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|library_id=CNhs12628
|library_id=CNhs12628
|library_id_phase_based=2:CNhs12628
|library_id_phase_based=2:CNhs12628
|microRNAs=
|microRNAs_nn=
|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2016/vis_viewer/#/mouse#cage;sample;11717
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2016/vis_viewer_novel/#/mouse#cage;sample;11717
|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.hCAGE/Mouse%2520Mesenchymal%2520stem%2520cells%2520-%2520bone%2520marrow%2520derived%252c%2520donor1.CNhs12628.11717-123C7.mm10.nobarcode.bam
|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.hCAGE/Mouse%2520Mesenchymal%2520stem%2520cells%2520-%2520bone%2520marrow%2520derived%252c%2520donor1.CNhs12628.11717-123C7.mm10.nobarcode.bam
|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.hCAGE/Mouse%2520Mesenchymal%2520stem%2520cells%2520-%2520bone%2520marrow%2520derived%252c%2520donor1.CNhs12628.11717-123C7.mm10.nobarcode.ctss.bed.gz
|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.hCAGE/Mouse%2520Mesenchymal%2520stem%2520cells%2520-%2520bone%2520marrow%2520derived%252c%2520donor1.CNhs12628.11717-123C7.mm10.nobarcode.ctss.bed.gz

Revision as of 21:17, 18 May 2017


Name:Mouse Mesenchymal stem cells - bone marrow derived, donor1
Species:Mouse (Mus musculus)
Library ID:CNhs12628
Sample type:primary cells
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuebone marrow
dev stageNA
sexNA
ageNA
cell typemesenchymal stem cell
cell lineNA
companySciencell/3H
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberRNAMCS1
catalog numbercustom
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-TRIzol-isopropanol-v1.0

CAGE Accession numbers
MethodSample accession id
CAGE  SAMD00005198
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs12628 CAGE DRX008825 DRR009697
Accession ID Mm9

Library idBAMCTSS
CNhs12628 DRZ001122 DRZ002507
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

CNhs12628

00
10
100
1000
10000.0678
1001-0.0749
10020.168
1003-0.0137
10040
10050
10060.304
1007-0.451
10080
1009-0.00295
101-0.507
10100
10110.00323
10120
10130.175
1014-0.0874
10150.0682
1016-0.187
10170
10180
10190
1020
10200.447
10210.279
1022-0.124
10230
1024-0.14
1025-0.0611
10260
10270
10280
1029-0.176
1030.0455
10300
1031-0.18
1032-0.177
1033-0.0382
10340
10350
1036-0.0244
10370
1038-0.0333
1039-5.195984e-4
1040
1040-0.0413
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: CNhs12628

Jaspar motifP-value
MA0002.28.47186e-6
MA0003.10.135
MA0004.10.302
MA0006.10.528
MA0007.10.609
MA0009.10.385
MA0014.10.704
MA0017.10.248
MA0018.20.0973
MA0019.10.592
MA0024.10.00552
MA0025.10.694
MA0027.10.703
MA0028.10.846
MA0029.10.821
MA0030.10.335
MA0031.10.84
MA0035.20.232
MA0038.17.88839e-5
MA0039.20.812
MA0040.10.606
MA0041.10.466
MA0042.10.92
MA0043.10.141
MA0046.11.94943e-7
MA0047.20.939
MA0048.10.536
MA0050.11.72552e-7
MA0051.16.99951e-5
MA0052.10.051
MA0055.10.729
MA0057.10.23
MA0058.10.139
MA0059.10.232
MA0060.19.6513e-14
MA0061.10.0305
MA0062.20.097
MA0065.20.0102
MA0066.10.0164
MA0067.10.816
MA0068.10.483
MA0069.10.986
MA0070.10.237
MA0071.10.0996
MA0072.10.271
MA0073.10.683
MA0074.10.0346
MA0076.10.502
MA0077.10.581
MA0078.10.601
MA0079.20.689
MA0080.22.26373e-13
MA0081.18.84382e-4
MA0083.10.342
MA0084.10.75
MA0087.10.54
MA0088.10.317
MA0090.10.815
MA0091.10.327
MA0092.10.453
MA0093.10.295
MA0099.21.76179e-4
MA0100.10.884
MA0101.10.0935
MA0102.20.549
MA0103.10.968
MA0104.20.806
MA0105.10.00866
MA0106.10.21
MA0107.10.0671
MA0108.20.0673
MA0111.10.308
MA0112.27.36373e-5
MA0113.10.331
MA0114.10.334
MA0115.10.573
MA0116.10.0026
MA0117.10.719
MA0119.10.295
MA0122.10.5
MA0124.10.76
MA0125.10.0698
MA0131.10.153
MA0135.10.219
MA0136.12.53605e-12
MA0137.20.973
MA0138.20.644
MA0139.10.123
MA0140.10.18
MA0141.10.0159
MA0142.10.818
MA0143.10.0965
MA0144.10.448
MA0145.10.0367
MA0146.10.00674
MA0147.10.793
MA0148.10.667
MA0149.10.232
MA0150.10.00547
MA0152.10.363
MA0153.14.37683e-5
MA0154.10.00494
MA0155.10.403
MA0156.11.76814e-4
MA0157.10.535
MA0159.10.00733
MA0160.10.0992
MA0162.10.182
MA0163.16.19654e-6
MA0164.10.863
MA0258.10.00814
MA0259.10.599



