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|fonse_treatment_closure=
|fonse_treatment_closure=
|top_motifs=CRX:2.56430744781;SOX{8,9,10}:2.44720722183;SOX2:2.03062613025;LHX3,4:1.82856511638;PAX1,9:1.68529477615;NANOG:1.64911047805;NKX2-1,4:1.58823806781;HSF1,2:1.58744564991;RBPJ:1.5772470319;GFI1:1.53665965173;NFY{A,B,C}:1.48568916852;TAL1_TCF{3,4,12}:1.41647420827;MZF1:1.34589396945;ZNF143:1.34492034823;SOX17:1.32597551574;NRF1:1.20473606578;LEF1_TCF7_TCF7L1,2:1.19844992295;POU5F1:1.1754418333;TFDP1:1.14249117764;SOX5:1.12293360521;PATZ1:1.10001758935;NANOG{mouse}:1.09477938656;OCT4_SOX2{dimer}:1.09448573949;TOPORS:1.09414579349;BREu{core}:1.09266519971;NKX2-3_NKX2-5:1.08740903087;HMX1:1.07892759563;DBP:1.06306002965;HOX{A4,D4}:1.05157532477;GFI1B:1.04939021611;ATF2:1.03301460391;MAZ:0.993150087604;RORA:0.969328359784;TGIF1:0.965710809319;RXR{A,B,G}:0.962112708375;IKZF1:0.954764512067;SMAD1..7,9:0.942073676452;MED-1{core}:0.889190919111;RREB1:0.871204662299;AHR_ARNT_ARNT2:0.858790374153;NHLH1,2:0.855063184335;MYBL2:0.849297438849;KLF4:0.839760806171;PRDM1:0.836554624891;VSX1,2:0.823520794024;TFAP2B:0.817457820848;MYOD1:0.809194523689;E2F1..5:0.807820052608;EP300:0.805653616962;GTF2I:0.800575283365;PAX6:0.739495308904;HIC1:0.735772523701;CDC5L:0.717434049344;ZFP161:0.715176693607;PAX8:0.705051263143;ZNF384:0.683753597402;RFX1:0.677250500846;ZNF238:0.666569896429;PRRX1,2:0.66019868379;FOXN1:0.639459330799;POU6F1:0.627212000176;TFAP4:0.616347540063;MTE{core}:0.613166331734;ESR1:0.599550111922;NKX6-1,2:0.594447424605;ZIC1..3:0.593047845418;ADNP_IRX_SIX_ZHX:0.590015224091;GATA4:0.581893728294;NKX3-2:0.575312427134;CUX2:0.558358798807;NKX3-1:0.54273959506;POU2F1..3:0.537176891306;TBP:0.53143004921;YY1:0.525019199436;SP1:0.520108484698;MAFB:0.508836667532;HAND1,2:0.497042860976;EGR1..3:0.495085042029;ELK1,4_GABP{A,B1}:0.485320611389;IKZF2:0.479235088948;JUN:0.46313586465;GTF2A1,2:0.433560336198;PBX1:0.420014766958;POU3F1..4:0.419046949098;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:0.416293138208;RFX2..5_RFXANK_RFXAP:0.414278578723;ONECUT1,2:0.412126245125;GCM1,2:0.388831890532;HIF1A:0.379914556035;FOXD3:0.375156355794;TLX2:0.360691955079;UFEwm:0.358151994087;TEAD1:0.346808392178;TFCP2:0.34375881588;TFAP2{A,C}:0.330006821786;POU1F1:0.318183684834;STAT5{A,B}:0.313384615268;MYFfamily:0.30344781893;XCPE1{core}:0.299533275698;NR3C1:0.280161815655;REST:0.25564557121;BPTF:0.236409134349;ALX1:0.194870400631;STAT1,3:0.172923558531;MYB:0.13343606454;NFATC1..3:0.132327550915;AIRE:0.131047597223;HES1:0.130438375707;ZNF423:0.125820680833;ATF4:0.106523315936;PITX1..3:0.0820768492932;EN1,2:0.0771580507163;NFE2L1:0.0561230860979;FOX{I1,J2}:0.0519964754001;MTF1:0.0328468008536;ZBTB6:0.0321458065993;NFE2:0.0262375052265;FOXL1:0.0260779363258;MEF2{A,B,C,D}:0.00765008072414;PAX5:0.00282032530258;NFIX:0.00278730925605;FOXM1:-0.00252702601897;CREB1:-0.0413974574917;HOX{A5,B5}:-0.0436587791786;HOXA9_MEIS1:-0.0467215915693;T:-0.055455290982;ATF6:-0.0564513451374;ZBTB16:-0.0722113147