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|top_motifs=GATA6:3.80253752489;PAX1,9:2.63421146581;E2F1..5:1.8553956644;NFY{A,B,C}:1.83294080329;FOX{F1,F2,J1}:1.68673189805;CEBPA,B_DDIT3:1.43780900823;PBX1:1.36813828589;RXR{A,B,G}_{NR1H2,PPAR}dimers:1.26584454961;HNF1A:1.21028397964;STAT5{A,B}:1.18581866812;ZNF423:1.18149097104;ARID5B:1.17238570612;YY1:1.16638078309;FOXA2:1.16453676378;NFE2L2:1.03307124702;HOXA9_MEIS1:1.00805975084;MYB:0.881442922716;FOX{D1,D2}:0.802596627972;NFE2:0.776535483236;NR6A1:0.721076957458;AIRE:0.706426530652;HNF4A_NR2F1,2:0.644437483174;ZNF143:0.601676163301;ELF1,2,4:0.541275770203;NKX3-2:0.531235367943;ONECUT1,2:0.53023818475;GFI1:0.505384389187;NFIL3:0.442280776179;ZNF148:0.441572230517;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:0.427632189009;SPIB:0.414255942955;POU1F1:0.39850431362;ZBTB16:0.347600427131;HLF:0.336098930788;TLX2:0.332758551037;EN1,2:0.313408638772;SPI1:0.273347260006;PITX1..3:0.269896961732;STAT2,4,6:0.264250368642;PDX1:0.256848825714;ALX4:0.252544307276;NKX2-2,8:0.25122270429;PPARG:0.187361841797;CUX2:0.172371016881;ETS1,2:0.165126909161;NRF1:0.149774950692;ELK1,4_GABP{A,B1}:0.146566374679;BACH2:0.111789084426;SOX17:0.108613966928;RUNX1..3:0.103365505861;CDX1,2,4:0.0841571319137;STAT1,3:0.0804648052867;PAX6:0.0769345278536;bHLH_family:0.0562591210619;TBP:0.0513145197817;TFDP1:0.0490929633514;FOXM1:0.0234622983286;PAX2:0.0224327556217;HES1:0.0117425503984;OCT4_SOX2{dimer}:-0.02786587128;FOXL1:-0.0397665706531;RXR{A,B,G}:-0.0403394535393;FOXO1,3,4:-0.0658969975359;RORA:-0.0776529986682;EBF1:-0.0781000225386;GZF1:-0.0791544438497;ATF5_CREB3:-0.0866931032736;ATF4:-0.0960534900007;HOX{A5,B5}:-0.102667594743;RXRA_VDR{dimer}:-0.107004809082;EVI1:-0.108994806461;NANOG{mouse}:-0.136104483022;TEF:-0.14056856347;LMO2:-0.169881338714;XCPE1{core}:-0.189646974296;SRF:-0.193285161095;NFIX:-0.234081896398;TBX4,5:-0.261065044806;ESRRA:-0.262629855424;NKX3-1:-0.293088637754;TOPORS:-0.295805886424;HIF1A:-0.299859006216;SREBF1,2:-0.302586507724;SOX{8,9,10}:-0.307532487502;CRX:-0.307900582667;RREB1:-0.310551296908;PAX8:-0.314066606688;IRF7:-0.343617069216;FOX{I1,J2}:-0.349733690412;POU2F1..3:-0.385165196816;SNAI1..3:-0.403208101546;IRF1,2:-0.404000398812;FOXP3:-0.404726897583;GCM1