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|fonse_treatment_closure=
|fonse_treatment_closure=
|top_motifs=NKX2-2,8:3.76745366504;FOX{F1,F2,J1}:3.15381156154;FOX{D1,D2}:2.79280630993;CEBPA,B_DDIT3:2.24134533612;FOXM1:2.21955935537;FOXA2:2.04363599697;GATA6:2.00213320209;PITX1..3:1.93821802878;NR6A1:1.92284880213;RXR{A,B,G}_{NR1H2,PPAR}dimers:1.86162802686;HNF1A:1.78647658134;NFIL3:1.66515697461;HNF4A_NR2F1,2:1.48351972541;ARID5B:1.46972573041;HLF:1.41992434144;NR3C1:1.39507484514;ZNF423:1.36040615477;UFEwm:1.32230939094;RXRA_VDR{dimer}:1.30656531505;STAT2,4,6:1.29380263494;EBF1:1.25050982414;ALX4:1.22507070727;HMGA1,2:1.22197961001;AIRE:1.09154544622;ZBTB16:1.07613992604;GZF1:1.02692122493;PAX1,9:0.937813489836;FOXQ1:0.933530035423;POU1F1:0.929980745756;NANOG{mouse}:0.861548048827;STAT5{A,B}:0.853194803341;FOXD3:0.842527866506;BPTF:0.836702730138;FOXP1:0.814463159008;E2F1..5:0.794979042391;NR1H4:0.771151056942;EVI1:0.727871049104;PDX1:0.711798690925;SPIB:0.706921651981;HOXA9_MEIS1:0.656804939785;ONECUT1,2:0.599527462571;bHLH_family:0.487955682622;IRF1,2:0.46800397712;PAX6:0.46008901459;SPI1:0.457889550335;RXR{A,B,G}:0.430166838604;RBPJ:0.404567638142;ESRRA:0.367624994556;PBX1:0.366810769968;TP53:0.361575949726;CUX2:0.314381626524;GCM1,2:0.310743477743;MYB:0.295179228227;HAND1,2:0.295108334879;IKZF1:0.281892583574;PAX4:0.279666299593;DBP:0.277196733874;IRF7:0.264816534127;CDX1,2,4:0.258512491513;EN1,2:0.252226119129;ETS1,2:0.237064169317;FOXO1,3,4:0.188086782328;AR:0.172163170655;NR5A1,2:0.169159551661;NFIX:0.150673623967;ELF1,2,4:0.137502681834;NFY{A,B,C}:0.0833221590505;NKX3-2:0.0650494601598;NFE2:0.0622199709377;SNAI1..3:0.0519110032684;TEF:0.0432081896519;DMAP1_NCOR{1,2}_SMARC:0.0278043781885;MYBL2:-0.0230810272032;MYOD1:-0.0448029019769;ZNF148:-0.0654094045868;RUNX1..3:-0.128368991926;TLX2:-0.1459374587;ZIC1..3:-0.21027537202;ZBTB6:-0.272827465299;NFE2L2:-0.27475773683;TBP:-0.27584665279;IKZF2:-0.312665139787;HIF1A:-0.33622680642;TLX1..3_NFIC{dimer}:-0.359524491444;SREBF1,2:-0.371908501458;MTF1:-0.3761878682;AHR_ARNT_ARNT2:-0.383867763964;PPARG:-0.384512166482;CREB1:-0.398025543755;GFI1B:-0.405793496299;NFE2L1:-0.439745588376;TFAP4:-0.450936077031;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:-0.470195500938;YY1:-0.48256233099;MYFfamily:-0.492069606491;NKX6-1,2:-0.501175619371;PAX2:-0.524516374454;ATF5_CREB3:-0.526110396586;BACH2:-0.534615414015;SRF:-0.5399592388;POU3F1..4:-0.563531624557;ATF4:-0.564485534824;NKX2-1,4:-0.567067571761;KLF4:-0.577068178468;ZEB1:-0.596438533674;TOPORS:-0.598471869226;FOXL1:-0.60704924755;NFKB1_REL_RELA:-0.612724167366;RREB1:-0.628200289093;RORA:-0.661108741714;XCPE1{core}:-0.667585134236;TEAD1:-0.669694173145;FOX{I1,J2}:-0.700673685299;GATA4:-0.715206804274;EGR1..3:-0.728245295601;TFCP2:-0.729606911693;GFI1:-0.736410769281;PAX5:-0.740467054475;SP1:-0.768163654092;MEF2{A,B,C,D}:-0.786602704735;NHLH1,2:-0.787397720039;FOXN1:-0.791345439717;MAZ:-0.802992919625;HMX1:-0.812893959233;REST:-0.819848439206;LMO2:-0.883621254178