;IRF1,2:-1.03407025596;HAND1,2:-1.05374522184;TEF:-1.07867794953;BACH2:-1.0834644962;FOSL2:-1.10902583824;CEBPA,B_DDIT3:-1.1374238384;ESRRA:-1.13852257154;ALX4:-1.15707030341;STAT2,4,6:-1.24836378519;PPARG:-1.25833162184;FOXO1,3,4:-1.43421773846;NKX2-2,8:-1.66310194204
|top_motifs=SOX2:2.35028826135;VSX1,2:2.26436560215;MZF1:2.15172554045;SOX5:2.00388378697;TFDP1:1.98704448322;PRRX1,2:1.86848715597;NFY{A,B,C}:1.80914405071;RREB1:1.80884139896;SOX{8,9,10}:1.78907252152;STAT5{A,B}:1.57810825623;NANOG:1.57096179571;SOX17:1.55203349387;GFI1:1.54741528305;PATZ1:1.54707072956;ZNF143:1.54208254253;LEF1_TCF7_TCF7L1,2:1.52383517818;BREu{core}:1.48021672573;ZNF384:1.41440298035;PBX1:1.40868300032;MED-1{core}:1.35814975129;GFI1B:1.30599393945;MAZ:1.29058052263;FOXD3:1.24628905516;EP300:1.2030761263;ZNF238:1.18357721394;SMAD1..7,9:1.1683047046;AHR_ARNT_ARNT2:1.15457893164;NKX2-1,4:1.14950448401;PRDM1:1.13625109458;PAX6:1.12880604729;NKX2-3_NKX2-5:1.12227264879;GZF1:1.12173937012;NANOG{mouse}:1.10898861519;TOPORS:1.10440989557;OCT4_SOX2{dimer}:1.09097675228;TFAP2B:1.04978645019;NHLH1,2:1.04179934417;HIC1:0.978096717173;GTF2I:0.972758249008;GATA6:0.963990783075;ZBTB6:0.938795211974;LHX3,4:0.929033140535;MTE{core}:0.92494299914;NRF1:0.911262454636;GATA4:0.898656865488;POU5F1:0.883017101707;DBP:0.851010170161;EN1,2:0.848772378411;ONECUT1,2:0.847169664743;FOX{I1,J2}:0.840244320669;CUX2:0.837862147609;PITX1..3:0.829555916657;HBP1_HMGB_SSRP1_UBTF:0.814862212076;TGIF1:0.809735070677;E2F1..5:0.803801161052;RBPJ:0.785351553409;EGR1..3:0.755466453255;ZFP161:0.742699031179;HSF1,2:0.726401002236;KLF4:0.724953530196;TFAP2{A,C}:0.690865716855;TFAP4:0.682904582991;HMX1:0.656056859061;ATF2:0.63235385513;REST:0.557348005675;HOX{A4,D4}:0.557124816547;POU6F1:0.553745143528;ZNF423:0.525268063944;UFEwm:0.516852048378;PAX5:0.513793404362;IKZF2:0.509032455867;XCPE1{core}:0.495878711709;GTF2A1,2:0.494867011036;NKX3-2:0.471028503403;RXR{A,B,G}:0.45893568242;NKX3-1:0.458372476703;HOXA9_MEIS1:0.448308517775;POU1F1:0.447796133462;FOXN1:0.434187449908;MTF1:0.423837587281;MYBL2:0.420511368793;JUN:0.399624878255;RFX1:0.387041676283;POU3F1..4:0.372384808527;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:0.363878400066;MYFfamily:0.361972964295;HMGA1,2:0.353039598792;ZIC1..3:0.32292410946;SP1:0.316885986003;TLX2:0.304172673464;ZNF148:0.282941030614;CRX:0.27717796619;TEAD1:0.275187468777;ELK1,4_GABP{A,B1}:0.269495