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|top_motifs=NKX3-1:1.50212014292;E2F1..5:1.28795587918;SPZ1:1.19190999714;NFY{A,B,C}:1.00891143145;TLX2:0.908350076992;GFI1:0.906643354183;STAT1,3:0.846838615509;RUNX1..3:0.838068386188;CDC5L:0.828674327269;ELF1,2,4:0.796380593657;SPIB:0.757859953851;STAT5{A,B}:0.753187669839;ZNF384:0.74405381108;FOXD3:0.728982618594;RXR{A,B,G}:0.692148128366;ETS1,2:0.637190589759;HES1:0.627771547915;ZNF148:0.598187750114;NFKB1_REL_RELA:0.560311855823;HSF1,2:0.544951169247;HMGA1,2:0.536888403959;NANOG{mouse}:0.529597072623;FOXP1:0.528692869313;ZNF423:0.507269679463;ALX4:0.50581589181;TBX4,5:0.504893390749;IKZF1:0.484093378179;POU2F1..3:0.482740043318;VSX1,2:0.475568278153;SPI1:0.466645397342;MYBL2:0.454907745656;ZIC1..3:0.444894216882;TP53:0.443794617929;RREB1:0.434429778322;FOXM1:0.411877585902;BREu{core}:0.401599957158;ZNF143:0.400895075919;EP300:0.400766195245;PATZ1:0.381811571221;SNAI1..3:0.378524446121;ELK1,4_GABP{A,B1}:0.368092186975;NANOG:0.358090548278;IKZF2:0.351554882868;DMAP1_NCOR{1,2}_SMARC:0.327482535471;HMX1:0.327464107478;MYB:0.322889131005;KLF4:0.31091276134;ZNF238:0.309915381764;NRF1:0.270884778242;SOX2:0.265332579139;GATA4:0.258257182205;XCPE1{core}:0.236459567987;LEF1_TCF7_TCF7L1,2:0.236433137899;NKX6-1,2:0.234582959818;RXR{A,B,G}_{NR1H2,PPAR}dimers:0.202744109543;GCM1,2:0.200969749143;SOX{8,9,10}:0.197379075261;ZEB1:0.183753466162;T:0.181450976032;PPARG:0.169892728889;TOPORS:0.159092733664;SOX17:0.145981731605;TFDP1:0.142403673411;HOXA9_MEIS1:0.138763124816;EN1,2:0.12215913989;TBP:0.121797433286;MAZ:0.11556419411;ZBTB16:0.113120548855;DBP:0.111558005005;CUX2:0.101649148406;POU5F1:0.0766754458263;FOXL1:0.0660751441928;PAX4:0.0615907720303;TLX1..3_NFIC{dimer}:0.0592251129948;ADNP_IRX_SIX_ZHX:0.0587991898249;ALX1:0.055844816312;TAL1_TCF{3,4,12}:0.0532339006732;MZF1:0.0518119100867;IRF1,2:0.051787903873;ESR1:0.0505832521916;PITX1..3:0.0390061431534;PAX1,9:0.0242225754787;SRF:0.0227982201886;EBF1:0.0147635730026;YY1:0.0116694754095;TFCP2:0.00561175387688;UFEwm:0.00198209422869;PAX6:-0.0038061202046;GZF1:-0.0166467445836;TFAP4:-0.0287175305374;PAX8:-0.0463131817757;HIC1:-0.052132563274;NKX2-2,8:-0.058466241698;MTF1:-0.0586249245894;EVI1:-0.0615124908256;ATF6:-0.0741563480967;IRF7:-0.0765823222293;NKX2-1,4:-0.0826931598291;PRRX1,2:-0.0866767571275;NFE2L1:-0.101353340644;TEAD1:-0.111240405219;TEF:-0.117182030842;GATA6:-0.12821027821;BACH2:-0.131790090914;GTF2I:-0.135517744998;NFIX:-0.138520042208;TFAP2{A,C}:-0.149341044509;SP1:-0.155048725905;HOX{A5,B5}:-0.162376741536;bHLH_family:-0.175352333322;NKX2-3_NKX2-5:-0.179801664938;CDX1,2,4:-0.184110554143;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:-0.199311544103;SOX5:-0.203944546154;ARID5B:-0.206339900296;OCT4_SOX2{dimer}:-0.220824282124;STAT2,4,6:-0.239740634246;ZFP161:-0.258858866623;RXRA_VDR{dimer}:-0.261737254517;LMO2:-0.279468374193;HIF1A:-0.282531445896;MTE{core}:-0.295508500089;MED-1{core}:-0.307936053195;PRDM1:-0.317583319533;GFI1B:-0.31949307856;RFX1:-0.343353181542;POU1F1:-0.344317922688;ATF2:-0.354806021117;AHR_ARNT_ARNT2:-0.374254669063;HLF:-0.379061161712;MYOD1:-0.388382941651;PAX5:-0.393004663964;FOS_FOS{B,L1}_JUN{B,D}:-0.398060260328;RBPJ:-0.409517064356;NR6A1:-0.418524793944;TGIF1:-0.427361776364;REST:-0.429390173774;GLI1..3:-0.438892164398;HAND1,2:-0.450780004323;NFE2L2:-0.452240705421;SMAD1..7,9:-0.452530022633;EGR1..3:-0.454449668841;PBX1:-0.464897951344;TFAP2B:-0.472718401396;MAFB:-0.485380208957;NHLH1,2:-0.504705314428;NFATC1..3:-0.516481886625;NR5A1,2:-0.534961215908;HNF4A_NR2F1,2:-0.540985854533;FOX{I1,J2}:-0.542662338375;HNF1A:-0.550122818779;POU6F1:-0.55140691588;PDX1:-0.555204411808;HBP1_HMGB_SSRP1_UBTF:-0.582104531937;MEF2{A,B,C,D}:-0.583273594058;JUN:-0.58565945589;POU3F1..4:-0.626332007492;HOX{A4,D4}:-0.638845261204;RFX2..5_RFXANK_RFXAP:-0.645325879703;CEBPA,B_DDIT3:-0.647936881336;FOXP3:-0.65558594883;NKX3-2:-0.660099650057;BPTF:-0.663799913347;CRX:-0.686918380206;CREB1:-0.703843409418;ATF5_CREB3:-0.723425186028;AR:-0.754884159352;FOX{F1,F2,J1}:-0.768318796696;NFE2:-0.784088039084;FOSL2:-0.796027793306;NR3C1:-0.81148983434;NFIL3:-0.830035359487;PAX2:-0.831247752145;ZBTB6:-0.837296952231;FOXN1:-0.842348616139;RORA:-0.867780997433;ONECUT1,2:-0.89366077244;ATF4:-0.909585329527;GTF2A1,2:-0.928406987932;FOXA2:-0.944814836413;MYFfamily:-0.957666991689;LHX3,4:-1.03412113444;AIRE:-1.09461255575;FOX{D1,D2}:-1.15912170354;ESRRA:-1.18320172896;SREBF1,2:-1.25357721094;NR1H4:-1.29083160237;FOXO1,3,4:-1.6021762835;FOXQ1:-1.65237874073
}}
}}

