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|fonse_treatment_closure=
|fonse_treatment_closure=
|top_motifs=CRX:9.18018866797;RORA:5.69795518841;MAFB:3.03904850998;PITX1..3:2.70896616486;TAL1_TCF{3,4,12}:2.68186917175;NFIL3:2.48020518961;NFE2L2:2.38235280187;CDC5L:2.28673516961;NANOG:2.15417250639;TGIF1:2.01685127507;SOX5:1.95380068466;TOPORS:1.69967666122;VSX1,2:1.69418680542;SPZ1:1.58468743444;POU6F1:1.56819143378;NKX2-1,4:1.56639092583;NHLH1,2:1.53169261713;ESRRA:1.49410220266;SMAD1..7,9:1.47325976765;MYFfamily:1.47088390995;FOXP1:1.42418070529;POU3F1..4:1.37820266706;NR5A1,2:1.35693112909;MYOD1:1.2932145873;GTF2A1,2:1.25771819414;ADNP_IRX_SIX_ZHX:1.25461138261;HOX{A5,B5}:1.22970488056;SOX{8,9,10}:1.19681998845;KLF4:1.19139279723;BPTF:1.14645378852;IKZF1:1.11900345265;PAX2:1.10750397053;REST:1.1025151424;TLX1..3_NFIC{dimer}:1.10146427149;HOX{A4,D4}:1.02174889593;GTF2I:1.01920798949;RXR{A,B,G}:0.99514020159;NFE2L1:0.992703521576;AHR_ARNT_ARNT2:0.989682322518;NKX6-1,2:0.966619798978;ZEB1:0.962832001636;PAX6:0.960431075769;CUX2:0.897570671314;ZBTB6:0.879963656171;NFIX:0.858539147049;NKX2-3_NKX2-5:0.856325970967;PRDM1:0.851209620354;MTE{core}:0.834239306667;PAX5:0.827969447132;TFAP2{A,C}:0.824441315719;TFCP2:0.823647976035;PPARG:0.812997730325;GFI1:0.812437987131;SREBF1,2:0.80020089262;MED-1{core}:0.789481721988;MYBL2:0.760138676648;PATZ1:0.757140243629;DBP:0.739539728388;MEF2{A,B,C,D}:0.732418228768;MZF1:0.732122802807;GCM1,2:0.728229569888;ZFP161:0.723091209557;MAZ:0.720274869631;BREu{core}:0.707812113947;ATF2:0.700851462332;HIC1:0.698954822636;PRRX1,2:0.688680046015;GFI1B:0.659885270343;NFE2:0.657147352076;FOX{I1,J2}:0.654698823126;GATA4:0.649858602103;HIF1A:0.628312758417;EVI1:0.615463540196;NKX3-2:0.609814344528;NKX2-2,8:0.598632470746;NR3C1:0.591171563021;TFAP2B:0.565515961075;ZIC1..3:0.558402216839;HAND1,2:0.550293415347;RFX2..5_RFXANK_RFXAP:0.546045744236;ARID5B:0.539038177624;SNAI1..3:0.522490096411;NFATC1..3:0.481847515366;EGR1..3:0.473771331869;SP1:0.465222149693;PAX1,9:0.416933457504;PAX8:0.412654289935;ZNF384:0.39785060452;LMO2:0.39620726008;FOXA2:0.389607107155;SOX2:0.375092793081;TFAP4:0.372917661796;HSF1,2:0.340986436886;PAX4:0.296978091511;RFX1:0.270172107565;FOXD3:0.267498488166;ZBTB16:0.25552780982;FOSL2:0.247414088387;bHLH_family:0.238603770364;TEAD1:0.233446906025;XCPE1{core}:0.204869887932;POU1F1:0.198267869404;HBP1_HMGB_SSRP1_UBTF:0.190369556818;RREB1:0.181491827917;ESR1:0.163439202959;FOXP3:0.160515675899;UFEwm:0.146903413288;ATF6:0.110931920541;FOXL1:0.109291517792;TBP:0.100853586268;AIRE:0.0135382013981;FOXN1:0.0100063334876;RBPJ:-0.00955033541005;ATF5_CREB3:-0.0198029882806;FOX{F1,F2,J1}:-0.0456940086518;MTF1:-0.0477519939446;RXRA_VDR{dimer}:-0.0520557154253;PBX1:-0.0640967263361;STAT5{A,B}:-0.102830660099;ZNF143:-0.104340142505;CREB1:-0.120750506385;YY1:-0.129074607622;HMX1:-0.156255438726;GZF1:-0.156324764419;ZNF238:-0.159222416183;STAT2,4,6:-0.162023920551;LHX3,4:-0.187520639007;TP53:-0.223560187973;HES1:-0.228623360178;JUN:-0.230239325852;SRF:-0.231375761609;NRF1:-0.264647628719;POU5F1:-0.284551891557;HMGA1,2:-0.307437379649;FOXO1,3,4:-0.311391021927;GLI1..3:-0.317551214496;IRF7:-0.344665752854;GATA6:-0.36114529104;FOS_FOS{B,L1}_JUN{B,D}:-0.376423579494;AR:-0.37808876502;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:-0.395252306679;NKX3-1:-0.410187057124;POU2F1..3:-0.424756252918;NANOG{mouse}:-0.461321103685;ATF4:-0.483566654815;STAT1,3:-0.48542878383;TBX4,5:-0.485682069092;IKZF2:-0.491329062095;IRF1,2:-0.495055093067;EP300:-0.501990503729;ALX1:-0.506515458712;FOXM1:-0.523346086079;T:-0.54878492403;TLX2:-0.571023825196;EN1,2:-0.584903151016;HNF4A_NR2F1,2:-0.585038673838;FOX{D1,D2}:-0.587297829348;LEF1_TCF7_TCF7L1,2:-0.589079199731;NR6A1:-0.594387869065;ZNF148:-0.596601033338;SOX17:-0.629768029776;TEF:-0.659349420232;FOXQ1:-0.730877053432;TFDP1:-0.753240640056;BACH2:-0.773231615587;HOXA9_MEIS1:-0.824594731585;MYB:-0.833829429714;OCT4_SOX2{dimer}:-0.900814688111;HLF:-0.925268238562;RXR{A,B,G}_{NR1H2,PPAR}dimers:-0.927350972934;NR1H4:-0.937652001161;CEBPA,B_DDIT3:-0.94675299514;EBF1:-0.951193200068;ONECUT1,2:-0.979325351502;HNF1A:-0.999318579408;ZNF423:-1.04723424105;NFKB1_REL_RELA:-1.07269675136;NFY{A,B,C}:-1.07576816222;SPI1:-1.105312155;ETS1,2:-1.17958488561;DMAP1_NCOR{1,2}_SMARC:-1.20811059576;ELK1,4_GABP{A,B1}:-1.22305984441;PDX1:-1.23931454598;ALX4:-1.24996869984;SPIB:-1.36364137684;RUNX1..3:-1.40074897462;E2F1..5:-1.48187721517;ELF1,2,4:-1.69069076893;CDX1,2,4:-2.43429646322