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: CNhs12628

Novel motifP-value
10.103
100.0593
1000.787
1010.803
1020.591
1030.113
1040.916
1050.444
1060.0215
1070.352
1080.561
1090.0204
110.055
1100.1
1110.0211
1120.0711
1130.759
1140.0176
1150.388
1160.146
1170.0289
1180.297
1190.229
120.674
1200.0439
1210.383
1220.911
1230.644
1240.824
1250.174
1260.526
1270.276
1280.0501
1290.192
130.0926
1300.509
1310.0933
1320.535
1330.129
1340.722
1350.923
1360.604
1370.462
1380.379
1390.188
140.568
1400.0653
1410.191
1420.327
1430.0108
1440.89
1450.151
1460.673
1470.801
1480.15
1490.0146
150.0894
1500.136
1510.237
1520.0951
1530.854
1540.519
1550.396
1560.314
1570.588
1580.391
1590.739
1600.468
1610.0826
1620.825
1630.913
1640.139
1650.101
1660.629
1670.392
1680.51
1690.00462
170.0319
180.117
190.134
20.693
200.268
210.34
220.114
230.113
240.124
250.849
260.00947
270.656
280.734
290.0855
30.0204
300.725
310.298
320.119
330.313
340.403
350.62
360.0173
370.0401
380.15
390.669
40.316
400.0641
410.276
420.238
430.0444
440.0475
450.504
460.0695
470.252
480.234
490.075
50.206
500.454
510.738
520.446
530.945
540.695
550.589
560.145
570.551
580.385
590.00514
61
600.114
610.331
620.123
630.105
640.324
650.0472
660.779
670.179
680.0536
690.208
70.469
702.89002e-4
710.0313
720.11
730.034
740.837
750.074
760.337
770.117
780.0305
790.729
80.0625
800.852
810.166
820.213
830.936
840.539
850.06
860.442
870.143
880.954
890.0809
90.479
900.51
910.2
920.0753
930.239
940.894
950.039
960.888
970.876
980.123
990.747



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: CNhs12628


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)
0002092 (bone marrow cell)
0002540 (mesenchymal stem cell of the bone marrow)

UBERON: Anatomy
0000468 (multi-cellular organism)
0002371 (bone marrow)
0001474 (bone element)
0002384 (connective tissue)
0000479 (tissue)
0000062 (organ)
0004120 (mesoderm-derived structure)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0004765 (skeletal element)
0010317 (germ layer / neural crest derived structure)
0002204 (musculoskeletal system)
0001434 (skeletal system)
0002390 (hematopoietic system)
0002193 (hemolymphoid system)
0002405 (immune system)

FF: FANTOM5
0000102 (sample by type)
0000002 (in vivo cell sample)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000112 (mouse mesenchymal stem cell of bone marrow 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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