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|library_id=CNhs13519
|library_id=CNhs13519
|library_id_phase_based=2:CNhs13519
|library_id_phase_based=2:CNhs13519
|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.timecourse.hCAGE/trophoblast%2520stem%2520cell%2520line%2520Rybp%2520differentiation%252c%2520day00%252c%2520biol_rep1.CNhs13519.13290-142G5.mm10.nobarcode.bam
|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.timecourse.hCAGE/trophoblast%2520stem%2520cell%2520line%2520Rybp%2520differentiation%252c%2520day00%252c%2520biol_rep1.CNhs13519.13290-142G5.mm10.nobarcode.ctss.bed.gz
|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.timecourse.hCAGE/trophoblast%2520stem%2520cell%2520line%2520Rybp%2520differentiation%252c%2520day00%252c%2520biol_rep1.CNhs13519.13290-142G5.mm9.nobarcode.bam
|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.timecourse.hCAGE/trophoblast%2520stem%2520cell%2520line%2520Rybp%2520differentiation%252c%2520day00%252c%2520biol_rep1.CNhs13519.13290-142G5.mm9.ctss.bed.gz
|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.timecourse.hCAGE/trophoblast%2520stem%2520cell%2520line%2520Rybp%2520differentiation%252c%2520day00%252c%2520biol_rep1.CNhs13519.13290-142G5.mm9.nobarcode.rdna.fa.gz
|name=trophoblast stem cell line Rybp differentiation
|name=trophoblast stem cell line Rybp differentiation
|namespace=
|namespace=

Revision as of 17:41, 17 May 2017


Name:trophoblast stem cell line Rybp differentiation
Species:Mouse (Mus musculus)
Library ID:CNhs13519
Sample type:time courses
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 numberRybp +d0
catalog numberNA
sample typeNA
extraction protocol (Details)NA

CAGE Accession numbers
MethodSample accession id
CAGE  SAMD00004700
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs13519 CAGE DRX008918 DRR009792
Accession ID Mm9

Library idBAMCTSS
CNhs13519 DRZ001217 DRZ002600
Download raw sequence, BAM & CTSS
Mm9
FastaBAMCTSS
downloaddownloaddonwload
Mm10
BAMCTSS
downloaddonwload


Relative expression to median (log10)

Transcription factors with enriched expression in this sampleRanked list of transcription factor promoter expression in this sample relative to the median expression in the FANTOM5 collection is shown. Value is log10 transformed.



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

CNhs13519

00
10
100
1000
1000-0.00178
1001-0.0631
1002-0.0941
1003-0.175
10040
1005-0.111
1006-0.248
1007-0.124
10080
1009-0.19
1010.318
10100
1011-0.0725
10120
1013-0.115
1014-0.0874
1015-0.063
1016-0.327
10170
10180.793
10190
1020
10200.177
10210.077
1022-0.124
10230
1024-0.14
10250
10260
1027-0.048
10280
1029-0.0989
103-0.0861
10300
1031-0.521
1032-0.458
10330.0595
10340
10350
1036-0.0321
10370
1038-0.0973
1039-0.281
1040
1040-0.0535
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



