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|top_motifs=HOX{A4,D4}:3.04039727014;FOS_FOS{B,L1}_JUN{B,D}:2.84529433955;TBP:2.6883336281;NANOG:2.57268020987;VSX1,2:2.5067209033;LEF1_TCF7_TCF7L1,2:2.31691500811;FOSL2:2.26970409476;TP53:2.09510165515;TFCP2:1.97052056551;T:1.92425996086;SPZ1:1.85247350355;BACH2:1.85035814239;GLI1..3:1.80595867919;TOPORS:1.78422602823;PDX1:1.52745828502;GCM1,2:1.52051451254;HMX1:1.48442287506;ZNF148:1.466240846;NKX2-3_NKX2-5:1.45545868842;ZNF238:1.39257008715;TEAD1:1.38606657579;FOX{I1,J2}:1.36297082091;EN1,2:1.33594508201;SP1:1.32264470134;GFI1:1.30624347073;TFAP4:1.29222577945;SMAD1..7,9:1.26742064055;TFAP2{A,C}:1.25448685074;GFI1B:1.21768226022;HLF:1.19470509554;XCPE1{core}:1.17727239033;NFATC1..3:1.13729446011;NKX2-1,4:1.10387372831;PITX1..3:1.09673235437;MYOD1:1.07135313962;CDC5L:1.0452463468;IKZF1:1.04442089576;GATA4:1.04282925772;TBX4,5:1.02831458988;TAL1_TCF{3,4,12}:1.00489404743;SOX5:0.965839671341;ATF2:0.956320187422;EP300:0.935003799468;FOXO1,3,4:0.89156619908;CRX:0.879737138717;TEF:0.875677590725;HSF1,2:0.845427853222;NFE2:0.837183022509;GTF2I:0.799684346276;AIRE:0.780776507204;SNAI1..3:0.734709928531;NKX3-2:0.721960649375;FOXQ1:0.705554025978;ATF4:0.703646099735;CEBPA,B_DDIT3:0.699378241349;PAX5:0.696767181952;EBF1:0.695051689417;SREBF1,2:0.684866533405;MAZ:0.66674081357;ZNF384:0.660579380492;MYFfamily:0.647936753686;MEF2{A,B,C,D}:0.641857524837;NFE2L2:0.638326465553;ESR1:0.624617210473;ALX4:0.607841067305;TLX1..3_NFIC{dimer}:0.592855991497;ALX1:0.567861403968;RBPJ:0.542967878938;MYBL2:0.542902429168;GTF2A1,2:0.539255375933;PAX2:0.538589474346;ZEB1:0.538581826196;TGIF1:0.538180914812;E2F1..5:0.534083695591;POU3F1..4:0.527329551835;ATF6:0.517265171263;SRF:0.514014763904;POU2F1..3:0.474662118651;HIC1:0.446416429188;MAFB:0.441415269838;POU6F1:0.393598933503;IKZF2:0.381001681206;FOXP3:0.365668772645;FOXP1:0.359432211668;FOXL1:0.357638487493;RORA:0.354980260994;HIF1A:0.350298380536;KLF4:0.343027480179;TFDP1:0.300599015649;bHLH_family:0.300309269731;PATZ1:0.292444515534;EGR1..3:0.272967860543;PRRX1,2:0.260074524099;TFAP2B:0.205804366754;SOX{8,9,10}:0.195425367975;FOXN1:0.185663539279;ZNF143:0.180341447523;MZF1:0.173619621794;MTF1:0.169551438811;STAT5{A,B}:0.155411389739;BREu{core}:0.147623256561;TLX2:0.145480100168;LHX3,4:0.118487236313;NFY{A,B,C}:0.0751596238714;SOX2:0.0740621863699;DBP:0.0708930547375;PRDM1:0.0667419540969;NKX2-2,8:0.0643411888979;IRF7:0.0486119267562;NKX3-1:0.0395140423936;NFE2L1:0.0237473421742;PAX8:0.0187644851032;MTE{core}:0.00570206143988;STAT2,4,6:0.000679199482281;HES1:-0.000954904356127;ZIC1..3:-0.0109025207419;NR3C1:-0.0121893732823;SOX17:-0.0162641877109;RFX2..5_RFXANK_RFXAP:-0.0318441442504;NHLH1,2:-0.041280738926;NFKB1_REL_RELA:-0.0468400655122;SPI1:-0.0610464534056;MED-1{core}:-0.0662626025678;POU5F1:-0.0678853144443;NKX6-1,2:-0.0756572125683;PAX6:-0.0862092446056;SPIB:-0.090391521966;HAND1,2:-0.111309214846;HOX{A5,B5}:-0.11404666908;HOXA9_MEIS1:-0.125375940153;ELK1,4_GABP{A,B1}:-0.130015367