;GTF2I:-0.904264900163;HOX{A4,D4}:-0.924620752349;FOXP3:-0.927948426495;SOX{8,9,10}:-0.939481721965;ELK1,4_GABP{A,B1}:-0.941654422012;TAL1_TCF{3,4,12}:-0.945657634057;BREu{core}:-0.955483801969;PRDM1:-1.00633634463;ATF6:-1.01209502384;SOX17:-1.02197134855;PATZ1:-1.02320734895;MZF1:-1.03432728903;TGIF1:-1.03771241984;SOX5:-1.0438199065;TFAP2{A,C}:-1.0491749309;OCT4_SOX2{dimer}:-1.05104299307;FOS_FOS{B,L1}_JUN{B,D}:-1.06102570719;PAX8:-1.06841321773;ZFP161:-1.09665772178;POU2F1..3:-1.09678540112;MAFB:-1.10985820514;T:-1.11095486053;TFAP2B:-1.11243503381;MTE{core}:-1.12490348036;TFDP1:-1.13167370309;CDC5L:-1.13550886699;ESR1:-1.13937395021;NKX3-1:-1.14871478578;HSF1,2:-1.16379692849;LEF1_TCF7_TCF7L1,2:-1.1919456512;HIC1:-1.19309147635;POU5F1:-1.20886702904;CRX:-1.21475751881;MED-1{core}:-1.21622549464;TBX4,5:-1.24757918498;ZNF143:-1.25163462675;RFX1:-1.29798951109;GLI1..3:-1.32279049829;LHX3,4:-1.39119979362;SOX2:-1.42287046986;RFX2..5_RFXANK_RFXAP:-1.42560802919;ZNF238:-1.42676776385;ADNP_IRX_SIX_ZHX:-1.42764908062;POU6F1:-1.44398453209;VSX1,2:-1.4444248884;ZNF384:-1.47076087695;SMAD1..7,9:-1.49186042945;PRRX1,2:-1.51541015139;ALX1:-1.51960223638;NRF1:-1.54954965761;HES1:-1.61334866127;ATF2:-1.61726320296;HOX{A5,B5}:-1.63240940738;STAT1,3:-1.63407905162;GTF2A1,2:-1.63522843061;JUN:-1.66766309524;NFATC1..3:-1.71465838017;FOSL2:-1.72723395837;EP300:-1.87374808956;NKX2-3_NKX2-5:-1.91192464901;SPZ1:-1.94555731761;NANOG:-2.16211224175;HBP1_HMGB_SSRP1_UBTF:-3.28130585394
|top_motifs=NKX2-2,8:3.76745366504;FOX{F1,F2,J1}:3.15381156154;FOX{D1,D2}:2.79280630993;CEBPA,B_DDIT3:2.24134533612;FOXM1:2.21955935537;FOXA2:2.04363599697;GATA6:2.00213320209;PITX1..3:1.93821802878;NR6A1:1.92284880213;RXR{A,B,G}_{NR1H2,PPAR}dimers:1.86162802686;HNF1A:1.78647658134;NFIL3:1.66515697461;HNF4A_NR2F1,2:1.48351972541;ARID5B:1.46972573041;HLF:1.41992434144;NR3C1:1.39507484514;ZNF423:1.36040615477;UFEwm:1.32230939094;RXRA_VDR{dimer}:1.30656531505;STAT2,4,6:1.29380263494;EBF1:1.25050982414;ALX4:1.22507070727;HMGA1,2:1.22197961001;AIRE:1.09154544622;ZBTB16:1.07613992604;GZF1:1.02692122493;PAX1,9:0.937813489836;FOXQ1:0.933530035423;POU1F1:0.929980745756;NANOG{mouse}:0.861548048827;STAT5{A,B}:0.853194803341;FOXD3:0.842527866506;BPTF:0.836702730138;FOXP1:0.814463159008;E2F1..5:0.794979042391;NR1H4:0.771151056942;EVI1:0.727871049104;PDX1:0.711798690925;SPIB:0.706921651981;HOXA9_MEIS1:0.656804939785;ONECUT1,2:0.599527462571;bHLH_family:0.487955682622;IRF1,2:0.46800397712;PAX6:0.46008901459;SPI1:0.457889550335;RXR{A,B,G}:0.430166838604;RBPJ:0.404567638142;ESRRA:0.367624994556;PBX1:0.366810769968;TP53:0.361575949726;CUX2:0.314381626524;GCM1,2:0.310743477743;MYB:0.295179228227;HAND1,2:0.295108334879;IKZF1:0.281892583574;PAX4:0.279666299593;DBP:0.277196733874;IRF7:0.264816534127;CDX1,2,4:0.258512491513;EN1,2:0.252226119129;ETS1,2:0.237064169317;FOXO1,3,4:0.188086782328;AR:0.172163170655;NR5A1,2:0.169159551661;NFIX:0.150673623967;ELF1,2,4:0.137502681834;NFY{A,B,C}:0.0833221590505;NKX3-2:0.0650494601598;NFE2:0.0