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|top_motifs=GATA6:3.66355968782;STAT5{A,B}:1.88527578944;E2F1..5:1.84127796232;PAX1,9:1.81686713297;NFY{A,B,C}:1.69059481898;RXR{A,B,G}_{NR1H2,PPAR}dimers:1.27271153425;ZNF423:1.20791539503;YY1:1.09411991298;ARID5B:1.061125144;ZNF143:1.02576055503;PBX1:0.892632135566;HOX{A5,B5}:0.878735452205;FOX{F1,F2,J1}:0.875033177417;MYB:0.826274255396;HOXA9_MEIS1:0.752248281894;AIRE:0.736513614325;ELF1,2,4:0.729568585323;NFE2L2:0.725946306791;ELK1,4_GABP{A,B1}:0.677277868184;PAX8:0.668178939419;GFI1:0.64063039218;NRF1:0.637961007359;ONECUT1,2:0.635228245869;bHLH_family:0.568424207519;ZBTB16:0.547761343154;NFE2:0.543383182695;HNF1A:0.538696472509;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:0.524877196086;NR6A1:0.522426188658;NKX3-2:0.484707583679;FOXA2:0.467876605184;EN1,2:0.462045101476;HES1:0.457574432855;SOX17:0.430010603783;PITX1..3:0.37548467278;STAT1,3:0.364163148317;TFDP1:0.359542748713;POU1F1:0.340303235035;SPIB:0.338762523966;CUX2:0.337190700153;RXR{A,B,G}:0.298639661447;CEBPA,B_DDIT3:0.271912682428;ALX4:0.243210784744;ZNF148:0.228706416518;FOX{I1,J2}:0.225016144397;TOPORS:0.189484597781;PAX6:0.160945445913;SRF:0.155983562953;SOX{8,9,10}:0.128983481184;HNF4A_NR2F1,2:0.118901352339;SPI1:0.108278610157;TBX4,5:0.100286577918;NANOG{mouse}:0.0961022439356;EVI1:0.0899085878436;GZF1:0.0798206807608;RUNX1..3:0.0755735250453;GATA4:0.0650855264372;HMGA1,2:0.0625572341453;NKX3-1:0.0461534311633;ATF4:0.036003058358;RREB1:0.00338149670532;ETS1,2:-0.00516232798452;ATF5_CREB3:-0.0103529371725;HIF1A:-0.0177305299411;FOXD3:-0.023142356939;OCT4_SOX2{dimer}:-0.0419371924978;IKZF2:-0.0529294934207;TBP:-0.0661944101745;BACH2:-0.0924606149849;AHR_ARNT_ARNT2:-0.09894195438;PPARG:-0.11198594708;CRX:-0.126923373656;FOX{D1,D2}:-0.135294191532;PDX1:-0.144534898927;LHX3,4:-0.160823835246;BREu{core}:-0.162689933178;MZF1:-0.163772556703;RORA:-0.164326294989;PAX2:-0.171977081436;ZIC1..3:-0.179199885536;NR1H4:-0.179456653231;HLF:-0.180780767734;PRRX1,2:-0.190167184021;UFEwm:-0.207257139162;HSF1,2:-0.228499487649;POU2F1..3:-0.230366431269;MEF2{A,B,C,D}:-0.241336783665;FOXM1:-0.245319321238;NFIL3:-0.252197561754;KLF4:-0.271798568119;XCPE1{core}:-0.273077799138;CDX1,2,4:-0.274647172841;NR5A1,2:-0.290820792292