743;RREB1:-0.139585542635;HMGA1,2:-0.154241727796;NFIX:-0.177995141843;STAT1,3:-0.189899594691;NANOG{mouse}:-0.192924911044;ELF1,2,4:-0.19811834263;FOX{D1,D2}:-0.230412844764;ETS1,2:-0.23437810454;DMAP1_NCOR{1,2}_SMARC:-0.271507729799;NRF1:-0.283437408583;ZFP161:-0.292336245229;IRF1,2:-0.295162820185;REST:-0.313605763114;POU1F1:-0.322898347653;MYB:-0.333883024893;PAX1,9:-0.346356945996;RUNX1..3:-0.395251645904;RXR{A,B,G}_{NR1H2,PPAR}dimers:-0.406821000876;FOX{F1,F2,J1}:-0.412911982272;ATF5_CREB3:-0.45711517489;GZF1:-0.462704365993;ADNP_IRX_SIX_ZHX:-0.479033898152;HNF4A_NR2F1,2:-0.492685874704;ZBTB6:-0.496740336497;CREB1:-0.504040697599;AHR_ARNT_ARNT2:-0.526985816328;CUX2:-0.535586045849;ESRRA:-0.562184537495;HBP1_HMGB_SSRP1_UBTF:-0.571287701205;FOXA2:-0.573717226859;ZNF423:-0.588046353222;PPARG:-0.591619049743;RXRA_VDR{dimer}:-0.597858135725;LMO2:-0.63264245846;NR6A1:-0.65107579567;RFX1:-0.704384888664;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:-0.715017254791;PAX4:-0.716701713052;ONECUT1,2:-0.726019364749;RXR{A,B,G}:-0.732469211594;HNF1A:-0.733406307321;GATA6:-0.745750759927;FOXM1:-0.780997455429;NFIL3:-0.804347789435;CDX1,2,4:-0.812887877986;ZBTB16:-0.826623468315;AR:-0.878066495125;FOXD3:-0.891258488935;JUN:-0.904649552749;BPTF:-0.913663067208;NR5A1,2:-0.940726501014;OCT4_SOX2{dimer}:-0.941001267233;UFEwm:-1.01446979168;PBX1:-1.23270941873;YY1:-1.29091270401;NR1H4:-1.33405805479;ARID5B:-1.39650508089;EVI1:-1.54901879254
|top_motifs=HOX{A4,D4}:3.04039727014;FOS_FOS{B,L1}_JUN{B,D}:2.84529433955;TBP:2.6883336281;NANOG:2.57268020987;VSX1,2:2.5067209033;LEF1_TCF7_TCF7L1,2:2.31691500811;FOSL2:2.26970409476;TP53:2.09510165515;TFCP2:1.97052056551;T:1.92425996086;SPZ1:1.85247350355;BACH2:1.85035814239;GLI1..3:1.80595867919;TOPORS:1.78422602823;PDX1:1.52745828502;GCM1,2:1.52051451254;HMX1:1.48442287506;ZNF148:1.466240846;NKX2-3_NKX2-5:1.45545868842;ZNF238:1.39257008715;TEAD1:1.38606657579;FOX{I1,J2}:1.36297082091;EN1,2:1.33594508201;SP1:1.32264470134;GFI1:1.30624347073;TFAP4:1.29222577945;SMAD1..7,9:1.26742064055;TFAP2{A,C}:1.25448685074;GFI1B:1.21768226022;HLF:1.19470509554;XCPE1{core}:1.17727239033;NFATC1..3:1.13729446011;NKX2-1,4:1.10387372831;PITX1..3:1.09673235437;MYOD1:1.07135313962;CDC5L:1.0452463468;IKZF1:1.04442089576;GATA4:1.04282925772;TBX4,5:1.02831458988;TAL1_TCF{3,4,12}:1.00489404743;SOX5:0.965839671341;ATF2:0.956320187422;EP300:0.935003799468;FOXO1,3,4:0.89156619908;CRX:0.879737138717;TEF:0.875677590725;HSF1,2:0.845427853222;NFE2:0.837183022509;GTF2I:0.799684346276;AIRE:0.780776507204;SNAI1..3:0.734709928531;NKX3-2:0.721960649375;FOXQ1:0.705554025978;ATF4:0.703646099735;CEBPA,B_DDIT3:0.699378241349;PAX5:0.696767181952;EBF1:0.695051689417;SREBF1,2:0.684866533405;MAZ:0.66674081357;ZNF384:0.660579380492;MYFfamily:0.647936753686;MEF2{A,B,C,D}:0.641857524837;NFE2L2:0.638326465553;ESR1:0.624617210473;ALX4:0.607841067305;TLX1..3_NFIC{dimer}:0.592855991497;ALX1:0.567861403968;RBPJ:0.542967878938;MYBL2:0.542902429168;GTF2A1,2:0.539255375933;PAX2:0.538589474