971;HBP1_HMGB_SSRP1_UBTF:-0.0978954797348;ARID5B:-0.108733769089;CDX1,2,4:-0.116228342079;FOXP3:-0.133917535227;SRF:-0.160635212893;FOSL2:-0.169408504126;LMO2:-0.169447914294;TBX4,5:-0.169867644702;PAX4:-0.187078725427;PDX1:-0.199277343822;ZNF148:-0.221488872525;bHLH_family:-0.226356745735;ATF5_CREB3:-0.246609205331;PAX2:-0.255663679161;TLX1..3_NFIC{dimer}:-0.256007709;SPZ1:-0.265259580915;FOXA2:-0.26544948488;ALX4:-0.26760079646;RXR{A,B,G}_{NR1H2,PPAR}dimers:-0.276227663762;HMGA1,2:-0.308831290689;FOXQ1:-0.33189411898;SNAI1..3:-0.371708255564;NFE2L2:-0.405399915165;PPARG:-0.414510371675;BACH2:-0.432611174945;TEF:-0.440935412303;TP53:-0.442648533875;GZF1:-0.44451684458;EVI1:-0.448231321299;FOS_FOS{B,L1}_JUN{B,D}:-0.455777934285;ELF1,2,4:-0.461996573376;SPIB:-0.472479839994;FOXP1:-0.478942596366;GLI1..3:-0.483613532579;NFIL3:-0.484877816456;SPI1:-0.514413786174;EBF1:-0.54018918659;HNF4A_NR2F1,2:-0.570638317646;NKX2-2,8:-0.579497915262;RUNX1..3:-0.628540191693;SREBF1,2:-0.646228528593;GATA6:-0.651001144751;RXRA_VDR{dimer}:-0.657237655374;NR5A1,2:-0.688863084966;ZEB1:-0.698406227609;NFKB1_REL_RELA:-0.703276532165;AR:-0.711156858628;ESRRA:-0.72475459192;HNF1A:-0.739751455225;ETS1,2:-0.813965799758;CEBPA,B_DDIT3:-0.823178261582;IRF1,2:-0.945091397854;HLF:-0.950598304062;FOX{F1,F2,J1}:-1.02135330789;IRF7:-1.02215445988;DMAP1_NCOR{1,2}_SMARC:-1.03184466552;FOX{D1,D2}:-1.04745605758;FOXO1,3,4:-1.11061822129;NR1H4:-1.19808395706;STAT2,4,6:-1.30942162527;NR6A1:-1.62306258298
|top_motifs=CRX:2.56430744781;SOX{8,9,10}:2.44720722183;SOX2:2.03062613025;LHX3,4:1.82856511638;PAX1,9:1.68529477615;NANOG:1.64911047805;NKX2-1,4:1.58823806781;HSF1,2:1.58744564991;RBPJ:1.5772470319;GFI1:1.53665965173;NFY{A,B,C}:1.48568916852;TAL1_TCF{3,4,12}:1.41647420827;MZF1:1.34589396945;ZNF143:1.34492034823;SOX17:1.32597551574;NRF1:1.20473606578;LEF1_TCF7_TCF7L1,2:1.19844992295;POU5F1:1.1754418333;TFDP1:1.14249117764;SOX5:1.12293360521;PATZ1:1.10001758935;NANOG{mouse}:1.09477938656;OCT4_SOX2{dimer}:1.09448573949;TOPORS:1.09414579349;BREu{core}:1.09266519971;NKX2-3_NKX2-5:1.08740903087;HMX1:1.07892759563;DBP:1.06306002965;HOX{A4,D4}:1.05157532477;GFI1B:1.04939021611;ATF2:1.03301460391;MAZ:0.993150087604;RORA:0.969328359784;TGIF1:0.965710809319;RXR{A,B,G}:0.962112708375;IKZF1:0.954764512067;SMAD1..7,9:0.942073676452;MED-1{core}:0.889190919111;RREB1:0.871204662299;AHR_ARNT_ARNT2:0.858790374153;NHLH1,2:0.855063184335;MYBL2:0.849297438849;KLF4:0.839760806171;PRDM1:0.836554624891;VSX1,2:0.823520794024;TFAP2B:0.817457820848;MYOD1:0.809194523689;E2F1..5:0.807820052608;EP300:0.805653616962;GTF2I:0.800575283365;PAX6:0.739495308904;HIC1:0.735772523701;CDC5L:0.717434049344;ZFP161:0.715176693607;PAX8:0.705051263143;ZNF384:0.683753597402;RFX1:0.677250500846;ZNF238:0.666569896429;PRRX1,2:0.66019868379;FOXN1:0.639459330799;POU6F1:0.627212000176;TFAP4:0.616347540063;MTE{core}:0.613166331734;ESR1:0.599550111922;NKX6-1,2:0.594447424605;ZIC1..3:0.593047845418;ADNP_IRX_SIX_ZHX:0.590015224091;GATA4:0.581893728294;NKX3-2:0.575312