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|is_obsolete=
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|library_id=CNhs13506
|library_id=CNhs13506
|library_ids=CNhs13506
|name=CD41+ megakaryocyte cancer, donor3
|name=CD41+ megakaryocyte cancer, donor3
|namespace=
|namespace=

Revision as of 16:23, 25 October 2013


Name:CD41+ megakaryocyte cancer, donor3
Species:Mouse (Mus musculus)
Library ID:CNhs13506
Sample type:primary cells
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuebone marrow
dev stageNA
sexNA
ageNA
cell typemegakaryocyte
cell lineNA
companyNA
collaborationHozumi Motohashi (Tohoku University Graduate School of Medicine)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot number3LL-4
catalog numberNA
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0

CAGE Accession numbers
MethodSample accession id
CAGE  DRS008689
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs13506 CAGE DRX008799 DRR009671
Accession ID Mm9

Library idBAMCTSS
CNhs13506 DRZ001096 DRZ002481
Download raw sequence, BAM & CTSS
Mm9
BAMCTSS
[{{{mm9bam}}} download][{{{mm9ctss}}} donwload]
Mm10
BAMCTSS
[{{{mm10bam}}} download][{{{mm10ctss}}} donwload]


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

CNhs13506

00
10
100
1000
10000.0436
1001-0.0749
1002-0.116
1003-0.102
10040
1005-0.0389
1006-0.235
1007-0.318
10080
1009-0.19
1010.0256
10100
10110
10120
1013-0.108
1014-0.0874
1015-0.222
1016-0.594
10170
10180
10190
1020
10200.386
10210.38
1022-0.16
10230
1024-0.307
1025-0.0611
10260
1027-0.048
10280
1029-0.115
103-0.0887
10300
1031-0.911
1032-0.184
1033-0.0752
10340
10350
10360.47
10370
1038-0.475
1039-0.348
1040
1040-0.718
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: CNhs13506

Jaspar motifP-value
MA0002.20.0237
MA0003.10.344
MA0004.10.5
MA0006.10.757
MA0007.10.847
MA0009.10.538
MA0014.10.924
MA0017.10.176
MA0018.20.306
MA0019.10.521
MA0024.12.21887e-8
MA0025.10.246
MA0027.10.566
MA0028.10.0289
MA0029.10.485
MA0030.10.366
MA0031.10.837
MA0035.21.9254e-5
MA0038.10.986
MA0039.20.995
MA0040.10.212
MA0041.10.758
MA0042.10.63
MA0043.10.132
MA0046.14.04355e-5
MA0047.20.974
MA0048.10.0963
MA0050.10.189
MA0051.10.257
MA0052.19.70639e-5
MA0055.10.0287
MA0057.10.661
MA0058.10.5
MA0059.10.0616
MA0060.10.0132
MA0061.10.0585
MA0062.20.00168
MA0065.20.0788
MA0066.10.105
MA0067.10.64
MA0068.10.31
MA0069.10.356
MA0070.10.291
MA0071.10.437
MA0072.10.814
MA0073.10.954
MA0074.10.688
MA0076.10.0925
MA0077.10.465
MA0078.10.831
MA0079.20.0186
MA0080.24.42372e-4
MA0081.10.47
MA0083.10.0122
MA0084.10.531
MA0087.10.214
MA0088.10.0793
MA0090.10.0975
MA0091.10.113
MA0092.10.84
MA0093.10.591
MA0099.20.616
MA0100.10.00618
MA0101.10.144
MA0102.20.833
MA0103.10.611
MA0104.20.203
MA0105.11.1806e-4
MA0106.10.365
MA0107.10.337
MA0108.20.0224
MA0111.10.916
MA0112.20.0152
MA0113.10.37
MA0114.10.341
MA0115.10.305
MA0116.10.00578
MA0117.10.542
MA0119.10.259
MA0122.10.45
MA0124.10.973
MA0125.10.063
MA0131.10.494
MA0135.10.298
MA0136.10.00835
MA0137.20.746
MA0138.20.0546
MA0139.10.357
MA0140.11.29776e-25
MA0141.10.0409
MA0142.10.301
MA0143.10.295
MA0144.10.856
MA0145.10.714
MA0146.10.306
MA0147.10.123
MA0148.10.709
MA0149.10.0187
MA0150.10.00424
MA0152.10.181
MA0153.10.0101
MA0154.10.0441
MA0155.10.418
MA0156.10.0239
MA0157.10.931
MA0159.10.0234
MA0160.10.264
MA0162.10.389
MA0163.13.12106e-4
MA0164.10.274
MA0258.10.0651
MA0259.10.409



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: CNhs13506

Novel motifP-value
10.0728
100.022
1000.344
1010.799
1020.71
1030.00572
1040.922
1050.799
1060.456
1070.833
1080.987
1090.0555
110.154
1100.0766
1110.034
1120.0277
1130.743
1140.307
1150.95
1160.635
1177.41646e-4
1180.112
1190.372
120.867
1200.981
1210.311
1220.662
1230.273
1240.239
1250.091
1260.199
1270.334
1280.499
1290.407
130.00899
1300.66
1310.657
1320.232
1330.762
1340.136
1350.29
1360.878
1370.362
1380.61
1390.467
140.889
1400.408
1410.816
1420.362
1430.309
1440.985
1450.0313
1460.962
1470.839
1480.488
1490.675
150.0535
1500.34
1510.536
1520.334
1530.891
1540.758
1550.191
1564.86729e-82
1570.901
1580.0337
1590.572
1600.623
1610.0466
1620.824
1630.496
1640.017
1650.48
1660.251
1670.0283
1680.875
1690.36
170.436
180.0771
190.734
20.208
200.0191
210.284
220.862
230.22
240.638
250.213
260.00343
270.828
280.418
290.00632
30.0557
300.515
310.73
320.709
330.11
340.668
350.394
360.0171
370.151
380.589
390.952
40.881
400.124
410.314
420.117
430.198
440.471
450.5
460.139
470.173
480.313
490.0937
50.00553
500.834
510.719
520.839
530.525
540.728
550.0747
560.664
570.167
580.485
590.455
60.702
600.493
610.553
620.177
630.564
640.614
650.698
660.189
670.337
680.279
690.926
70.0756
700.128
710.0129
720.355
730.313
740.566
750.0194
760.123
770.993
780.0472
790.618
80.0193
800.0728
810.607
820.555
830.379
840.875
850.577
860.542
870.691
880.741
890.611
90.939
900.0466
910.181
920.478
930.572
940.188
950.135
960.163
970.975
980.548
990.488



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: CNhs13506


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)
0000988 (hematopoietic cell)
0000548 (animal cell)
0000763 (myeloid cell)
0002371 (somatic cell)
0000255 (eukaryotic cell)
0000556 (megakaryocyte)
0002027 (CD9-positive, CD41-positive megakaryocyte cell)

DOID: Disease
4 (disease)
162 (cancer)
14566 (disease of cellular proliferation)

UBERON: Anatomy
0000468 (multi-cellular organism)
0002371 (bone marrow)
0001474 (bone element)
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)
0011131 (mouse CD41-positive megakaryocyte cancer 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:0000049 (common myeloid progenitor)
CL:0000134 (mesenchymal cell)
CL:0002006 (Kit-positive, CD34-negative megakaryocyte erythroid progenitor cell)

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