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|microRNAs=
|microRNAs=
|microRNAs_nn=
|microRNAs_nn=
|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2016/vis_viewer/#/mouse#cage;sample;12124
|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;12124
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2016/vis_viewer_novel/#/mouse#cage;sample;12124
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;12124
|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_rep2.CNhs12535.12124-128C9.mm10.nobarcode.bam
|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_rep2.CNhs12535.12124-128C9.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_rep2.CNhs12535.12124-128C9.mm10.nobarcode.ctss.bed.gz
|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_rep2.CNhs12535.12124-128C9.mm10.nobarcode.ctss.bed.gz

Revision as of 17:31, 4 August 2017


Name:stem cell (cKit+ Sca1- lineage-) KSL, biol_rep2
Species:Mouse (Mus musculus)
Library ID:CNhs12535
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 numberrep2
catalog numberNA
sample typetotal RNA
extraction protocol (Details)NA

CAGE Accession numbers
MethodSample accession id
CAGE  SAMD00005977
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs12535 CAGE DRX008785 DRR009657
Accession ID Mm9

Library idBAMCTSS
CNhs12535 DRZ001082 DRZ002467
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

CNhs12535

00
10
100
1000
1000-0.00703
1001-0.0631
1002-0.116
1003-0.111
10040
10050.0569
1006-0.143
1007-0.17
10080
1009-0.0804
1010.254
10100
10110.0569
10120
1013-0.169
1014-0.0851
10150.00923
1016-0.266
10170
10180.107
10190
1020.107
10200
10210
1022-0.0704
10230.76
10240.979
1025-0.0611
10260
1027-0.048
10280
1029-0.115
103-0.0887
10300
1031-0.854
1032-0.184
10330.199
10340
10350
10360.464
10370
1038-0.241
1039-0.102
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: CNhs12535

Jaspar motifP-value
MA0002.21.63896e-7
MA0003.10.763
MA0004.10.211
MA0006.10.88
MA0007.10.833
MA0009.10.273
MA0014.10.871
MA0017.10.337
MA0018.21.68121e-11
MA0019.10.601
MA0024.17.39556e-4
MA0025.15.0228e-4
MA0027.10.0391
MA0028.12.88778e-8
MA0029.10.384
MA0030.10.247
MA0031.10.00385
MA0035.20.917
MA0038.10.00607
MA0039.20.244
MA0040.10.0286
MA0041.10.504
MA0042.10.532
MA0043.11.57493e-7
MA0046.15.93308e-15
MA0047.20.579
MA0048.10.0229
MA0050.11.3056e-15
MA0051.12.52363e-9
MA0052.10.396
MA0055.10.0278
MA0057.10.764
MA0058.10.087
MA0059.10.103
MA0060.10.357
MA0061.14.15816e-13
MA0062.21.93427e-22
MA0065.20.756
MA0066.10.275
MA0067.11.17581e-5
MA0068.10.0132
MA0069.10.628
MA0070.10.669
MA0071.10.926
MA0072.10.592
MA0073.10.647
MA0074.10.778
MA0076.13.46685e-8
MA0077.10.325
MA0078.10.947
MA0079.20.432
MA0080.22.5526e-14
MA0081.12.12769e-5
MA0083.10.515
MA0084.10.142
MA0087.10.99
MA0088.10.483
MA0090.10.00583
MA0091.10.285
MA0092.10.276
MA0093.10.16
MA0099.24.06301e-24
MA0100.10.00397
MA0101.17.08398e-18
MA0102.20.0197
MA0103.10.131
MA0104.20.0965
MA0105.12.18381e-6
MA0106.10.722
MA0107.15.45564e-20
MA0108.20.482
MA0111.10.8
MA0112.20.874
MA0113.10.762
MA0114.10.012
MA0115.10.782
MA0116.10.0621
MA0117.10.0041
MA0119.10.0568
MA0122.10.131
MA0124.10.994
MA0125.10.0686
MA0131.10.167
MA0135.10.843
MA0136.12.51251e-30
MA0137.20.00259
MA0138.21.8912e-5
MA0139.10.892
MA0140.10.698
MA0141.10.0941
MA0142.10.518
MA0143.10.0498
MA0144.10.0638
MA0145.10.461
MA0146.10.1
MA0147.10.112
MA0148.10.988
MA0149.10.339
MA0150.12.87117e-7
MA0152.10.859
MA0153.11.8033e-5
MA0154.10.833
MA0155.10.335
MA0156.11.23664e-27
MA0157.10.0265
MA0159.10.455
MA0160.10.746
MA0162.10.592
MA0163.10.00257
MA0164.10.745
MA0258.10.447
MA0259.10.358



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: CNhs12535

Novel motifP-value
10.872
100.234
1000.969
1010.465
1020.84
1030.411
1040.582
1050.525
1060.0695
1070.689
1080.623
1090.642
110.966
1100.606
1110.968
1120.27
1130.797
1140.0998
1150.624
1160.631
1172.17724e-4
1180.176
1190.611
120.472
1200.366
1210.263
1220.545
1230.163
1240.336
1250.945
1260.53
1270.876
1280.208
1290.892
130.00308
1300.57
1310.211
1320.391
1330.257
1340.907
1350.697
1360.0908
1370.00684
1380.973
1390.6
140.573
1400.698
1410.557
1420.503
1430.247
1440.845
1450.499
1460.668
1470.49
1480.361
1490.175
150.195
1500.818
1510.744
1520.156
1530.329
1540.571
1550.523
1560.292
1570.748
1580.0336
1590.702
1600.0839
1610.435
1620.515
1630.0437
1640.0542
1650.136
1660.215
1670.535
1680.156
1690.192
170.845
180.956
190.0758
20.0168
200.0228
210.957
220.995
230.402
240.0869
250.559
260.0935
270.382
280.687
290.271
30.638
300.191
310.444
320.0382
330.146
340.653
350.944
360.2
370.0583
380.676
390.364
40.488
400.314
410.114
420.66
430.871
440.983
450.7
460.986
470.642
480.682
490.949
50.868
500.62
510.609
520.606
530.803
540.551
550.995
560.963
570.535
580.342
590.696
60.786
600.537
610.368
620.395
630.552
640.641
650.97
660.431
670.779
680.436
690.574
70.69
700.562
710.261
720.453
730.0329
740.569
750.00883
760.115
770.00552
780.352
790.596
80.899
800.746
810.792
820.163
830.00591
840.552
850.087
860.225
870.0105
880.414
890.233
90.727
900.535
910.403
920.439
930.153
940.789
950.00349
960.376
970.92
980.604
990.026



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: CNhs12535


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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