Revision as of 15:21, 15 February 2012


Name:thymus, embryo E14, 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
tissuethymus
dev stage14 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

CNhs11041

00
10
100
1000
10000
1001-0.0749
10020.215
1003-0.105
10040
10050
1006-0.143
10070.0425
10080
1009-0.112
1010.122
10100
10110.00849
10120
1013-0.191
10140.163
10150.187
10160.13
10170
10180.584
10190
1020
10200
10210.148
1022-0.303
10230
10240.00826
10250.0492
10260
10270
10280
1029-0.0989
1030.148
10300
10310.22
1032-0.0964
10330
10340
10350
10360.147
10370
1038-0.275
1039-0.136
1040
1040-0.0407
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: CNhs11041

Jaspar motifP-value
MA0002.20.11
MA0003.10.791
MA0004.10.907
MA0006.10.907
MA0007.10.635
MA0009.10.364
MA0014.10.65
MA0017.16.90554e-4
MA0018.20.00633
MA0019.10.506
MA0024.14.80313e-13
MA0025.10.00581
MA0027.10.0149
MA0028.14.73825e-5
MA0029.10.906
MA0030.10.0178
MA0031.10.00881
MA0035.20.86
MA0038.10.672
MA0039.20.713
MA0040.10.357
MA0041.10.157
MA0042.10.371
MA0043.10.204
MA0046.13.9621e-18
MA0047.24.77842e-4
MA0048.10.00253
MA0050.10.0457
MA0051.10.354
MA0052.15.11058e-8
MA0055.18.02599e-6
MA0057.10.706
MA0058.10.743
MA0059.10.017
MA0060.18.12152e-9
MA0061.11.03842e-4
MA0062.28.43065e-10
MA0065.20.0391
MA0066.10.732
MA0067.10.225
MA0068.10.17
MA0069.10.233
MA0070.10.919
MA0071.10.00108
MA0072.10.00252
MA0073.10.936
MA0074.10.539
MA0076.16.51296e-5
MA0077.10.835
MA0078.10.994
MA0079.20.918
MA0080.28.64602e-10
MA0081.10.00265
MA0083.10.347
MA0084.10.782
MA0087.10.333
MA0088.10.0759
MA0090.10.58
MA0091.10.599
MA0092.10.891
MA0093.10.957
MA0099.20.138
MA0100.10.636
MA0101.13.03044e-5
MA0102.20.167
MA0103.10.87
MA0104.20.0918
MA0105.11.0466e-4
MA0106.10.265
MA0107.11.09412e-4
MA0108.20.604
MA0111.10.908
MA0112.20.846
MA0113.10.935
MA0114.13.67061e-5
MA0115.10.0309
MA0116.10.00855
MA0117.10.02
MA0119.10.33
MA0122.10.975
MA0124.10.403
MA0125.10.354
MA0131.10.0737
MA0135.10.231
MA0136.12.75251e-13
MA0137.20.0574
MA0138.21.77516e-6
MA0139.10.16
MA0140.10.723
MA0141.12.7823e-4
MA0142.10.623
MA0143.10.777
MA0144.10.458
MA0145.10.522
MA0146.10.376
MA0147.10.0122
MA0148.16.66331e-4
MA0149.10.473
MA0150.10.00396
MA0152.10.194
MA0153.17.38999e-5
MA0154.10.0821
MA0155.10.378
MA0156.14.12348e-13
MA0157.10.102
MA0159.10.772
MA0160.10.00339
MA0162.10.0878
MA0163.10.00213
MA0164.10.956
MA0258.10.889
MA0259.10.34