;NFE2L1:-0.29387556222;TEAD1:-0.302250557916;ESRRA:-0.305244454992;TEF:-0.306994991162;TLX2:-0.325304401317;FOXL1:-0.345746954646;FOXP3:-0.353238469776;GCM1,2:-0.359964579713;CREB1:-0.367325833666;PATZ1:-0.377135814947;EGR1..3:-0.38626687064;SOX2:-0.394269816124;ALX1:-0.410040633757;EBF1:-0.424220016994;MAZ:-0.437329084343;HOX{A4,D4}:-0.437654841321;TGIF1:-0.438959631371;MYBL2:-0.45551610687;NFKB1_REL_RELA:-0.463989211269;DMAP1_NCOR{1,2}_SMARC:-0.480411786547;NKX2-1,4:-0.486323645687;AR:-0.493800375463;GLI1..3:-0.501800872476;STAT2,4,6:-0.502999586029;RFX1:-0.505584850914;RXRA_VDR{dimer}:-0.513226583329;VSX1,2:-0.516457130007;PRDM1:-0.535173194046;NKX2-2,8:-0.541332591759;RFX2..5_RFXANK_RFXAP:-0.546029126421;ADNP_IRX_SIX_ZHX:-0.546111614696;ATF2:-0.552784556024;MAFB:-0.554420731794;FOXP1:-0.577668148578;ZFP161:-0.587053595949;RBPJ:-0.59020422273;MTF1:-0.596038534646;DBP:-0.603152177627;POU3F1..4:-0.609022584359;IKZF1:-0.62644614028;MED-1{core}:-0.640610873728;NANOG:-0.648900459123;ZNF384:-0.652335184149;IRF1,2:-0.655873644215;MYOD1:-0.662679450162;GTF2I:-0.663149855404;TP53:-0.681515859222;REST:-0.685479304062;T:-0.687847403898;LMO2:-0.68966668493;EP300:-0.689937981003;LEF1_TCF7_TCF7L1,2:-0.705715689512;FOXN1:-0.71235228389;FOS_FOS{B,L1}_JUN{B,D}:-0.715785490793;SNAI1..3:-0.717889648604;TFAP2{A,C}:-0.718465208111;TFAP4:-0.719541953679;GFI1B:-0.722720841159;HAND1,2:-0.731707338163;PAX4:-0.737778930101;HMX1:-0.738441145981;SREBF1,2:-0.754105105673;TFCP2:-0.759515701152;JUN:-0.766099778329;SPZ1:-0.77490292699;NR3C1:-0.780745285555;MYFfamily:-0.824791025624;TAL1_TCF{3,4,12}:-0.832542037894;TLX1..3_NFIC{dimer}:-0.834985735389;HIC1:-0.835205111489;IRF7:-0.837951125567;FOXQ1:-0.838672808532;NFIX:-0.842908373956;POU6F1:-0.888856113887;FOXO1,3,4:-0.898008208761;NHLH1,2:-0.90672642505;MTE{core}:-0.91031029417;FOSL2:-0.926543961847;SMAD1..7,9:-0.941160268339;ZBTB6:-0.950421050801;NKX2-3_NKX2-5:-0.957067239157;ZEB1:-0.998445678132;TFAP2B:-1.00253186057;POU5F1:-1.02182868845;ZNF238:-1.02739031819;NFATC1..3:-1.09446632375;SP1:-1.10505693256;SOX5:-1.1519675402;CDC5L:-1.23646705445;NKX6-1,2:-1.2637791195;ESR1:-1.31597078609;GTF2A1,2:-1.3160329979;BPTF:-1.40848151769;HBP1_HMGB_SSRP1_UBTF:-1.41237731009;PAX5:-1.43254325502;ATF6:-1.74427440173
}}
}}