622199709377;SNAI1..3:0.0519110032684;TEF:0.0432081896519;DMAP1_NCOR{1,2}_SMARC:0.0278043781885;MYBL2:-0.0230810272032;MYOD1:-0.0448029019769;ZNF148:-0.0654094045868;RUNX1..3:-0.128368991926;TLX2:-0.1459374587;ZIC1..3:-0.21027537202;ZBTB6:-0.272827465299;NFE2L2:-0.27475773683;TBP:-0.27584665279;IKZF2:-0.312665139787;HIF1A:-0.33622680642;TLX1..3_NFIC{dimer}:-0.359524491444;SREBF1,2:-0.371908501458;MTF1:-0.3761878682;AHR_ARNT_ARNT2:-0.383867763964;PPARG:-0.384512166482;CREB1:-0.398025543755;GFI1B:-0.405793496299;NFE2L1:-0.439745588376;TFAP4:-0.450936077031;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:-0.470195500938;YY1:-0.48256233099;MYFfamily:-0.492069606491;NKX6-1,2:-0.501175619371;PAX2:-0.524516374454;ATF5_CREB3:-0.526110396586;BACH2:-0.534615414015;SRF:-0.5399592388;POU3F1..4:-0.563531624557;ATF4:-0.564485534824;NKX2-1,4:-0.567067571761;KLF4:-0.577068178468;ZEB1:-0.596438533674;TOPORS:-0.598471869226;FOXL1:-0.60704924755;NFKB1_REL_RELA:-0.612724167366;RREB1:-0.628200289093;RORA:-0.661108741714;XCPE1{core}:-0.667585134236;TEAD1:-0.669694173145;FOX{I1,J2}:-0.700673685299;GATA4:-0.715206804274;EGR1..3:-0.728245295601;TFCP2:-0.729606911693;GFI1:-0.736410769281;PAX5:-0.740467054475;SP1:-0.768163654092;MEF2{A,B,C,D}:-0.786602704735;NHLH1,2:-0.787397720039;FOXN1:-0.791345439717;MAZ:-0.802992919625;HMX1:-0.812893959233;REST:-0.819848439206;LMO2:-0.883621254178;GTF2I:-0.904264900163;HOX{A4,D4}:-0.924620752349;FOXP3:-0.927948426495;SOX{8,9,10}:-0.939481721965;ELK1,4_GABP{A,B1}:-0.941654422012;TAL1_TCF{3,4,12}:-0.945657634057;BREu{core}:-0.955483801969;PRDM1:-1.00633634463;ATF6:-1.01209502384;SOX17:-1.02197134855;PATZ1:-1.02320734895;MZF1:-1.03432728903;TGIF1:-1.03771241984;SOX5:-1.0438199065;TFAP2{A,C}:-1.0491749309;OCT4_SOX2{dimer}:-1.05104299307;FOS_FOS{B,L1}_JUN{B,D}:-1.06102570719;PAX8:-1.06841321773;ZFP161:-1.09665772178;POU2F1..3:-1.09678540112;MAFB:-1.10985820514;T:-1.11095486053;TFAP2B:-1.11243503381;MTE{core}:-1.12490348036;TFDP1:-1.13167370309;CDC5L:-1.13550886699;ESR1:-1.13937395021;NKX3-1:-1.14871478578;HSF1,2:-1.16379692849;LEF1_TCF7_TCF7L1,2:-1.1919456512;HIC1:-1.19309147635;POU5F1:-1.20886702904;CRX:-1.21475751881;MED-1{core}:-1.21622549464;TBX4,5:-1.24757918498;ZNF143:-1.25163462675;RFX1:-1.29798951109;GLI1..3:-1.32279049829;LHX3,4:-1.39119979362;SOX2:-1.42287046986;RFX2..5_RFXANK_RFXAP:-1.42560802919;ZNF238:-1.42676776385;ADNP_IRX_SIX_ZHX:-1.42764908062;POU6F1:-1.44398453209;VSX1,2:-1.4444248884;ZNF384:-1.47076087695;SMAD1..7,9:-1.49186042945;PRRX1,2:-1.51541015139;ALX1:-1.51960223638;NRF1:-1.54954965761;HES1:-1.61334866127;ATF2:-1.61726320296;HOX{A5,B5}:-1.63240940738;STAT1,3:-1.63407905162;GTF2A1,2:-1.63522843061;JUN:-1.66766309524;NFATC1..3:-1.71465838017;FOSL2:-1.72723395837;EP300:-1.87374808956;NKX2-3_NKX2-5:-1.91192464901;SPZ1:-1.94555731761;NANOG:-2.16211224175;HBP1_HMGB_SSRP1_UBTF:-3.28130585394
|comment=
|created_by=
|creation_date=
|def=
|has_quality=
|is_a=EFO:0002091;;FF:0000004;;FF:0000103;;FF:0011395
|namespace=FANTOM5
|part_of=
}}
}}