427134;CUX2:0.558358798807;NKX3-1:0.54273959506;POU2F1..3:0.537176891306;TBP:0.53143004921;YY1:0.525019199436;SP1:0.520108484698;MAFB:0.508836667532;HAND1,2:0.497042860976;EGR1..3:0.495085042029;ELK1,4_GABP{A,B1}:0.485320611389;IKZF2:0.479235088948;JUN:0.46313586465;GTF2A1,2:0.433560336198;PBX1:0.420014766958;POU3F1..4:0.419046949098;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:0.416293138208;RFX2..5_RFXANK_RFXAP:0.414278578723;ONECUT1,2:0.412126245125;GCM1,2:0.388831890532;HIF1A:0.379914556035;FOXD3:0.375156355794;TLX2:0.360691955079;UFEwm:0.358151994087;TEAD1:0.346808392178;TFCP2:0.34375881588;TFAP2{A,C}:0.330006821786;POU1F1:0.318183684834;STAT5{A,B}:0.313384615268;MYFfamily:0.30344781893;XCPE1{core}:0.299533275698;NR3C1:0.280161815655;REST:0.25564557121;BPTF:0.236409134349;ALX1:0.194870400631;STAT1,3:0.172923558531;MYB:0.13343606454;NFATC1..3:0.132327550915;AIRE:0.131047597223;HES1:0.130438375707;ZNF423:0.125820680833;ATF4:0.106523315936;PITX1..3:0.0820768492932;EN1,2:0.0771580507163;NFE2L1:0.0561230860979;FOX{I1,J2}:0.0519964754001;MTF1:0.0328468008536;ZBTB6:0.0321458065993;NFE2:0.0262375052265;FOXL1:0.0260779363258;MEF2{A,B,C,D}:0.00765008072414;PAX5:0.00282032530258;NFIX:0.00278730925605;FOXM1:-0.00252702601897;CREB1:-0.0413974574917;HOX{A5,B5}:-0.0436587791786;HOXA9_MEIS1:-0.0467215915693;T:-0.055455290982;ATF6:-0.0564513451374;ZBTB16:-0.0722113147971;HBP1_HMGB_SSRP1_UBTF:-0.0978954797348;ARID5B:-0.108733769089;CDX1,2,4:-0.116228342079;FOXP3:-0.133917535227;SRF:-0.160635212893;FOSL2:-0.169408504126;LMO2:-0.169447914294;TBX4,5:-0.169867644702;PAX4:-0.187078725427;PDX1:-0.199277343822;ZNF148:-0.221488872525;bHLH_family:-0.226356745735;ATF5_CREB3:-0.246609205331;PAX2:-0.255663679161;TLX1..3_NFIC{dimer}:-0.256007709;SPZ1:-0.265259580915;FOXA2:-0.26544948488;ALX4:-0.26760079646;RXR{A,B,G}_{NR1H2,PPAR}dimers:-0.276227663762;HMGA1,2:-0.308831290689;FOXQ1:-0.33189411898;SNAI1..3:-0.371708255564;NFE2L2:-0.405399915165;PPARG:-0.414510371675;BACH2:-0.432611174945;TEF:-0.440935412303;TP53:-0.442648533875;GZF1:-0.44451684458;EVI1:-0.448231321299;FOS_FOS{B,L1}_JUN{B,D}:-0.455777934285;ELF1,2,4:-0.461996573376;SPIB:-0.472479839994;FOXP1:-0.478942596366;GLI1..3:-0.483613532579;NFIL3:-0.484877816456;SPI1:-0.514413786174;EBF1:-0.54018918659;HNF4A_NR2F1,2:-0.570638317646;NKX2-2,8:-0.579497915262;RUNX1..3:-0.628540191693;SREBF1,2:-0.646228528593;GATA6:-0.651001144751;RXRA_VDR{dimer}:-0.657237655374;NR5A1,2:-0.688863084966;ZEB1:-0.698406227609;NFKB1_REL_RELA:-0.703276532165;AR:-0.711156858628;ESRRA:-0.72475459192;HNF1A:-0.739751455225;ETS1,2:-0.813965799758;CEBPA,B_DDIT3:-0.823178261582;IRF1,2:-0.945091397854;HLF:-0.950598304062;FOX{F1,F2,J1}:-1.02135330789;IRF7:-1.02215445988;DMAP1_NCOR{1,2}_SMARC:-1.03184466552;FOX{D1,D2}:-1.04745605758;FOXO1,3,4:-1.11061822129;NR1H4:-1.19808395706;STAT2,4,6:-1.30942162527;NR6A1:-1.62306258298
|comment=
|created_by=
|creation_date=
|def=
|has_quality=
|is_a=EFO:0002091;;FF:0000004;;FF:0000103;;FF:0011344
|namespace=FANTOM5
|part_of=
}}
}}