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: CNhs13519

Jaspar motifP-value
MA0002.20.21
MA0003.10.738
MA0004.10.239
MA0006.10.987
MA0007.10.869
MA0009.10.336
MA0014.10.0949
MA0017.10.761
MA0018.20.00107
MA0019.10.525
MA0024.10.00164
MA0025.10.347
MA0027.10.843
MA0028.19.22102e-8
MA0029.12.56211e-4
MA0030.10.268
MA0031.10.0398
MA0035.20.173
MA0038.10.851
MA0039.23.27972e-6
MA0040.10.904
MA0041.10.185
MA0042.10.613
MA0043.10.00613
MA0046.11.78922e-12
MA0047.20.00571
MA0048.10.0248
MA0050.15.59512e-5
MA0051.10.0799
MA0052.12.43036e-5
MA0055.16.18729e-6
MA0057.10.525
MA0058.10.119
MA0059.10.0358
MA0060.10.00204
MA0061.10.826
MA0062.21.13817e-10
MA0065.20.31
MA0066.10.837
MA0067.10.248
MA0068.10.00301
MA0069.10.857
MA0070.10.53
MA0071.10.0803
MA0072.10.329
MA0073.10.575
MA0074.10.414
MA0076.13.85008e-7
MA0077.10.796
MA0078.10.235
MA0079.20.192
MA0080.20.378
MA0081.10.862
MA0083.10.0261
MA0084.10.598
MA0087.10.554
MA0088.10.155
MA0090.10.407
MA0091.10.778
MA0092.10.541
MA0093.10.217
MA0099.22.86627e-9
MA0100.10.0307
MA0101.10.215
MA0102.20.759
MA0103.10.0804
MA0104.20.081
MA0105.10.446
MA0106.10.00284
MA0107.10.688
MA0108.20.172
MA0111.10.394
MA0112.20.745
MA0113.10.425
MA0114.10.961
MA0115.10.00624
MA0116.10.654
MA0117.10.871
MA0119.10.00133
MA0122.10.581
MA0124.10.382
MA0125.10.663
MA0131.10.0609
MA0135.10.798
MA0136.10.0198
MA0137.20.0197
MA0138.20.00707
MA0139.10.273
MA0140.10.0237
MA0141.10.891
MA0142.10.694
MA0143.10.835
MA0144.10.174
MA0145.10.784
MA0146.10.00548
MA0147.10.0386
MA0148.10.00651
MA0149.10.0368
MA0150.10.231
MA0152.10.0555
MA0153.14.59169e-6
MA0154.10.456
MA0155.10.443
MA0156.10.0111
MA0157.10.049
MA0159.10.361
MA0160.10.157
MA0162.10.691
MA0163.10.977
MA0164.10.0215
MA0258.10.75
MA0259.10.043



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: CNhs13519

Novel motifP-value
10.418
100.409
1000.427
1010.0394
1020.0654
1030.942
1040.705
1050.303
1060.257
1070.0809
1080.826
1090.453
110.913
1100.845
1110.0434
1120.863
1130.566
1140.901
1150.587
1160.794
1172.98606e-4
1180.346
1190.653
120.596
1200.746
1210.769
1220.396
1230.0115
1240.0796
1250.777
1260.441
1270.338
1280.136
1290.689
130.00622
1300.0677
1310.00449
1320.196
1330.0429
1340.256
1350.00932
1360.019
1370.565
1380.54
1390.706
140.396
1400.316
1410.91
1420.729
1430.294
1440.697
1450.585
1460.533
1470.923
1480.0349
1490.0517
150.379
1500.637
1510.174
1520.0503
1530.909
1540.855
1550.0513
1560.00987
1570.538
1580.456
1590.891
1600.583
1610.0905
1620.32
1630.192
1640.0193
1650.742
1660.0224
1670.865
1680.0764
1690.34
170.957
180.422
190.478
20.161
200.00903
210.385
220.84
230.118
240.215
250.951
260.573
270.0308
280.837
290.00671
30.746
300.495
310.238
320.0297
330.722
340.697
350.242
360.575
370.268
380.88
390.785
40.0966
400.437
410.171
420.708
430.368
440.222
450.531
460.953
470.649
480.754
490.448
50.306
500.685
510.605
520.258
530.0572
540.816
550.335
560.589
570.752
580.966
590.278
60.611
600.573
610.136
620.881
630.339
640.389
650.533
660.534
670.3
680.358
690.265
70.802
700.369
710.696
720.88
730.0078
740.211
750.0462
760.0256
770.766
780.242
790.851
80.663
800.308
810.224
820.424
830.722
840.376
850.455
860.553
870.0497
880.0234
890.763
90.437
900.704
910.433
920.497
930.101
940.322
950.0128
960.845
970.908
980.0171
990.184



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: CNhs13519


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

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

UBERON: Anatomy
0000468 (multi-cellular organism)
0000922 (embryo)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0002050 (embryonic structure)
0005423 (developing anatomical structure)
0001062 (anatomical entity)
0000358 (blastocyst)
0000307 (blastula)

FF: FANTOM5
0000102 (sample by type)
0000003 (cell line sample)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000350 (experimentally modified sample)
0000380 (0 days sample)
0000626 (trophoblast cell line sample)
0000644 (trophoblast cell line differentiation sample)
0000642 (mouse trophoblast stem cell line Rybp sample)
0011201 (mouse trophoblast stem cell line Rybp differentiation- day00 sample)

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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