131497;PAX1,9:0.242839460053;YY1:0.24232735943;PDX1:0.241769509207;ADNP_IRX_SIX_ZHX:0.233840419879;TBX4,5:0.227459260483;IKZF1:0.143390905176;RFX2..5_RFXANK_RFXAP:0.138592430216;HIF1A:0.102201702305;MAFB:0.0822781937148;POU2F1..3:0.0787554512506;ZBTB16:0.066234763749;MYB:0.065057096686;PAX2:0.0562380181026;CREB1:0.0485470604921;TAL1_TCF{3,4,12}:0.040686755135;RXR{A,B,G}_{NR1H2,PPAR}dimers:0.0334415339362;SRF:0.012273380424;HOX{A5,B5}:-0.0154646722239;FOX{F1,F2,J1}:-0.019825317589;NKX6-1,2:-0.0287652089737;CDC5L:-0.0369355293345;TFCP2:-0.0411572357347;NR6A1:-0.0788020833359;ATF5_CREB3:-0.0864720922886;FOXP3:-0.0898535931626;ATF6:-0.0923034528293;T:-0.101727388649;bHLH_family:-0.11515642323;GCM1,2:-0.126989364245;RORA:-0.135735437952;NFIX:-0.140077156422;FOXM1:-0.144859669785;NR3C1:-0.148295662703;PAX8:-0.150567095547;AIRE:-0.176487728148;TBP:-0.188050155814;MEF2{A,B,C,D}:-0.206591651668;STAT1,3:-0.21384824949;ATF4:-0.226262642808;NR1H4:-0.230721810345;BPTF:-0.243545277494;FOXA2:-0.261970034204;SPIB:-0.27153925859;LMO2:-0.277734987799;HNF1A:-0.288496180656;RUNX1..3:-0.291638175706;SPI1:-0.305139972704;ELF1,2,4:-0.318849083563;SNAI1..3:-0.32581541097;TLX1..3_NFIC{dimer}:-0.354937385136;ESR1:-0.362049198415;HES1:-0.3800192242;FOXQ1:-0.387342495372;EVI1:-0.393571539208;NFE2L1:-0.394073888588;CDX1,2,4:-0.394197213413;GLI1..3:-0.394955544456;NFATC1..3:-0.412209584955;MYOD1:-0.418921182059;HNF4A_NR2F1,2:-0.439130214824;FOXP1:-0.445586811672;PAX4:-0.513573484667;DMAP1_NCOR{1,2}_SMARC:-0.515339401212;ARID5B:-0.553197698276;AR:-0.587892223997;FOXL1:-0.594296991408;SREBF1,2:-0.618658725962;NFKB1_REL_RELA:-0.618661118549;HLF:-0.684150309695;ETS1,2:-0.691997673333;NR5A1,2:-0.695447877329;TP53:-0.700955939406;NFE2:-0.710755267568;NFIL3:-0.750800784101;IRF7:-0.765611374702;EBF1:-0.776865481805;ZEB1:-0.805493200162;SPZ1:-0.805525949269;RXRA_VDR{dimer}:-0.846329831579;ALX1:-0.863467592596;FOS_FOS{B,L1}_JUN{B,D}:-0.876585680567;NFE2L2:-0.927305456141;FOX{D1,D2}:-1.01807471943;IRF1,2:-1.03407025596;HAND1,2:-1.05374522184;TEF:-1.07867794953;BACH2:-1.0834644962;FOSL2:-1.10902583824;CEBPA,B_DDIT3:-1.1374238384;ESRRA:-1.13852257154;ALX4:-1.15707030341;STAT2,4,6:-1.24836378519;PPARG:-1.25833162184;FOXO1,3,4:-1.43421773846;NKX2-2,8:-1.66310194204
|xref=
|xref=
|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_mouse;search_select_hide=table111:857-27C9;search_select_hide=table117:857-27C9
}}
}}