|top_motifs=CRX:9.18018866797;RORA:5.69795518841;MAFB:3.03904850998;PITX1..3:2.70896616486;TAL1_TCF{3,4,12}:2.68186917175;NFIL3:2.48020518961;NFE2L2:2.38235280187;CDC5L:2.28673516961;NANOG:2.15417250639;TGIF1:2.01685127507;SOX5:1.95380068466;TOPORS:1.69967666122;VSX1,2:1.69418680542;SPZ1:1.58468743444;POU6F1:1.56819143378;NKX2-1,4:1.56639092583;NHLH1,2:1.53169261713;ESRRA:1.49410220266;SMAD1..7,9:1.47325976765;MYFfamily:1.47088390995;FOXP1:1.42418070529;POU3F1..4:1.37820266706;NR5A1,2:1.35693112909;MYOD1:1.2932145873;GTF2A1,2:1.25771819414;ADNP_IRX_SIX_ZHX:1.25461138261;HOX{A5,B5}:1.22970488056;SOX{8,9,10}:1.19681998845;KLF4:1.19139279723;BPTF:1.14645378852;IKZF1:1.11900345265;PAX2:1.10750397053;REST:1.1025151424;TLX1..3_NFIC{dimer}:1.10146427149;HOX{A4,D4}:1.02174889593;GTF2I:1.01920798949;RXR{A,B,G}:0.99514020159;NFE2L1:0.992703521576;AHR_ARNT_ARNT2:0.989682322518;NKX6-1,2:0.966619798978;ZEB1:0.962832001636;PAX6:0.960431075769;CUX2:0.897570671314;ZBTB6:0.879963656171;NFIX:0.858539147049;NKX2-3_NKX2-5:0.856325970967;PRDM1:0.851209620354;MTE{core}:0.834239306667;PAX5:0.827969447132;TFAP2{A,C}:0.824441315719;TFCP2:0.823647976035;PPARG:0.812997730325;GFI1:0.812437987131;SREBF1,2:0.80020089262;MED-1{core}:0.789481721988;MYBL2:0.760138676648;PATZ1:0.757140243629;DBP:0.739539728388;MEF2{A,B,C,D}:0.732418228768;MZF1:0.732122802807;GCM1,2:0.728229569888;ZFP161:0.723091209557;MAZ:0.720274869631;BREu{core}:0.707812113947;ATF2:0.700851462332;HIC1:0.698954822636;PRRX1,2:0.688680046015;GFI1B:0.659885270343;NFE2:0.657147352076;FOX{I1,J2}:0.654698823126;GATA4:0.649858602103;HIF1A:0.628312758417;EVI1:0.615463540196;NKX3-2:0.609814344528;NKX2-2,8:0.598632470746;NR3C1:0.591171563021;TFAP2B:0.565515961075;ZIC1..3:0.558402216839;HAND1,2:0.550293415347;RFX2..5_RFXANK_RFXAP:0.546045744236;ARID5B:0.539038177624;SNAI1..3:0.522490096411;NFATC1..3:0.481847515366;EGR1..3:0.473771331869;SP1:0.465222149693;PAX1,9:0.416933457504;PAX8:0.412654289935;ZNF384:0.39785060452;LMO2:0.39620726008;FOXA2:0.389607107155;SOX2:0.375092793081;TFAP4:0.372917661796;HSF1,2:0.340986436886;PAX4:0.296978091511;RFX1:0.270172107565;FOXD3:0.267498488166;ZBTB16:0.25552780982;FOSL2:0.247414088387;bHLH_family:0.238603770364;TEAD1:0.233446906025;XCPE1{core}:0.204869887932;POU1F1:0.198267869404;HBP1_HMGB