,2:-0.409825774173;FOXD3:-0.413912608166;HMGA1,2:-0.421100551694;NFKB1_REL_RELA:-0.4475240991;AHR_ARNT_ARNT2:-0.448116256823;LHX3,4:-0.456608766802;DMAP1_NCOR{1,2}_SMARC:-0.464030245937;DBP:-0.468886593958;TLX1..3_NFIC{dimer}:-0.488991389799;MEF2{A,B,C,D}:-0.489375910164;MYOD1:-0.501220030134;HOX{A4,D4}:-0.501572308433;MTF1:-0.506530023778;POU3F1..4:-0.507628174221;NR1H4:-0.513022133993;TGIF1:-0.51492098397;PRRX1,2:-0.520051764858;RBPJ:-0.529370717171;NR5A1,2:-0.536058112656;ZIC1..3:-0.53755262164;BREu{core}:-0.554310748145;ADNP_IRX_SIX_ZHX:-0.555346846421;EGR1..3:-0.560004336278;GLI1..3:-0.560845859081;VSX1,2:-0.574043178814;TAL1_TCF{3,4,12}:-0.579611840971;IKZF2:-0.598023269299;NFE2L1:-0.612157687263;NR3C1:-0.620184705794;FOXQ1:-0.620523514239;GFI1B:-0.636204617858;NKX2-1,4:-0.641348713295;MYFfamily:-0.650693259583;POU5F1:-0.655492701341;TEAD1:-0.671095673486;CREB1:-0.673598973556;UFEwm:-0.676149763611;FOS_FOS{B,L1}_JUN{B,D}:-0.695196800449;MYBL2:-0.698015603555;RFX2..5_RFXANK_RFXAP:-0.702969668955;KLF4:-0.704573557908;FOXP1:-0.711398806486;ZEB1:-0.718979940949;HSF1,2:-0.731564234006;TFAP4:-0.738366322544;TP53:-0.749431108356;RFX1:-0.752596315504;MZF1:-0.77262605584;REST:-0.775009213953;MAZ:-0.776508502487;ALX1:-0.785767490766;SP1:-0.789404731191;MAFB:-0.830166326819;TFCP2:-0.831540850278;IKZF1:-0.835399757733;NHLH1,2:-0.836132630997;HMX1:-0.846898627713;GTF2I:-0.865208394438;ZFP161:-0.866590860921;T:-0.8697465165;LEF1_TCF7_TCF7L1,2:-0.886437223041;PATZ1:-0.888991689076;PAX5:-0.901384274737;SPZ1:-0.906866822079;ZBTB6:-0.90733408961;SOX2:-0.9266671483;EP300:-0.948444781911;MED-1{core}:-0.957910059797;PRDM1:-0.961445166034;SMAD1..7,9:-0.970781643395;PAX4:-0.993057280734;POU6F1:-0.999182015114;ATF2:-1.02361127692;JUN:-1.04544395177;MTE{core}:-1.09384695224;AR:-1.11091775144;ESR1:-1.13485990186;NKX2-3_NKX2-5:-1.14915559309;BPTF:-1.15934804775;ZNF238:-1.17832502621;TFAP2{A,C}:-1.18022446355;NANOG:-1.19903857806;HIC1:-1.21122142369;HAND1,2:-1.25120029775;TFAP2B:-1.26992939123;GATA4:-1.29774188879;ZNF384:-1.310362952;FOSL2:-1.38700238203;FOXN1:-1.4468236021;NFATC1..3:-1.4575942444;GTF2A1,2:-1.49184455283;SOX5:-1.85948175563;HBP1_HMGB_SSRP1_UBTF:-1.87755982019;ATF6:-1.89721989184;CDC5L:-1.89755608317;NKX6-1,2:-1.96511851191
}}
}}

