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|ancestors_in_disease_facet=
|ancestors_in_disease_facet=
|sample_description=
|sample_description=
|fonse_cell_line=FF:0000626
|fonse_cell_line=FF:0000626
|fonse_cell_line_closure=FF:0000626
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|fonse_treatment=EFO:0000369,FF:0000644,FF:0011194,FF:13283-142F7
|fonse_treatment=EFO:0000369,FF:0000644,FF:0011194,FF:13283-142F7
|fonse_treatment_closure=EFO:0000369,FF:0000644,FF:0011194,FF:13283-142F7
|fonse_treatment_closure=EFO:0000369,FF:0000644,FF:0011194,FF:13283-142F7
|top_motifs=ELK1,4_GABP{A,B1}:2.12599411136;PAX8:1.59083413084;ZBTB16:1.52740274738;PAX1,9:1.522351274;AIRE:1.46370201655;E2F1..5:1.43455225886;NFE2L1:1.31929886685;RXR{A,B,G}_{NR1H2,PPAR}dimers:1.30458183148;PITX1..3:1.25909990334;PPARG:1.2096181709;NFE2:1.19279511023;ALX1:1.18743827581;NRF1:1.13020320896;TP53:1.08428723944;YY1:1.067067179;FOXP3:0.95974939465;BACH2:0.874957119639;RXR{A,B,G}:0.833754527814;UFEwm:0.798674380587;bHLH_family:0.752089053446;HSF1,2:0.71944682428;ZNF143:0.708821390571;NFY{A,B,C}:0.708009854775;TEF:0.673640688426;EVI1:0.626759846888;MYB:0.620583070209;ONECUT1,2:0.569619094758;ELF1,2,4:0.554124835077;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:0.534783238516;HES1:0.526054379612;ZNF148:0.522337921177;HMX1:0.505023343955;PDX1:0.447309276383;NKX3-1:0.424198131965;FOS_FOS{B,L1}_JUN{B,D}:0.36689240839;EN1,2:0.363850479808;CREB1:0.334442164072;TFDP1:0.301784239847;T:0.236775917677;CDX1,2,4:0.217163119873;ATF4:0.207829569334;FOSL2:0.158814740506;NANOG:0.146097867025;POU3F1..4:0.135551738662;NKX6-1,2:0.128087533955;NFKB1_REL_RELA:0.0940987061934;ZIC1..3:0.0934799048642;NANOG{mouse}:0.0930937541347;CRX:0.0702783731709;KLF4:0.0698595078816;ALX4:0.0599120536585;HIF1A:0.0554915137327;ZEB1:0.0405347449067;POU1F1:0.0240948051026;IKZF2:0.0216499428591;NFE2L2:-0.00700023202853;SOX17:-0.0434181728429;NKX3-2:-0.0486833720654;HOXA9_MEIS1:-0.060241539826;NKX2-1,4:-0.0693332331366;TFAP2{A,C}:-0.0766904781804;RORA:-0.0947509665407;ESRRA:-0.0965692751468;OCT4_SOX2{dimer}:-0.140683371344;AHR_ARNT_ARNT2:-0.157399357368;RFX2..5_RFXANK_RFXAP:-0.160623241254;RFX1:-0.160704248379;POU2F1..3:-0.188538357146;JUN:-0.205405606347;PAX4:-0.211610833688;STAT5{A,B}:-0.222828771733;TEAD1:-0.227078206788;IKZF1:-0.232265314306;CDC5L:-0.246796290257;SPIB:-0.258069922058;LHX3,4:-0.286864404555;STAT1,3:-0.292724099909;SP1:-0.296540814037;NKX2-3_NKX2-5:-0.314474577236;ETS1,2:-0.317686312435;CEBPA,B_DDIT3:-0.320580831815;RUNX1