Latest revision as of 19:21, 4 June 2020


Name:whole body, embryo E12
Species:Mouse (Mus musculus)
Library ID:CNhs10587
Sample type:developmental
Genomic View: UCSC
CAGEd-oPOSSUM:link
ZENBU report :link
Additional information
Sample information
strainC57BL/6J
tissuewhole body
dev stage12 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  SAMD00005965
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs10587 CAGE DRX009143 DRR010017
Accession ID Mm9

Library idBAMCTSS
CNhs10587 DRZ001442 DRZ002825
Accession ID Mm10

Library idBAMCTSS
CNhs10587 DRZ012792 DRZ014175
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

CNhs10587

00
10.112
100
1000.146
10000
1001-0.0749
10020.309
10030.0362
10040.255
1005-0.0507
1006-0.00509
10070.107
10080
1009-0.143
1010.101
10100
10110.122
10120
1013-0.124
10140.0585
10150.251
10160.439
10170
10180.0503
10190
1020
10200
1021-0.0487
1022-0.0924
10230
1024-0.0523
10250.146
10260
10270.353
10280
10290.237
1030
10300
10310.231
1032-0.184
10330.0912
10340
10350
10360.0659
10370
10380.0417
1039-0.238
1040
10400.0835
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: CNhs10587

Jaspar motifP-value
MA0002.28.29221e-4
MA0003.10.254
MA0004.10.788
MA0006.10.319
MA0007.10.133
MA0009.10.391
MA0014.10.167
MA0017.19.60547e-6
MA0018.20.149
MA0019.10.801
MA0024.10.00235
MA0025.10.174
MA0027.10.179
MA0028.10.579
MA0029.10.495
MA0030.10.733
MA0031.10.0569
MA0035.20.745
MA0038.10.0121
MA0039.20.0788
MA0040.10.829
MA0041.10.24
MA0042.10.722
MA0043.10.109
MA0046.11.45241e-4
MA0047.20.0164
MA0048.10.469
MA0050.13.79834e-8
MA0051.14.73854e-4
MA0052.10.236
MA0055.10.809
MA0057.10.0816
MA0058.10.809
MA0059.10.333
MA0060.13.57506e-16
MA0061.10.0699
MA0062.20.132
MA0065.21.51986e-5
MA0066.10.104
MA0067.10.737
MA0068.10.713
MA0069.10.688
MA0070.10.3
MA0071.10.0433
MA0072.10.0282
MA0073.10.968
MA0074.10.445
MA0076.10.939
MA0077.10.0244
MA0078.10.686
MA0079.20.451
MA0080.26.86274e-11
MA0081.10.292
MA0083.10.717
MA0084.10.639
MA0087.10.893
MA0088.10.203
MA0090.10.353
MA0091.10.748
MA0092.10.374
MA0093.10.832
MA0099.23.60048e-4
MA0100.10.982
MA0101.10.125
MA0102.20.791
MA0103.10.00612
MA0104.20.993
MA0105.10.00643
MA0106.10.0811
MA0107.10.0892
MA0108.20.0114
MA0111.10.37
MA0112.23.59556e-6
MA0113.10.222
MA0114.11.61361e-4
MA0115.10.00539
MA0116.10.00889
MA0117.10.572
MA0119.10.0161
MA0122.10.804
MA0124.10.658
MA0125.10.0114
MA0131.10.652
MA0135.10.0417
MA0136.16.02806e-9
MA0137.20.0734
MA0138.20.321
MA0139.10.0532
MA0140.10.2
MA0141.11.6363e-4
MA0142.10.219
MA0143.10.00825
MA0144.10.063
MA0145.10.0475
MA0146.10.114
MA0147.10.765
MA0148.10.00211
MA0149.10.00131
MA0150.10.0144
MA0152.10.946
MA0153.12.86602e-4
MA0154.10.00295
MA0155.10.735
MA0156.10.00213
MA0157.10.0836
MA0159.10.00364
MA0160.10.00414
MA0162.10.307
MA0163.12.14579e-4
MA0164.10.994
MA0258.14.73581e-4
MA0259.10.973



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: CNhs10587

Novel motifP-value
10.039
100.0687
1000.942
1010.735
1020.64
1030.0304
1040.904
1050.313
1060.0324
1070.197
1080.782
1090.0139
110.0393
1100.068
1110.0207
1120.00814
1130.958
1140.0169
1150.484
1160.28
1170.0225
1180.565
1190.127
120.954
1200.924
1210.464
1220.895
1230.61
1240.653
1250.273
1260.209
1270.226
1280.0524
1290.147
130.00838
1300.883
1310.781
1320.26
1330.42
1340.983
1350.718
1360.093
1370.582
1380.852
1390.0139
140.471
1400.0138
1410.208
1420.852
1430.196
1440.799
1450.129
1460.672
1470.627
1480.0864
1490.155
150.0751
1500.356
1510.328
1520.0722
1530.193
1540.542
1550.585
1560.0538
1570.731
1580.359
1590.551
1600.365
1610.223
1620.979
1630.436
1640.0267
1650.344
1660.84
1670.306
1680.898
1690.00198
170.051
180.612
190.147
20.999
200.589
210.596
220.201
230.262
240.171
250.371
260.0378
270.592
280.478
290.12
30.0807
300.825
310.594
320.2
330.24
340.891
350.332
360.14
370.0204
380.274
390.345
40.72
400.191
410.44
420.332
430.119
440.0169
450.788
460.139
470.079
480.0535
490.115
50.135
500.85
510.473
520.51
530.946
540.602
550.354
560.397
570.293
580.168
590.0893
60.562
600.1
610.231
620.0623
630.113
640.431
650.155
660.902
670.665
680.18
690.623
70.106
702.14811e-4
710.0446
720.498
730.0341
740.351
750.021
760.554
770.178
780.115
790.0875
80.0524
800.559
810.536
820.0834
830.117
840.711
850.0331
860.251
870.263
880.553
890.176
90.553
900.00561
910.352
920.0787
930.454
940.582
950.0553
960.379
970.604
980.482
990.565



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: CNhs10587


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)
0000295 (mouse embryonic day 12 sample)
0011434 (mouse whole body- embryo E12 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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