346;ZEB1:0.538581826196;TGIF1:0.538180914812;E2F1..5:0.534083695591;POU3F1..4:0.527329551835;ATF6:0.517265171263;SRF:0.514014763904;POU2F1..3:0.474662118651;HIC1:0.446416429188;MAFB:0.441415269838;POU6F1:0.393598933503;IKZF2:0.381001681206;FOXP3:0.365668772645;FOXP1:0.359432211668;FOXL1:0.357638487493;RORA:0.354980260994;HIF1A:0.350298380536;KLF4:0.343027480179;TFDP1:0.300599015649;bHLH_family:0.300309269731;PATZ1:0.292444515534;EGR1..3:0.272967860543;PRRX1,2:0.260074524099;TFAP2B:0.205804366754;SOX{8,9,10}:0.195425367975;FOXN1:0.185663539279;ZNF143:0.180341447523;MZF1:0.173619621794;MTF1:0.169551438811;STAT5{A,B}:0.155411389739;BREu{core}:0.147623256561;TLX2:0.145480100168;LHX3,4:0.118487236313;NFY{A,B,C}:0.0751596238714;SOX2:0.0740621863699;DBP:0.0708930547375;PRDM1:0.0667419540969;NKX2-2,8:0.0643411888979;IRF7:0.0486119267562;NKX3-1:0.0395140423936;NFE2L1:0.0237473421742;PAX8:0.0187644851032;MTE{core}:0.00570206143988;STAT2,4,6:0.000679199482281;HES1:-0.000954904356127;ZIC1..3:-0.0109025207419;NR3C1:-0.0121893732823;SOX17:-0.0162641877109;RFX2..5_RFXANK_RFXAP:-0.0318441442504;NHLH1,2:-0.041280738926;NFKB1_REL_RELA:-0.0468400655122;SPI1:-0.0610464534056;MED-1{core}:-0.0662626025678;POU5F1:-0.0678853144443;NKX6-1,2:-0.0756572125683;PAX6:-0.0862092446056;SPIB:-0.090391521966;HAND1,2:-0.111309214846;HOX{A5,B5}:-0.11404666908;HOXA9_MEIS1:-0.125375940153;ELK1,4_GABP{A,B1}:-0.130015367743;RREB1:-0.139585542635;HMGA1,2:-0.154241727796;NFIX:-0.177995141843;STAT1,3:-0.189899594691;NANOG{mouse}:-0.192924911044;ELF1,2,4:-0.19811834263;FOX{D1,D2}:-0.230412844764;ETS1,2:-0.23437810454;DMAP1_NCOR{1,2}_SMARC:-0.271507729799;NRF1:-0.283437408583;ZFP161:-0.292336245229;IRF1,2:-0.295162820185;REST:-0.313605763114;POU1F1:-0.322898347653;MYB:-0.333883024893;PAX1,9:-0.346356945996;RUNX1..3:-0.395251645904;RXR{A,B,G}_{NR1H2,PPAR}dimers:-0.406821000876;FOX{F1,F2,J1}:-0.412911982272;ATF5_CREB3:-0.45711517489;GZF1:-0.462704365993;ADNP_IRX_SIX_ZHX:-0.479033898152;HNF4A_NR2F1,2:-0.492685874704;ZBTB6:-0.496740336497;CREB1:-0.504040697599;AHR_ARNT_ARNT2:-0.526985816328;CUX2:-0.535586045849;ESRRA:-0.562184537495;HBP1_HMGB_SSRP1_UBTF:-0.571287701205;FOXA2:-0.573717226859;ZNF423:-0.588046353222;PPARG:-0.591619049743;RXRA_VDR{dimer}:-0.597858135725;LMO2:-0.63264245846;NR6A1:-0.65107579567;RFX1:-0.704384888664;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:-0.715017254791;PAX4:-0.716701713052;ONECUT1,2:-0.726019364749;RXR{A,B,G}:-0.732469211594;HNF1A:-0.733406307321;GATA6:-0.745750759927;FOXM1:-0.780997455429;NFIL3:-0.804347789435;CDX1,2,4:-0.812887877986;ZBTB16:-0.826623468315;AR:-0.878066495125;FOXD3:-0.891258488935;JUN:-0.904649552749;BPTF:-0.913663067208;NR5A1,2:-0.940726501014;OCT4_SOX2{dimer}:-0.941001267233;UFEwm:-1.01446979168;PBX1:-1.23270941873;YY1:-1.29091270401;NR1H4:-1.33405805479;ARID5B:-1.39650508089;EVI1:-1.54901879254
|xref=
|xref=
|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_mouse;search_select_hide=table111:662-22H3;search_select_hide=table117:662-22H3
}}
}}