Revision as of 15:19, 15 February 2012


Name:liver, embryo E12, 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 stage12 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

CNhs10601

00
10
100
1000
1000-0.0355
1001-0.0119
10020.0674
1003-0.152
10040
1005-0.0389
1006-0.0976
10070.0314
10080
1009-0.133
1010.244
10100
1011-0.0343
10120
1013-0.0943
10140.176
10150.00886
1016-0.044
10170
10180
10190
1020
10200
10210.176
1022-0.248
10230
1024-0.0145
10250.144
10260
10270
10280
10292.64663e-4
103-0.035
10300
10310.0165
1032-0.318
10330.125
10340
10350
10360.395
10370
1038-0.267
1039-0.151
1040
1040-0.142
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: CNhs10601

Jaspar motifP-value
MA0002.20.195
MA0003.10.97
MA0004.10.0512
MA0006.10.86
MA0007.10.922
MA0009.10.222
MA0014.10.525
MA0017.12.1055e-6
MA0018.20.0389
MA0019.10.407
MA0024.11.04296e-17
MA0025.10.327
MA0027.10.479
MA0028.17.01873e-7
MA0029.10.0146
MA0030.10.962
MA0031.10.237
MA0035.22.15279e-37
MA0038.10.0651
MA0039.20.749
MA0040.10.422
MA0041.10.16
MA0042.10.608
MA0043.10.361
MA0046.13.62489e-17
MA0047.20.327
MA0048.10.00251
MA0050.10.00184
MA0051.10.00176
MA0052.10.0018
MA0055.14.04903e-4
MA0057.10.927
MA0058.10.0317
MA0059.10.00234
MA0060.11.20975e-12
MA0061.10.394
MA0062.21.78831e-8
MA0065.20.00327
MA0066.10.119
MA0067.10.336
MA0068.10.0422
MA0069.10.00727
MA0070.10.973
MA0071.10.54
MA0072.10.377
MA0073.10.805
MA0074.10.722
MA0076.13.56772e-6
MA0077.10.812
MA0078.10.773
MA0079.20.0543
MA0080.20.0279
MA0081.10.281
MA0083.10.958
MA0084.10.288
MA0087.10.0617
MA0088.10.0226
MA0090.10.266
MA0091.10.278
MA0092.10.647
MA0093.10.0599
MA0099.20.665
MA0100.10.00572
MA0101.10.441
MA0102.20.928
MA0103.10.0277
MA0104.20.0163
MA0105.10.00314
MA0106.10.984
MA0107.10.957
MA0108.20.422
MA0111.10.526
MA0112.20.225
MA0113.10.226
MA0114.12.61278e-5
MA0115.18.70248e-4
MA0116.10.00544
MA0117.10.858
MA0119.10.928
MA0122.10.959
MA0124.10.959
MA0125.10.718
MA0131.10.295
MA0135.10.489
MA0136.10.00303
MA0137.20.599
MA0138.26.91924e-4
MA0139.10.517
MA0140.12.3086e-81
MA0141.10.362
MA0142.10.169
MA0143.10.21
MA0144.10.745
MA0145.10.292
MA0146.10.196
MA0147.10.00623
MA0148.10.0651
MA0149.10.298
MA0150.10.017
MA0152.10.535
MA0153.17.66012e-14
MA0154.10.286
MA0155.10.534
MA0156.12.05802e-4
MA0157.10.0412
MA0159.10.0587
MA0160.10.135
MA0162.10.395
MA0163.11.20157e-5
MA0164.10.174
MA0258.10.873
MA0259.10.0904



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: CNhs10601

Novel motifP-value
10.373
100.0976
1000.133
1010.206
1020.759
1030.247
1040.804
1050.743
1060.61
1070.583
1080.696
1090.0323
110.226
1100.066
1110.00887
1120.167
1130.443
1140.882
1150.661
1160.942
1170.00193
1180.037
1190.762
120.84
1200.972
1210.163
1220.708
1230.0127
1240.0608
1250.658
1260.114
1270.0614
1280.99
1290.61
134.84845e-6
1300.546
1310.81
1320.00609
1330.425
1340.0838
1350.19
1360.371
1370.303
1380.333
1390.464
140.268
1400.768
1410.0335
1420.185
1430.869
1440.525
1450.00803
1460.939
1470.617
1480.174
1490.174
150.114
1500.27
1510.72
1520.493
1530.724
1540.44
1550.589
1560.00635
1570.785
1580.0589
1590.854
1600.732
1610.0179
1620.62
1630.74
1640.00155
1650.253
1660.0774
1670.267
1680.809
1690.259
170.857
180.506
190.575
20.221
200.00383
210.493
220.869
230.113
240.638
250.482
266.82155e-4
270.601
280.806
290.00157
30.0782
300.63
310.603
320.996
330.305
340.807
350.665
360.123
370.386
380.957
390.536
40.384
400.264
410.646
420.0751
430.285
440.853
450.735
460.173
470.26
480.351
490.229
50.247
500.763
510.99
520.526
530.653
540.863
550.575
560.955
570.445
580.932
590.794
60.876
600.92
610.393
620.346
630.898
640.781
650.777
660.115
670.14
680.899
690.609
70.0331
700.439
710.00323
720.734
730.552
740.395
750.13
760.321
770.227
780.0162
790.0985
80.00793
800.0951
810.964
820.453
830.289
840.685
850.485
860.547
870.3
880.175
890.821
90.865
900.234
910.836
920.876
930.344
940.277
950.0366
960.231
970.229
980.611
990.848



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: CNhs10601


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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