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|library_id=CNhs12534
|library_id=CNhs12534
|library_id_phase_based=2:CNhs12534
|library_id_phase_based=2:CNhs12534
|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.LQhCAGE/stem%2520cell%2520%2528cKit%252b%2520Sca1-%2520lineage-%2529%2520KSL%252c%2520biol_rep1.CNhs12534.12121-128C6.mm10.nobarcode.bam
|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.LQhCAGE/stem%2520cell%2520%2528cKit%252b%2520Sca1-%2520lineage-%2529%2520KSL%252c%2520biol_rep1.CNhs12534.12121-128C6.mm10.nobarcode.ctss.bed.gz
|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.LQhCAGE/stem%2520cell%2520%2528cKit%252b%2520Sca1-%2520lineage-%2529%2520KSL%252c%2520biol_rep1.CNhs12534.12121-128C6.mm9.nobarcode.bam
|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.LQhCAGE/stem%2520cell%2520%2528cKit%252b%2520Sca1-%2520lineage-%2529%2520KSL%252c%2520biol_rep1.CNhs12534.12121-128C6.mm9.ctss.bed.gz
|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.LQhCAGE/stem%2520cell%2520%2528cKit%252b%2520Sca1-%2520lineage-%2529%2520KSL%252c%2520biol_rep1.CNhs12534.12121-128C6.mm9.nobarcode.rdna.fa.gz
|name=stem cell (cKit+ Sca1- lineage-) KSL, biol_rep1
|name=stem cell (cKit+ Sca1- lineage-) KSL, biol_rep1
|namespace=FANTOM5
|namespace=FANTOM5

Revision as of 17:05, 17 May 2017


Name:stem cell (cKit+ Sca1- lineage-) KSL, biol_rep1
Species:Mouse (Mus musculus)
Library ID:CNhs12534
Sample type:primary cells
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/8J
tissuebone marrow
dev stageNA
sexmale
age9-10weeks
cell typestem cell (cKit+ Sca1- lineage-)
cell lineNA
companyNA
collaborationKitamura/Nakahara
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberrep1
catalog numberNA
sample typetotal RNA
extraction protocol (Details)NA

CAGE Accession numbers
MethodSample accession id
CAGE  SAMD00005414
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs12534 CAGE DRX008784 DRR009656
Accession ID Mm9

Library idBAMCTSS
CNhs12534 DRZ001081 DRZ002466
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

CNhs12534

00
10
100
1000
1000-0.00139
1001-0.072
1002-0.116
1003-0.102
10040
10050
1006-0.143
1007-0.236
10080
1009-0.0273
1010.235
10100
10110
10120.0682
1013-0.149
1014-0.0874
10150.0772
1016-0.282
10170
10180
10190
1020.127
10200
10210
1022-0.111
10230.81
10241.012
1025-0.0611
10260
1027-0.048
10280
1029-0.115
103-0.0887
10300
1031-0.911
1032-0.28
10330.0682
10340
10350
10360.421
10370
1038-0.198
1039-0.0609
1040
1040-0.121
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: CNhs12534