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: CNhs11041

Novel motifP-value
10.247
100.278
1000.806
1010.437
1020.349
1030.965
1040.609
1050.427
1060.708
1070.47
1080.705
1090.232
110.301
1100.201
1110.584
1120.912
1130.221
1140.0238
1150.702
1160.359
1170.108
1180.913
1190.449
120.541
1200.675
1210.849
1220.899
1230.5
1240.889
1250.964
1260.795
1270.344
1280.916
1290.45
130.0369
1300.341
1310.993
1320.214
1330.375
1340.216
1350.781
1360.21
1370.0341
1380.987
1390.00162
140.111
1400.173
1410.787
1420.338
1430.153
1440.631
1450.271
1460.823
1470.141
1480.286
1490.738
150.597
1500.403
1510.746
1520.984
1530.4
1540.546
1550.659
1561.39665e-7
1570.198
1580.107
1590.13
1600.413
1610.223
1620.423
1630.0496
1640.17
1650.827
1660.26
1670.72
1680.113
1690.674
170.367
180.385
190.769
20.366
200.426
210.0125
220.914
230.19
240.0432
250.192
260.0268
270.996
280.0608
290.161
30.9
300.831
310.197
320.313
330.457
340.331
350.226
360.428
370.617
380.572
390.828
40.891
400.058
410.507
420.23
430.339
440.777
450.753
460.981
470.446
480.909
490.225
50.193
500.0189
510.674
520.78
530.868
540.147
550.745
560.723
570.756
580.92
590.0586
60.594
600.288
610.258
620.732
630.934
640.555
650.663
660.333
670.512
680.193
690.629
70.706
700.484
710.0382
720.247
730.284
740.536
750.256
760.311
770.904
780.845
790.753
80.805
800.552
810.401
820.392
830.972
840.0177
850.0423
860.616
870.114
880.261
890.212
90.884
900.402
910.659
920.0873
930.579
940.831
950.091
960.798
970.495
980.655
990.55



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: CNhs11041


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
0000061 (anatomical structure)
0000062 (organ)
0000063 (organ segment)
0000064 (organ part)
0000065 (respiratory tract)
0000072 (segment of respiratory tract)
0000077 (mixed endoderm/mesoderm-derived structure)
0000078 (mixed ectoderm/mesoderm/endoderm-derived structure)
0000119 (cell layer)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000475 (organism subdivision)
0000479 (tissue)
0000480 (anatomical group)
0000481 (multi-tissue structure)
0000483 (epithelium)
0000490 (unilaminar epithelium)
0000922 (embryo)
0000923 (germ layer)
0000924 (ectoderm)
0000925 (endoderm)
0000926 (mesoderm)
0000949 (endocrine system)
0000974 (neck)
0001004 (respiratory system)
0001007 (digestive system)
0001041 (foregut)
0001042 (chordate pharynx)
0001048 (primordium)
0001062 (anatomical entity)
0001555 (digestive tract)
0001557 (upper respiratory tract)
0002050 (embryonic structure)
0002193 (hemolymphoid system)
0002342 (neural crest)
0002346 (neurectoderm)
0002368 (endocrine gland)
0002370 (thymus)
0002390 (hematopoietic system)
0002405 (immune system)
0002530 (gland)
0002532 (epiblast (generic))
0003075 (neural plate)
0003104 (mesenchyme)
0003295 (pharyngeal gland)
0003351 (pharyngeal epithelium)
0003408 (gland of gut)
0003929 (gut epithelium)
0004119 (endoderm-derived structure)
0004120 (mesoderm-derived structure)
0004121 (ectoderm-derived structure)
0004177 (hemopoietic organ)
0004185 (endodermal part of digestive tract)
0004807 (respiratory system epithelium)
0004921 (subdivision of digestive tract)
0005057 (immune organ)
0005058 (hemolymphoid system gland)
0005291 (embryonic tissue)
0005423 (developing anatomical structure)
0005428 (vagal neural crest)
0005562 (thymus primordium)
0005911 (endo-epithelium)
0006562 (pharynx)
0006598 (presumptive structure)
0007026 (primitive gut)
0007284 (presumptive neural plate)
0007690 (early pharyngeal endoderm)
0009113 (thymic region)
0009142 (entire embryonic mesenchyme)
0009145 (pharyngeal region of foregut)

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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