..3:-0.323471177159;GATA4:-0.330779677079;TBX4,5:-0.333957291258;HOX{A4,D4}:-0.344546756438;FOXQ1:-0.349897273789;HLF:-0.356958409997;NFATC1..3:-0.357230452567;ATF5_CREB3:-0.396160715099;SNAI1..3:-0.398737512184;EP300:-0.41268705079;SREBF1,2:-0.420249853022;HAND1,2:-0.423999555009;GFI1:-0.425263286534;SPI1:-0.468876526224;HNF4A_NR2F1,2:-0.471164033078;PRRX1,2:-0.474050886366;PAX2:-0.488781260138;RXRA_VDR{dimer}:-0.508168067591;FOXM1:-0.528836350815;EGR1..3:-0.536166101317;FOXP1:-0.550804104415;TBP:-0.554241402023;XCPE1{core}:-0.558501264182;ADNP_IRX_SIX_ZHX:-0.559470457551;TOPORS:-0.570043634782;POU6F1:-0.570744615702;MTE{core}:-0.587876718125;BREu{core}:-0.598789218384;CUX2:-0.609510147733;MZF1:-0.619450094124;FOX{F1,F2,J1}:-0.62411002396;GZF1:-0.630702706945;NR3C1:-0.632421947708;SRF:-0.633647860897;HNF1A:-0.634970557119;FOXD3:-0.643011119858;FOXL1:-0.646282503273;HMGA1,2:-0.649989010722;NKX2-2,8:-0.661838468824;VSX1,2:-0.671140156739;MEF2{A,B,C,D}:-0.672277690244;REST:-0.680177336573;ZNF384:-0.682418357493;POU5F1:-0.696408394628;HIC1:-0.70262564866;SOX5:-0.713707757507;SOX{8,9,10}:-0.713967131028;MYOD1:-0.737174646655;GCM1,2:-0.739127049402;ZFP161:-0.750497548779;LEF1_TCF7_TCF7L1,2:-0.786437796206;GFI1B:-0.786667554669;TFAP2B:-0.788397591733;FOXO1,3,4:-0.792869298547;BPTF:-0.806729806208;TLX2:-0.819050132593;NFIL3:-0.819451253505;NR6A1:-0.823998830414;ESR1:-0.831478018097;GATA6:-0.841837124944;EBF1:-0.842190667525;ATF2:-0.843981162566;FOXA2:-0.846554727984;ZBTB6:-0.85823213329;STAT2,4,6:-0.859110190545;MAZ:-0.882114492073;MED-1{core}:-0.890423222673;ARID5B:-0.915958329914;PBX1:-0.919652487194;NR5A1,2:-0.932132486432;PATZ1:-0.949196085587;DMAP1_NCOR{1,2}_SMARC:-0.96230110746;PAX6:-0.966279645431;TFCP2:-1.00698363209;RREB1:-1.00797186799;SOX2:-1.01253512825;IRF1,2:-1.05162241445;FOX{D1,D2}:-1.08803854941;GLI1..3:-1.11067699754;ZNF423:-1.16012372347;MTF1:-1.16089211926;DBP:-1.17004056499;TAL1_TCF{3,4,12}:-1.17363405986;AR:-1.25969393898;NR1H4:-1.29556209732;HOX{A5,B5}:-1.30103484528;HBP1_HMGB_SSRP1_UBTF:-1.32322331774;ZNF238:-1.32427850553;SPZ1:-1.3281894174;IRF7:-1.33294045472;NFIX:-1.35359379871;GTF2A1,2:-1.36812742181;TFAP4:-1.38904938804;GTF2I:-1.38993090963;FOXN1:-1.43170213816;PRDM1:-1.44660839864;MAFB:-1.50338677447;TGIF1:-1.52824116196;LMO2:-1.52930442298;FOX{I1,J2}:-1.58394245362;NHLH1,2:-1.58511636772;MYFfamily:-1.61778216412;PAX5:-1.68647163395;SMAD1..7,9:-1.74908544515;RBPJ:-1.76176195731;TLX1..3_NFIC{dimer}:-1.91921834423;ATF6:-1.95590923754;MYBL2:-2.04285229836
}}
}}