Revision as of 16:02, 7 March 2012


Name:eyeball, embryo E15
Species:Mouse (Mus musculus)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissueeyeball
dev stage15 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
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

CNhs10593

00
10.0719
100
1000.0719
10000
1001-0.0303
10020.269
1003-0.0539
10040.497
1005-0.0389
10060.0416
10070.00775
10080
10090.0584
1010.0713
10100
10110.0204
10120
1013-0.147
10140.279
10150.224
10160.3
10170
10180.0719
10190
1020
10200
10210.0719
1022-0.0704
10230
1024-0.0322
10250
10260
10270.41
10280
1029-0.0424
1030.16
10300
10310.271
1032-7.9209e-4
10330.0584
10340
10350
10360.0278
10370
1038-0.0217
1039-0.176
1040
10400.0117
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: CNhs10593

Jaspar motifP-value
MA0002.26.74939e-5
MA0003.10.354
MA0004.10.623
MA0006.10.323
MA0007.10.276
MA0009.10.27
MA0014.10.188
MA0017.12.62133e-7
MA0018.20.0773
MA0019.10.641
MA0024.10.00207
MA0025.10.229
MA0027.10.462
MA0028.10.928
MA0029.10.913
MA0030.10.363
MA0031.10.0886
MA0035.20.0185
MA0038.19.04169e-4
MA0039.20.355
MA0040.10.0926
MA0041.10.166
MA0042.10.441
MA0043.10.12
MA0046.16.16473e-19
MA0047.27.44076e-4
MA0048.10.612
MA0050.11.0849e-7
MA0051.11.57441e-4
MA0052.10.69
MA0055.10.914
MA0057.10.131
MA0058.10.657
MA0059.10.332
MA0060.17.22073e-17
MA0061.10.0564
MA0062.20.298
MA0065.21.23956e-6
MA0066.10.079
MA0067.10.903
MA0068.10.25
MA0069.10.0602
MA0070.10.307
MA0071.10.265
MA0072.10.686
MA0073.10.922
MA0074.10.228
MA0076.10.51
MA0077.10.00171
MA0078.10.318
MA0079.20.374
MA0080.29.35648e-12
MA0081.10.228
MA0083.10.948
MA0084.10.0642
MA0087.10.0678
MA0088.10.313
MA0090.10.789
MA0091.10.4
MA0092.10.333
MA0093.10.658
MA0099.20.00219
MA0100.10.998
MA0101.10.151
MA0102.20.417
MA0103.10.00367
MA0104.20.901
MA0105.10.00406
MA0106.10.166
MA0107.10.0951
MA0108.21.99412e-7
MA0111.10.491
MA0112.21.20505e-5
MA0113.10.218
MA0114.16.00225e-6
MA0115.13.92795e-4
MA0116.10.00833
MA0117.10.673
MA0119.10.00977
MA0122.10.826
MA0124.10.41
MA0125.10.0023
MA0131.10.566
MA0135.10.0256
MA0136.11.5578e-8
MA0137.20.0445
MA0138.20.179
MA0139.10.0575
MA0140.10.00213
MA0141.11.90697e-4
MA0142.10.119
MA0143.10.0081
MA0144.10.0612
MA0145.10.0566
MA0146.10.154
MA0147.10.863
MA0148.13.33905e-5
MA0149.10.00296
MA0150.10.123
MA0152.10.989
MA0153.12.12946e-18
MA0154.10.00277
MA0155.10.741
MA0156.10.0026