Revision as of 15:19, 15 February 2012


Name:liver, embryo E15, biol_rep1
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 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

CNhs10520

00
10
100
1000
1000-0.0355
10017.556884e-4
1002-0.0941
1003-0.0538
10040
10050.0413
1006-0.132
1007-0.0756
10080
1009-0.0699
1010.107
10100
1011-0.0397
10120
1013-0.00524
10140
1015-0.0727
1016-0.183
10170
10180
10190
1020
10200
10210.0149
1022-0.0682
10230
1024-0.001
10250.206
10260
1027-0.048
10280
1029-0.0989
103-0.0617
10300
1031-0.234
1032-0.177
1033-0.0333
10340.0802
10350
10360.185
10370
1038-0.218
1039-0.0391
1040
1040-0.263
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: CNhs10520

Jaspar motifP-value
MA0002.20.0163
MA0003.10.511
MA0004.10.431
MA0006.10.306
MA0007.10.711
MA0009.10.169
MA0014.10.622
MA0017.15.53939e-12
MA0018.20.00141
MA0019.10.429
MA0024.18.37023e-9
MA0025.10.963
MA0027.10.897
MA0028.10.0127
MA0029.10.0379
MA0030.10.13
MA0031.10.603
MA0035.21.53258e-30
MA0038.10.368
MA0039.20.00993
MA0040.10.0651
MA0041.10.109
MA0042.10.425
MA0043.10.165
MA0046.11.99157e-44
MA0047.24.22322e-4
MA0048.10.0904
MA0050.10.888
MA0051.10.632
MA0052.14.75691e-4
MA0055.10.0524
MA0057.10.554
MA0058.10.306
MA0059.10.104
MA0060.13.03632e-9
MA0061.10.174
MA0062.24.03045e-4
MA0065.22.49641e-6
MA0066.10.0292
MA0067.10.237
MA0068.10.35
MA0069.10.0428
MA0070.10.558
MA0071.10.124
MA0072.10.0656
MA0073.10.764
MA0074.10.577
MA0076.10.0361
MA0077.10.329
MA0078.10.57
MA0079.20.176
MA0080.29.96336e-5
MA0081.10.251
MA0083.10.461
MA0084.10.135
MA0087.10.0193
MA0088.10.0261
MA0090.10.478
MA0091.10.419
MA0092.10.62
MA0093.10.427
MA0099.20.576
MA0100.10.0315
MA0101.10.417
MA0102.20.0966
MA0103.10.986
MA0104.20.438
MA0105.10.00262
MA0106.10.747
MA0107.10.793
MA0108.20.206
MA0111.10.926
MA0112.20.00739
MA0113.10.363
MA0114.11.71665e-10
MA0115.14.53376e-6
MA0116.10.00305
MA0117.10.774
MA0119.10.0341
MA0122.10.333
MA0124.10.624
MA0125.10.632
MA0131.10.507
MA0135.10.62
MA0136.11.20849e-4
MA0137.20.555
MA0138.20.045
MA0139.10.316
MA0140.12.69631e-65
MA0141.10.0679
MA0142.10.163
MA0143.10.213
MA0144.10.634
MA0145.10.974
MA0146.10.0597
MA0147.10.359
MA0148.13.56979e-6
MA0149.10.0156
MA0150.13.00529e-4
MA0152.10.524
MA0153.12.79903e-35
MA0154.10.056
MA0155.10.67
MA0156.18.60813e-4
MA0157.10.895
MA0159.10.0303
MA0160.10.0246
MA0162.10.478
MA0163.12.46622e-5
MA0164.10.571
MA0258.10.227
MA0259.10.614



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: CNhs10520

Novel motifP-value
10.118
100.0933
1000.299
1010.715
1020.602
1030.0227
1040.918
1050.722
1060.423
1070.561
1080.483
1090.0104
110.113
1100.116
1110.0182
1120.0151
1130.699
1140.657
1150.712
1160.985
1170.00202
1180.0464
1190.0869
120.9
1200.92
1210.2
1220.892
1230.0863
1240.642
1250.755
1260.116
1270.253
1280.154
1290.953
133.39724e-5
1300.428
1310.0789
1320.0552
1330.941
1340.227
1350.476
1360.187
1370.228
1380.99
1390.86
140.851
1400.626
1410.307
1420.127
1430.354
1440.94
1450.0183
1460.284
1470.871
1480.435
1490.837
150.0191
1500.215
1510.478
1520.645
1530.845
1540.446
1550.578
1560.0739
1570.859
1580.257
1590.776
1600.325
1610.186
1620.902
1630.758
1640.00281
1650.291
1660.444
1670.265
1680.682
1690.0236
170.423
180.575
190.193
20.679
200.0893
210.764
220.391
230.864
240.446
250.296
264.79882e-4
270.657
280.336
290.0183
30.0211
300.892
310.916
320.553
330.101
340.702
350.708
360.0253
370.233
380.602
390.908
40.493
400.073
410.638
420.0474
430.085
440.702
450.916
460.135
470.104
480.137
490.0649
50.0824
500.778
510.521
520.659
530.954
540.547
550.277
560.597
570.641
580.595
590.347
60.972
600.236
610.461
620.115
630.336
640.498
650.546
660.121
670.348
680.53
690.762
70.0198
700.663
710.0169
720.409
730.298
740.411
750.0527
760.817
770.943
780.0017
790.525
80.0096
800.0401
810.78
820.939
830.405
840.961
850.669
860.225
870.0481
880.841
890.699
90.689
900.161
910.323
920.571
930.81
940.377
950.0608
960.0833
970.644
980.247
990.716



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: CNhs10520


FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
{{{is_a}}}

part_of relathionship
{{{part_of}}}

has_quality relathionship
{{{has_quality}}}

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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