Latest revision as of 19:19, 4 June 2020


Name:skin, neonate N03
Species:Mouse (Mus musculus)
Library ID:CNhs11215
Sample type:developmental
Genomic View: UCSC
CAGEd-oPOSSUM:link
ZENBU report :link
Additional information
Sample information
strainC57BL/6J
tissueskin
dev stage3 days neonate
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  SAMD00004789
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11215 CAGE DRX009079 DRR009953
Accession ID Mm9

Library idBAMCTSS
CNhs11215 DRZ001378 DRZ002761
Accession ID Mm10

Library idBAMCTSS
CNhs11215 DRZ012728 DRZ014111
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

CNhs11215

00
10
100
1000
10000.0804
10010.0374
1002-0.0566
10030.121
10040
10050
10060.0495
10070.0759
10080
10090.21
1010.111
10100
10110.0254
10120
1013-0.058
10140.0836
1015-0.0122
10160.0979
10170
10180.467
10190
1020
10200
10210.0254
10220.153
10230
10240.0984
10250
10260
10270.0113
10280
1029-0.0267
1030.389
10300
10310.245
1032-0.0495
10330
10340.0495
10350.0254
10360.051
10370
10380.0376
1039-0.0756
1040
10400.14
10410.733



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: CNhs11215

Jaspar motifP-value
MA0002.20.123
MA0003.10.446
MA0004.10.496
MA0006.10.101
MA0007.10.303
MA0009.10.164
MA0014.10.725
MA0017.12.1883e-9
MA0018.20.239
MA0019.10.175
MA0024.10.161
MA0025.10.9
MA0027.10.995
MA0028.10.00487
MA0029.10.335
MA0030.10.321
MA0031.10.956
MA0035.25.15306e-4
MA0038.10.00233
MA0039.20.00412
MA0040.10.244
MA0041.10.287
MA0042.10.602
MA0043.10.493
MA0046.11.88659e-21
MA0047.20.0487
MA0048.10.438
MA0050.10.0181
MA0051.10.138
MA0052.11.22503e-9
MA0055.10.0449
MA0057.10.312
MA0058.10.262
MA0059.10.013
MA0060.10.00292
MA0061.10.0559
MA0062.29.58976e-5
MA0065.20.0246
MA0066.10.182
MA0067.10.909
MA0068.10.353
MA0069.10.81
MA0070.10.597
MA0071.10.00188
MA0072.10.615
MA0073.10.871
MA0074.10.0795
MA0076.10.0134
MA0077.10.56
MA0078.10.0316
MA0079.20.0326
MA0080.27.35174e-7
MA0081.10.00665
MA0083.10.00417
MA0084.10.88
MA0087.10.466
MA0088.10.647
MA0090.10.0157
MA0091.10.171
MA0092.10.269
MA0093.10.504
MA0099.22.3907e-10
MA0100.10.0469
MA0101.10.712
MA0102.20.111
MA0103.10.788
MA0104.20.049
MA0105.10.00457
MA0106.10.066
MA0107.10.913
MA0108.26.78402e-37
MA0111.10.393
MA0112.20.187
MA0113.10.136
MA0114.15.08266e-7
MA0115.17.43795e-5
MA0116.10.0179
MA0117.10.647
MA0119.10.776
MA0122.10.436
MA0124.10.404
MA0125.18.73086e-4
MA0131.10.827
MA0135.10.0149
MA0136.19.9065e-8
MA0137.20.414
MA0138.20.246
MA0139.10.014
MA0140.13.87348e-4
MA0141.12.6763e-8
MA0142.10.211
MA0143.10.0973
MA0144.10.973
MA0145.10.275
MA0146.10.352
MA0147.10.0166
MA0148.10.0378
MA0149.10.348
MA0150.10.392
MA0152.10.105
MA0153.14.97641e-13
MA0154.10.268
MA0155.10.664
MA0156.12.22717e-4
MA0157.10.346
MA0159.10.00462
MA0160.11.51697e-4
MA0162.10.485
MA0163.10.00929
MA0164.10.137
MA0258.10.0257
MA0259.10.343