Revision as of 16:03, 7 March 2012


Name:liver, neonate N00
Species:Mouse (Mus musculus)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissueliver
dev stage0 day 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
Download raw sequence, BAM & CTSS
Mm9
BAMCTSS
[{{{mm9bam}}} download][{{{mm9ctss}}} donwload]
Mm10
BAMCTSS
[{{{mm10bam}}} download][{{{mm10ctss}}} donwload]





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

CNhs11117

00
10
100
1000
1000-0.00285
10010.0581
10020.061
1003-0.102
10040
10050.219
1006-0.143
1007-0.0684
10080
1009-0.0406
1010.104
10100
1011-0.165
10120.0147
10130.0802
10140.208
1015-0.233
1016-0.261
10170
10180
10190
1020
10200
10210.0653
10220.0653
10230
10240.122
10250.454
10260
1027-0.00994
10280
10290.185
103-0.00602
10300.172
10310.00115
1032-0.21
1033-0.00124
10340.644
10350
10360.083
10370
1038-0.126
10390.353
1040
1040-0.0869
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 no result for this sample


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: CNhs11117

Jaspar motifP-value
MA0002.20.156
MA0003.10.702
MA0004.10.547
MA0006.10.26
MA0007.10.18
MA0009.10.189
MA0014.10.883
MA0017.11.02945e-12
MA0018.24.62858e-5
MA0019.10.301
MA0024.10.987
MA0025.10.78
MA0027.10.651
MA0028.10.781
MA0029.10.129
MA0030.10.0296
MA0031.10.04
MA0035.29.49523e-6
MA0038.10.0309
MA0039.20.621
MA0040.10.209
MA0041.10.369
MA0042.10.962
MA0043.10.01
MA0046.11.92565e-27
MA0047.24.44081e-6
MA0048.10.213
MA0050.10.0949
MA0051.10.488
MA0052.13.24587e-5
MA0055.10.55
MA0057.10.829
MA0058.10.579
MA0059.10.125
MA0060.10.00581
MA0061.10.214
MA0062.20.686
MA0065.23.03421e-9
MA0066.10.00572
MA0067.10.231
MA0068.10.973
MA0069.10.193
MA0070.10.777
MA0071.10.00209
MA0072.10.0345
MA0073.10.478
MA0074.10.15
MA0076.10.314
MA0077.10.0335
MA0078.10.455
MA0079.20.103
MA0080.20.00693
MA0081.10.688
MA0083.10.0382
MA0084.10.065
MA0087.10.0186
MA0088.10.596
MA0090.10.51
MA0091.10.316
MA0092.10.11
MA0093.10.618
MA0099.20.585
MA0100.10.995
MA0101.10.677
MA0102.20.144
MA0103.10.261
MA0104.20.956
MA0105.10.00123
MA0106.10.155
MA0107.10.918
MA0108.22.16129e-4
MA0111.10.781
MA0112.22.41757e-6
MA0113.10.129
MA0114.11.8395e-10
MA0115.14.4174e-8
MA0116.10.0125
MA0117.10.996
MA0119.10.0259
MA0122.10.134
MA0124.10.938
MA0125.10.575
MA0131.10.996
MA0135.10.049
MA0136.10.557
MA0137.20.997
MA0138.20.885
MA0139.10.125
MA0140.14.55036e-12
MA0141.13.84837e-5
MA0142.10.351
MA0143.10.227
MA0144.10.61
MA0145.10.487
MA0146.10.195
MA0147.10.738
MA0148.19.44022e-9
MA0149.10.00571
MA0150.10.0828
MA0152.10.283
MA0153.15.88437e-20
MA0154.10.0235
MA0155.10.445
MA0156.10.741
MA0157.10.0222
MA0159.10.00704
MA0160.10.00195
MA0162.10.314
MA0163.11.8764e-6
MA0164.10.431
MA0258.10.00361
MA0259.10.871