Jaspar motifP-value
MA0002.22.15094e-7
MA0003.10.658
MA0004.10.244
MA0006.10.887
MA0007.10.693
MA0009.10.35
MA0014.10.529
MA0017.10.413
MA0018.21.9578e-11
MA0019.10.698
MA0024.18.48169e-4
MA0025.14.30764e-4
MA0027.10.0348
MA0028.13.48273e-7
MA0029.10.546
MA0030.10.215
MA0031.10.00288
MA0035.20.906
MA0038.10.00225
MA0039.20.608
MA0040.10.0225
MA0041.10.127
MA0042.10.341
MA0043.11.1927e-7
MA0046.12.9056e-15
MA0047.20.543
MA0048.10.0141
MA0050.16.6821e-15
MA0051.14.66319e-8
MA0052.10.295
MA0055.10.0163
MA0057.10.784
MA0058.10.152
MA0059.10.0586
MA0060.10.914
MA0061.11.09498e-14
MA0062.23.20628e-20
MA0065.20.886
MA0066.10.143
MA0067.11.46181e-5
MA0068.10.00419
MA0069.10.612
MA0070.10.537
MA0071.10.702
MA0072.10.881
MA0073.10.705
MA0074.10.644
MA0076.14.80143e-7
MA0077.10.256
MA0078.10.891
MA0079.20.166
MA0080.24.66137e-14
MA0081.17.14077e-5
MA0083.10.4
MA0084.10.0502
MA0087.10.74
MA0088.10.615
MA0090.10.00925
MA0091.10.311
MA0092.10.379
MA0093.10.207
MA0099.24.9867e-27
MA0100.10.00452
MA0101.19.89916e-20
MA0102.20.0494
MA0103.10.197
MA0104.20.0794
MA0105.12.26708e-7
MA0106.10.839
MA0107.11.89918e-21
MA0108.20.831
MA0111.10.859
MA0112.20.476
MA0113.10.858
MA0114.10.0123
MA0115.10.914
MA0116.10.0328
MA0117.10.00965
MA0119.10.164
MA0122.10.0873
MA0124.10.947
MA0125.10.0939
MA0131.10.106
MA0135.10.399
MA0136.11.64025e-29
MA0137.20.00164
MA0138.21.63499e-5
MA0139.10.772
MA0140.10.617
MA0141.10.264
MA0142.10.344
MA0143.10.0966
MA0144.10.0489
MA0145.10.64
MA0146.10.133
MA0147.10.0792
MA0148.10.97
MA0149.10.185
MA0150.18.09947e-8
MA0152.10.75
MA0153.13.48843e-5
MA0154.10.908
MA0155.10.423
MA0156.12.15946e-26
MA0157.10.0154
MA0159.10.247
MA0160.10.954
MA0162.10.631
MA0163.17.87149e-4
MA0164.10.656
MA0258.10.166
MA0259.10.342



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: CNhs12534

Novel motifP-value
10.936
100.174
1000.884
1010.554
1020.917
1030.532
1040.564
1050.624
1060.0562
1070.843
1080.669
1090.588
110.926
1100.651
1110.898
1120.211
1130.827
1140.164
1150.57
1160.599
1172.82009e-4
1180.132
1190.691
120.548
1200.372
1210.208
1220.563
1230.205
1240.542
1250.99
1260.535
1270.954
1280.067
1290.581
130.0017
1300.507
1310.212
1320.339
1330.336
1340.879
1350.689
1360.14
1370.00463
1380.996
1390.838
140.524
1400.701
1410.489
1420.585
1430.297
1440.906
1450.427
1460.583
1470.625
1480.229
1490.244
150.0956
1500.776
1510.717
1520.27
1530.211
1540.503
1550.666
1560.0863
1570.825
1580.0308
1590.787
1600.11
1610.323
1620.337
1630.0782
1640.0384
1650.0958
1660.24
1670.297
1680.272
1690.178
170.828
180.87
190.101
20.0187
200.0218
210.883
220.958
230.482
240.0402
250.59
260.0542
270.431
280.716
290.173
30.508
300.175
310.491
320.0403
330.156
340.677
350.997
360.152
370.0547
380.711
390.482
40.48
400.241
410.0859
420.608
430.975
440.953
450.709
460.814
470.588
480.749
490.847
50.806
500.663
510.743
520.78
530.78
540.594
550.957
560.969
570.665
580.267
590.814
60.829
600.451
610.394
620.277
630.692
640.603
650.923
660.472
670.8
680.367
690.588
70.584
700.427
710.201
720.514
730.0507
740.81
750.00732
760.0822
770.00899
780.261
790.547
80.965
800.81
810.769
820.166
830.0174
840.501
850.149
860.199
870.0316
880.423
890.33
90.689
900.262
910.518
920.731
930.166
940.886
950.00628
960.555
970.966
980.776
990.0421



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: CNhs12534


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)
0000034 (stem cell)

FF: FANTOM5
0000102 (sample by type)
0000002 (in vivo cell sample)
0000101 (sample by species)
0000021 (hematopoietic stem cell sample)
0000103 (mouse sample)
0000001 (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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