MA0157.10.0944
MA0159.10.00594
MA0160.10.0205
MA0162.10.597
MA0163.13.24484e-4
MA0164.10.95
MA0258.10.00145
MA0259.10.919



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: CNhs10593

Novel motifP-value
10.0631
100.0639
1000.978
1010.755
1020.667
1030.0262
1040.775
1050.323
1060.0168
1070.0902
1080.893
1090.0323
110.0435
1100.0598
1113.85463e-4
1120.00918
1130.896
1140.019
1150.881
1160.52
1170.0396
1180.444
1190.0402
120.708
1200.384
1210.766
1220.893
1230.913
1240.534
1250.0338
1260.231
1270.0801
1280.0652
1290.331
130.0111
1300.758
1310.729
1320.272
1330.253
1340.672
1350.301
1360.503
1370.69
1380.577
1390.00677
140.699
1400.0631
1410.0528
1420.68
1430.512
1440.872
1450.0834
1460.544
1470.563
1480.0931
1490.232
150.0622
1500.344
1510.25
1520.0726
1530.338
1540.467
1550.31
1564.9982e-4
1570.857
1580.189
1590.0228
1600.377
1610.248
1620.761
1630.517
1640.00997
1650.0768
1660.794
1670.177
1680.702
1690.00113
170.0285
180.557
190.175
20.744
200.66
210.646
220.244
230.204
240.318
250.567
260.0311
270.505
280.373
290.157
30.0551
300.924
310.545
320.196
330.387
340.96
350.36
360.158
370.0242
380.23
390.304
40.576
400.328
410.651
420.295
430.117
440.135
450.566
460.145
470.0905
480.0814
490.102
50.0662
500.923
510.543
520.315
530.914
540.567
550.589
560.344
570.366
580.328
590.0908
60.721
600.0462
610.477
620.155
630.097
640.507
650.13
660.308
670.918
680.0409
690.603
70.118
700.00708
710.0416
720.443
730.0384
740.552
750.0266
760.458
770.169
780.114
790.128
80.0546
800.457
810.302
820.0183
830.693
840.961
850.0208
860.158
870.924
880.697
890.17
90.495
900.0504
910.557
920.111
930.234
940.514
950.0678
960.352
970.841
980.315
990.5



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: CNhs10593


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
0000019 (camera-type eye)
0000020 (sense organ)
0000033 (head)
0000047 (simple eye)
0000061 (anatomical structure)
0000062 (organ)
0000153 (anterior region of body)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000475 (organism subdivision)
0000479 (tissue)
0000480 (anatomical group)
0000922 (embryo)
0000970 (eye)
0001032 (sensory system)
0001062 (anatomical entity)
0001444 (subdivision of head)
0001456 (face)
0002104 (visual system)
0004456 (entire sense organ system)

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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