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: CNhs11117

Novel motifP-value
10.153
100.0893
1000.499
1010.376
1020.471
1030.00394
1040.917
1050.905
1060.0128
1070.0169
1080.883
1090.0714
110.098
1100.0784
1110.0297
1120.00167
1130.996
1140.0253
1150.719
1160.828
1170.0157
1180.106
1190.118
120.509
1200.945
1210.979
1220.658
1230.531
1240.104
1250.464
1260.118
1270.702
1280.00948
1290.471
130.00207
1300.791
1310.67
1320.759
1330.144
1340.971
1350.985
1360.442
1370.299
1380.303
1390.657
140.91
1400.00693
1410.498
1420.0538
1430.31
1440.798
1450.0168
1460.486
1470.733
1480.56
1490.71
150.0678
1500.157
1510.417
1520.186
1530.137
1540.544
1550.796
1560.156
1570.904
1580.851
1590.765
1600.131
1610.603
1620.637
1630.587
1640.0138
1650.353
1660.926
1670.169
1680.955
1690.00294
170.0334
180.455
190.0564
20.93
200.231
210.793
220.238
230.463
240.442
250.945
261.08956e-4
270.722
280.412
290.145
30.0169
300.805
310.348
320.143
330.23
340.957
350.504
360.0421
370.0579
380.616
390.211
40.389
400.274
410.627
420.157
430.0436
440.104
450.879
460.045
470.459
480.222
490.0424
50.0501
500.471
510.339
520.296
530.702
540.36
550.829
560.384
570.435
580.49
590.2
60.827
600.0788
610.151
620.112
630.115
640.46
650.326
660.706
670.662
680.132
690.348
70.164
700.172
710.0232
720.57
730.105
740.957
750.0225
760.539
770.599
780.00727
790.619
80.0106
800.246
810.728
820.103
830.454
840.905
850.131
860.185
870.676
880.927
890.566
90.702
900.061
910.184
920.0906
930.793
940.8
950.0998
960.0915
970.683
980.284
990.27



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: CNhs11117


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
0000015 (anatomical boundary)
0000061 (anatomical structure)
0000062 (organ)
0000077 (mixed endoderm/mesoderm-derived structure)
0000465 (material anatomical entity)
0000466 (immaterial anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000475 (organism subdivision)
0000479 (tissue)
0000480 (anatomical group)
0000481 (multi-tissue structure)
0000916 (abdomen)
0000922 (embryo)
0000923 (germ layer)
0000925 (endoderm)
0000926 (mesoderm)
0000949 (endocrine system)
0001007 (digestive system)
0001041 (foregut)
0001048 (primordium)
0001062 (anatomical entity)
0001555 (digestive tract)
0002050 (embryonic structure)
0002100 (trunk)
0002107 (liver)
0002330 (exocrine system)
0002365 (exocrine gland)
0002368 (endocrine gland)
0002405 (immune system)
0002417 (abdominal segment of trunk)
0002423 (hepatobiliary system)
0002530 (gland)
0002532 (epiblast (generic))
0003104 (mesenchyme)
0003894 (liver primordium)
0004119 (endoderm-derived structure)
0004120 (mesoderm-derived structure)
0004161 (septum transversum)
0004185 (endodermal part of digestive tract)
0004921 (subdivision of digestive tract)
0005057 (immune organ)
0005172 (abdomen element)
0005173 (abdominal segment element)
0005177 (trunk region element)
0005256 (trunk mesenchyme)
0005423 (developing anatomical structure)
0006235 (foregut-midgut junction)
0006925 (digestive gland)
0007026 (primitive gut)
0008835 (hepatic diverticulum)
0008836 (liver bud)
0009142 (entire embryonic mesenchyme)

FF: FANTOM5
NA

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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