_SSRP1_UBTF:0.190369556818;RREB1:0.181491827917;ESR1:0.163439202959;FOXP3:0.160515675899;UFEwm:0.146903413288;ATF6:0.110931920541;FOXL1:0.109291517792;TBP:0.100853586268;AIRE:0.0135382013981;FOXN1:0.0100063334876;RBPJ:-0.00955033541005;ATF5_CREB3:-0.0198029882806;FOX{F1,F2,J1}:-0.0456940086518;MTF1:-0.0477519939446;RXRA_VDR{dimer}:-0.0520557154253;PBX1:-0.0640967263361;STAT5{A,B}:-0.102830660099;ZNF143:-0.104340142505;CREB1:-0.120750506385;YY1:-0.129074607622;HMX1:-0.156255438726;GZF1:-0.156324764419;ZNF238:-0.159222416183;STAT2,4,6:-0.162023920551;LHX3,4:-0.187520639007;TP53:-0.223560187973;HES1:-0.228623360178;JUN:-0.230239325852;SRF:-0.231375761609;NRF1:-0.264647628719;POU5F1:-0.284551891557;HMGA1,2:-0.307437379649;FOXO1,3,4:-0.311391021927;GLI1..3:-0.317551214496;IRF7:-0.344665752854;GATA6:-0.36114529104;FOS_FOS{B,L1}_JUN{B,D}:-0.376423579494;AR:-0.37808876502;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:-0.395252306679;NKX3-1:-0.410187057124;POU2F1..3:-0.424756252918;NANOG{mouse}:-0.461321103685;ATF4:-0.483566654815;STAT1,3:-0.48542878383;TBX4,5:-0.485682069092;IKZF2:-0.491329062095;IRF1,2:-0.495055093067;EP300:-0.501990503729;ALX1:-0.506515458712;FOXM1:-0.523346086079;T:-0.54878492403;TLX2:-0.571023825196;EN1,2:-0.584903151016;HNF4A_NR2F1,2:-0.585038673838;FOX{D1,D2}:-0.587297829348;LEF1_TCF7_TCF7L1,2:-0.589079199731;NR6A1:-0.594387869065;ZNF148:-0.596601033338;SOX17:-0.629768029776;TEF:-0.659349420232;FOXQ1:-0.730877053432;TFDP1:-0.753240640056;BACH2:-0.773231615587;HOXA9_MEIS1:-0.824594731585;MYB:-0.833829429714;OCT4_SOX2{dimer}:-0.900814688111;HLF:-0.925268238562;RXR{A,B,G}_{NR1H2,PPAR}dimers:-0.927350972934;NR1H4:-0.937652001161;CEBPA,B_DDIT3:-0.94675299514;EBF1:-0.951193200068;ONECUT1,2:-0.979325351502;HNF1A:-0.999318579408;ZNF423:-1.04723424105;NFKB1_REL_RELA:-1.07269675136;NFY{A,B,C}:-1.07576816222;SPI1:-1.105312155;ETS1,2:-1.17958488561;DMAP1_NCOR{1,2}_SMARC:-1.20811059576;ELK1,4_GABP{A,B1}:-1.22305984441;PDX1:-1.23931454598;ALX4:-1.24996869984;SPIB:-1.36364137684;RUNX1..3:-1.40074897462;E2F1..5:-1.48187721517;ELF1,2,4:-1.69069076893;CDX1,2,4:-2.43429646322
|comment=
|created_by=
|creation_date=
|def=
|has_quality=
|is_a=EFO:0002091;;FF:0000004;;FF:0000103;;FF:0011423
|namespace=FANTOM5
|part_of=
}}
}}