Revision as of 15:21, 15 February 2012


Name:trophoblast stem cell line R1AB differentiation, day00, biol_rep1
Species:Mouse (Mus musculus)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueNA
dev stageNA
sexmale
ageNA
cell typeSELECT CELL TYPE
cell lineNA
companyNA
collaborationHirohiko Kodeki(RCAI)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberR1AB +d0
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

CNhs13481

00
10
100
1000
1000-0.0355
1001-0.0749
1002-0.0975
1003-0.156
10040.0717
1005-0.429
1006-0.143
1007-0.0573
10080
1009-0.188
1010.457
10100
1011-0.0801
10120
1013-0.145
1014-0.0874
1015-0.00286
1016-0.328
10170
10180.588
10190
1020
10200.0717
10210.0717
10220
10230
1024-0.14
10250
10260
1027-0.048
10280
1029-0.0775
103-0.0848
10300
1031-0.536
1032-0.583
10330.143
10340
10350
10360.28
10370
1038-0.123
1039-0.344
1040
1040-0.0865
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: CNhs13481

Jaspar motifP-value
MA0002.20.125
MA0003.10.861
MA0004.10.0967
MA0006.10.989
MA0007.10.977
MA0009.10.285
MA0014.10.41
MA0017.10.674
MA0018.20.0412
MA0019.10.483
MA0024.17.36205e-4
MA0025.10.141
MA0027.10.866
MA0028.14.95951e-9
MA0029.10.0281
MA0030.10.0455
MA0031.10.00799
MA0035.20.126
MA0038.10.511
MA0039.23.11489e-4
MA0040.10.485
MA0041.10.355
MA0042.10.875
MA0043.10.0262
MA0046.12.33362e-15
MA0047.21.29614e-4
MA0048.10.00571
MA0050.14.10606e-5
MA0051.10.0285
MA0052.16.12687e-6
MA0055.12.34921e-5
MA0057.10.955
MA0058.10.0431
MA0059.10.00385
MA0060.10.023
MA0061.10.76
MA0062.24.06262e-12
MA0065.20.225
MA0066.10.867
MA0067.10.506
MA0068.10.0526
MA0069.10.75
MA0070.10.329
MA0071.10.0589
MA0072.10.571
MA0073.10.682
MA0074.10.36
MA0076.17.43519e-9
MA0077.10.782
MA0078.10.274
MA0079.20.872
MA0080.20.424
MA0081.10.529
MA0083.10.00537
MA0084.10.14
MA0087.10.744
MA0088.10.344
MA0090.10.889
MA0091.10.899
MA0092.10.172
MA0093.10.102
MA0099.23.52375e-5
MA0100.10.0172
MA0101.10.23
MA0102.20.628
MA0103.10.467
MA0104.20.0346
MA0105.10.884
MA0106.10.0134
MA0107.10.824
MA0108.20.00281
MA0111.10.521
MA0112.20.835
MA0113.10.723
MA0114.10.882
MA0115.10.00389
MA0116.10.962
MA0117.10.881
MA0119.10.00762
MA0122.10.544
MA0124.10.484
MA0125.10.202
MA0131.10.0845
MA0135.10.172
MA0136.10.00225
MA0137.20.0669
MA0138.20.0021
MA0139.10.465
MA0140.10.0205
MA0141.10.308
MA0142.10.811
MA0143.10.646
MA0144.10.383
MA0145.10.516
MA0146.10.0548
MA0147.10.0114
MA0148.14.25595e-4
MA0149.10.0459
MA0150.10.212
MA0152.10.404
MA0153.12.15586e-7
MA0154.10.385
MA0155.10.568
MA0156.13.64395e-4
MA0157.10.00555
MA0159.10.339
MA0160.10.099
MA0162.10.615
MA0163.10.214
MA0164.10.0223
MA0258.10.511
MA0259.10.0369



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: CNhs13481

Novel motifP-value
10.673
100.224
1000.233
1010.0711
1020.14
1030.713
1040.717
1050.324
1060.239
1070.0738
1080.503
1090.328
110.715
1100.597
1110.0892
1120.878
1130.298
1140.803
1150.363
1160.512
1175.62093e-4
1180.34
1190.372
120.613
1200.478
1210.923
1220.254
1230.0306
1240.0236
1250.316
1260.395
1270.279
1280.187
1290.912
130.0109
1300.157
1310.0157
1320.241
1330.0467
1340.192
1350.0215
1360.0563
1370.61
1380.8
1390.532
140.392
1400.13
1410.61
1420.554
1430.322
1440.575
1450.301
1460.429
1470.853
1480.122
1490.00528
150.632
1500.665
1510.136
1520.122
1530.75
1540.699
1550.0565
1560.419
1570.9
1580.436
1590.678
1600.541
1610.318
1620.245
1630.281
1640.0158
1650.604
1660.0272
1670.987
1680.0645
1690.7
170.786
180.499
190.31
20.0531
200.00389
210.238
220.814
230.0636
240.29
250.881
260.303
270.0459
280.752
290.00555
30.753
300.366
310.292
320.0981
330.463
340.464
350.623
360.285
370.251
380.661
390.543
40.147
400.458
410.155
420.731
430.521
440.378
450.426
460.822
470.62
480.509
490.533
50.635
500.911
510.795
520.168
530.0493
540.788
550.491
560.464
570.731
580.822
590.329
60.814
600.372
610.107
620.803
630.406
640.599
650.449
660.733
670.348
680.335
690.444
70.768
700.411
710.332
720.921
730.00652
740.334
750.0502
760.015
770.696
780.382
790.67
80.382
800.158
810.138
820.22
830.54
840.563
850.33
860.48
870.183
880.0482
890.516
90.379
900.342
910.737
920.288
930.168
940.607
950.016
960.634
970.999
980.0645
990.262



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: CNhs13481


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

CL: Cell type
0000000 (cell), 0000000 (cell)
0000003 (native cell)
0000034 (stem cell)
0000255 (eukaryotic cell)
0000349 (extraembryonic cell)
0000351 (trophoblast cell)
0000548 (animal cell)
0002371 (somatic cell)

UBERON: Anatomy
0000061 (anatomical structure)
0000358 (blastocyst)
0000465 (material anatomical entity)
0000468 (multi-cellular organism)
0000922 (embryo)
0001062 (anatomical entity)
0002050 (embryonic structure)
0005423 (developing anatomical structure)

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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