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: CNhs11215

Novel motifP-value
10.235
100.356
1000.975
1010.93
1020.818
1030.0437
1040.176
1050.381
1060.526
1070.156
1080.943
1090.286
110.256
1100.429
1110.118
1120.106
1130.947
1140.233
1150.131
1160.637
1170.129
1180.0177
1190.374
120.497
1200.485
1210.446
1220.645
1230.726
1240.159
1250.533
1260.754
1270.352
1280.751
1290.433
130.172
1300.666
1310.277
1320.569
1330.35
1340.806
1350.215
1360.204
1370.465
1380.394
1390.0612
140.706
1400.388
1410.386
1420.948
1430.179
1440.93
1450.889
1460.816
1470.194
1480.0936
1490.462
150.0131
1500.526
1510.393
1520.0195
1530.675
1540.609
1550.434
1560.345
1570.00324
1580.132
1590.0794
1600.711
1610.2
1620.587
1630.764
1640.199
1650.273
1660.183
1670.00789
1680.322
1690.148
170.494
180.0978
190.763
20.197
200.141
210.99
220.869
230.371
240.971
250.224
260.0545
270.435
280.81
290.0583
30.158
300.0373
310.209
320.504
330.346
340.646
352.56414e-4
360.00992
370.769
380.586
390.272
40.615
400.223
410.473
420.694
430.269
440.0806
450.332
460.739
470.381
480.515
490.0414
50.151
500.571
510.781
520.139
530.287
540.885
550.745
560.719
570.776
580.833
590.758
60.977
600.29
610.998
620.363
630.921
640.184
650.329
660.871
670.985
680.0169
690.591
70.674
700.0854
710.527
720.648
730.499
740.823
750.0384
760.0012
770.427
780.0754
790.516
80.0744
800.22
810.29
820.271
830.251
840.61
850.912
860.232
870.0439
880.757
890.0963
90.528
900.186
910.484
920.394
930.674
940.673
950.72
960.622
970.0663
980.276
990.399



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: CNhs11215


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)
0000014 (zone of skin)
0001003 (skin epidermis)
0002097 (skin of body)
0002199 (integument)
0007029 (surface)
0000483 (epithelium)
0000479 (tissue)
0004121 (ectoderm-derived structure)
0000064 (organ part)
0000062 (organ)
0000475 (organism subdivision)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0000119 (cell layer)
0003102 (surface structure)
0007376 (outer epithelium)
0010371 (ecto-epithelium)
0010317 (germ layer / neural crest derived structure)
0002416 (integumental system)

FF: FANTOM5
0000102 (sample by type)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000004 (tissue sample)
0000303 (neonate sample - mouse)
0000311 (mouse neonate N3 sample)
0011400 (mouse skin- neonate N03 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
UBERON:0002532 (epiblast (generic))
UBERON:0006601 (presumptive ectoderm)
UBERON:0010316 (germ layer / neural crest)
FF:0000294 (mouse embryonic day 11 sample)

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