Revision as of 16:04, 7 March 2012


Name:eyeball, neonate N16
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 stage16 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
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

CNhs11188

00
10.315
100
1000
10000.428
10010.537
10020.38
10030.145
10040
10050
10060.524
10070.0262
10080
10090.0594
101-0.0531
10100
10110.142
10120.249
10130.21
1014-0.0874
1015-0.223
1016-0.128
10170
10180.0999
10190.826
1020
10200
10210
10220.415
10230
10240.0534
10250
10260
10270.359
10280
10290.632
1030.309
10300
10310.122
10320.0362
10330.0683
10340.0137
10350
1036-0.102
10370.873
10380.118
10390.184
1040
10400.0594
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: CNhs11188

Jaspar motifP-value
MA0002.20.0432
MA0003.10.925
MA0004.10.0591
MA0006.10.497
MA0007.10.376
MA0009.10.439
MA0014.10.193
MA0017.14.23705e-5
MA0018.20.224
MA0019.10.591
MA0024.11.29563e-4
MA0025.10.202
MA0027.10.0712
MA0028.11.09633e-6
MA0029.10.635
MA0030.10.84
MA0031.10.431
MA0035.20.194
MA0038.10.085
MA0039.20.001
MA0040.10.0944
MA0041.10.366
MA0042.10.857
MA0043.10.0726
MA0046.13.42394e-20
MA0047.20.0355
MA0048.10.00268
MA0050.10.0014
MA0051.10.00222
MA0052.13.02831e-5
MA0055.11.0938e-4
MA0057.10.592
MA0058.10.0443
MA0059.10.0094
MA0060.10.00518
MA0061.10.00141
MA0062.21.54222e-14
MA0065.20.0142
MA0066.10.508
MA0067.10.899
MA0068.10.253
MA0069.10.124
MA0070.10.624
MA0071.10.0348
MA0072.11.83047e-7
MA0073.10.87
MA0074.10.141
MA0076.11.01701e-7
MA0077.10.866
MA0078.10.0579
MA0079.20.633
MA0080.25.31992e-12
MA0081.15.65111e-4
MA0083.10.497
MA0084.10.545
MA0087.10.174
MA0088.10.322
MA0090.10.724
MA0091.10.0789
MA0092.10.658
MA0093.10.0755
MA0099.20.00947
MA0100.10.00654
MA0101.14.79221e-4
MA0102.20.143
MA0103.10.783
MA0104.20.156
MA0105.10.00223
MA0106.10.298
MA0107.10.00676
MA0108.20.5
MA0111.10.426
MA0112.20.172
MA0113.10.0545
MA0114.15.36783e-5
MA0115.17.17512e-4
MA0116.10.178
MA0117.10.831
MA0119.10.997
MA0122.10.413
MA0124.10.897
MA0125.10.0491
MA0131.10.291
MA0135.10.637
MA0136.12.96964e-22
MA0137.20.00295
MA0138.22.88863e-5
MA0139.10.368
MA0140.10.113
MA0141.10.147
MA0142.10.521
MA0143.10.457
MA0144.10.0025
MA0145.11
MA0146.10.0486
MA0147.10.0601
MA0148.10.00632
MA0149.10.328
MA0150.10.905
MA0152.10.93
MA0153.16.50512e-19
MA0154.10.203
MA0155.10.746
MA0156.14.28237e-18
MA0157.10.124
MA0159.10.175
MA0160.10.509
MA0162.10.549
MA0163.16.14381e-4
MA0164.10.851
MA0258.10.578
MA0259.10.361



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: CNhs11188

Novel motifP-value
10.981
100.213
1000.96
1010.702
1020.866
1030.636
1040.877
1050.918
1060.65
1070.638
1080.631
1090.16
110.216
1100.135
1110.0633
1120.186
1130.229
1140.85
1150.891
1160.298
1177.59083e-4
1180.00494
1190.57
120.154
1200.492
1210.885
1220.49
1230.019
1240.194
1250.677
1260.16
1270.699
1280.919
1290.884
131.1698e-6
1300.295
1310.303
1320.831
1330.881
1340.786
1350.557
1360.00119
1370.791
1380.0499
1390.567
140.159
1400.67
1410.763
1420.82
1430.0973
1440.97
1450.0254
1460.818
1470.705
1480.811
1490.713
150.131
1500.0635
1510.406
1520.0285
1530.92
1540.537
1550.163
1560.846
1570.466
1580.983
1590.176
1600.991
1610.215
1620.974
1630.953
1646.93209e-4
1650.0934
1660.696
1670.852
1680.59
1690.0413
170.451
180.694
190.906
20.193
200.00104
210.165
220.597
230.226
240.0398
250.353
263.37492e-4
270.465
280.826
290.00142
30.2
300.521
310.658
320.584
330.038
340.766
350.649
360.279
370.0745
380.453
390.536
40.547
400.285
410.321
420.224
430.668
440.631
450.897
460.445
470.722
480.396
490.744
50.299
500.592
510.822
520.973
530.0483
540.342
550.202
560.967
570.851
580.602
590.109
60.871
600.19
610.0778
620.509
630.419
640.915
650.609
660.828
670.415
680.327
690.271
70.101
700.842
710.00949
720.359
730.0012
740.406
750.0132
760.0666
770.981
780.0122
790.906
80.0498
800.591
810.316
820.92
830.199
840.768
850.931
860.225
870.00248
880.462
890.609
90.759
900.696
910.836
920.942
930.501
940.722
950.00261
960.768
970.961
980.396
990.628



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: CNhs11188


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)
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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