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FF:12582-133I8

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Name:ST2 (Mesenchymal stem cells) cells, medium change (without induction)
Species:Mouse (Mus musculus)
Library ID:CNhs13324
Sample type:time courses
Genomic View: UCSC
CAGEd-oPOSSUM:link
ZENBU report :link
Additional information
Sample information
strainNA
tissuebone marrow
dev stageNA
sexNA
ageNA
cell typemesenchymal stem cell
cell lineST2
companyNA
collaborationYasushi Okazaki (Saitama medical college)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberNA
sample typeNA
extraction protocol (Details)NA

CAGE Accession numbers
MethodSample accession id
CAGE  SAMD00005351
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs13324 CAGE DRX008907 DRR009781
Accession ID Mm9

Library idBAMCTSS
CNhs13324 DRZ001206 DRZ002589
Accession ID Mm10

Library idBAMCTSS
CNhs13324 DRZ012556 DRZ013939
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

CNhs13324

00
10
100
1000
10000.131
10010.0161
1002-0.116
10030.0794
10040
10050
1006-0.09
1007-0.0484
10080
10090.733
101-0.0667
10100
1011-0.166
10120
10130.0443
1014-0.0874
10150.221
10160.0754
10170
10180
10190
1020
10200
10210.232
1022-0.124
10230
1024-0.307
1025-0.0611
10260
10270
10280
1029-0.176
1030.442
10300
1031-0.395
1032-0.0522
1033-0.0322
10340
10350
10360.131
10370
10380.0377
1039-0.0317
1040
10400.406
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: CNhs13324

Jaspar motifP-value
MA0002.20.114
MA0003.10.649
MA0004.10.312
MA0006.10.529
MA0007.10.476
MA0009.10.578
MA0014.10.208
MA0017.10.366
MA0018.20.166
MA0019.10.911
MA0024.10.279
MA0025.10.914
MA0027.10.176
MA0028.10.00629
MA0029.10.554
MA0030.10.429
MA0031.10.29
MA0035.20.0248
MA0038.10.9
MA0039.20.976
MA0040.10.528
MA0041.10.78
MA0042.10.518
MA0043.10.669
MA0046.14.96545e-7
MA0047.20.527
MA0048.13.55386e-4
MA0050.10.814
MA0051.10.962
MA0052.10.00207
MA0055.12.43341e-4
MA0057.10.166
MA0058.10.11
MA0059.10.193
MA0060.10.0172
MA0061.10.389
MA0062.20.0017
MA0065.20.103
MA0066.10.199
MA0067.10.856
MA0068.10.258
MA0069.10.605
MA0070.10.239
MA0071.10.568
MA0072.10.739
MA0073.10.645
MA0074.10.706
MA0076.10.0213
MA0077.10.642
MA0078.10.237
MA0079.20.195
MA0080.20.0467
MA0081.10.339
MA0083.10.00175
MA0084.10.641
MA0087.10.704
MA0088.10.00632
MA0090.10.0941
MA0091.10.456
MA0092.10.142
MA0093.10.299
MA0099.22.01487e-4
MA0100.10.079
MA0101.10.505
MA0102.20.402
MA0103.16.11348e-5
MA0104.20.947
MA0105.10.0484
MA0106.10.00511
MA0107.10.865
MA0108.20.0796
MA0111.10.407
MA0112.20.00486
MA0113.10.865
MA0114.10.923
MA0115.10.585
MA0116.10.0286
MA0117.10.498
MA0119.10.282
MA0122.10.782
MA0124.10.562
MA0125.10.00334
MA0131.10.429
MA0135.10.0593
MA0136.10.649
MA0137.20.114
MA0138.29.49313e-4
MA0139.10.796
MA0140.10.00154
MA0141.10.142
MA0142.10.106
MA0143.10.79
MA0144.10.107
MA0145.10.423
MA0146.10.00247
MA0147.10.88
MA0148.10.729
MA0149.10.0686
MA0150.10.195
MA0152.10.0544
MA0153.18.5661e-5
MA0154.10.155
MA0155.10.935
MA0156.10.557
MA0157.10.775
MA0159.10.32
MA0160.10.558
MA0162.10.0538
MA0163.10.0433
MA0164.10.626
MA0258.10.177
MA0259.10.264



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: CNhs13324

Novel motifP-value
10.172
100.0068
1000.929
1010.472
1020.289
1030.141
1040.906
1050.621
1060.633
1070.743
1080.345
1090.0205
110.0997
1100.0288
1110.352
1120.898
1130.0812
1140.356
1150.703
1160.0283
1175.35328e-4
1180.895
1190.271
120.933
1200.152
1210.822
1220.207
1230.328
1240.24
1250.194
1260.276
1270.0548
1280.775
1290.59
130.00876
1300.524
1310.563
1320.476
1330.141
1340.624
1350.343
1360.575
1370.671
1380.545
1390.218
140.472
1400.546
1410.613
1420.958
1430.0409
1440.205
1450.117
1460.352
1470.983
1480.644
1490.265
150.849
1500.0309
1510.996
1520.118
1530.762
1540.48
1550.151
1567.1938e-60
1570.863
1580.717
1590.395
1600.486
1610.613
1620.893
1630.976
1640.00209
1650.809
1660.67
1670.171
1680.456
1690.00131
170.16
180.267
190.304
20.39
200.0461
210.0836
220.247
230.171
240.98
250.95
260.0399
270.441
280.644
290.00227
30.0778
300.491
310.772
320.395
330.328
340.788
350.356
360.0898
370.0151
380.574
390.366
40.588
400.473
410.16
420.287
430.425
440.201
450.649
460.307
470.166
480.269
490.9
50.0618
500.614
510.885
520.851
530.534
540.546
550.63
560.812
570.235
580.835
590.163
60.649
600.342
610.678
620.449
630.51
640.511
650.852
660.58
670.728
680.682
690.938
70.278
700.00256
718.21729e-4
720.918
730.0188
740.971
750.0465
760.175
770.226
780.048
790.756
80.0764
800.00944
810.7
820.2
830.589
840.662
850.561
860.659
870.178
880.675
890.869
90.867
900.0378
910.413
920.673
930.291
940.687
950.0189
960.411
970.689
980.309
990.853



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: CNhs13324


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)
0000723 (somatic stem cell)
0000048 (multi fate stem cell)
0000548 (animal cell)
0002320 (connective tissue cell)
0002371 (somatic cell)
0000219 (motile cell)
0000134 (mesenchymal cell)
0000255 (eukaryotic cell)
0000034 (stem cell)

UBERON: Anatomy
0002384 (connective tissue)
0000479 (tissue)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0001062 (anatomical entity)

FF: FANTOM5
0000102 (sample by type)
0000003 (cell line sample)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000350 (experimentally modified sample)
0000404 (mouse mesenchymal stem cell line: ST2 sample)
0000333 (medium change sample)
0000357 (0 hr sample)
0000488 (mouse ST2 Mesenchymal stem cells, cells 0hr after medium change , without induction 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
CL:0000134 (mesenchymal cell)

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