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{{f5samples
{{f5samples
|F5samples=
|ancestors_in_anatomy_facet=UBERON:0000061,UBERON:0000465,UBERON:0000479,UBERON:0001062,UBERON:0002384
|ancestors_in_anatomy_facet=UBERON:0000061,UBERON:0000465,UBERON:0000479,UBERON:0001062,UBERON:0002384
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000004,CL:0000012,CL:0000034,CL:0000037,CL:0000048,CL:0000049,CL:0000063,CL:0000134,CL:0000144,CL:0000219,CL:0000255,CL:0000548,CL:0000566,CL:0000723,CL:0000763,CL:0000837,CL:0000988,CL:0002032,CL:0002320,CL:0002371
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000004,CL:0000012,CL:0000034,CL:0000037,CL:0000048,CL:0000049,CL:0000063,CL:0000134,CL:0000144,CL:0000219,CL:0000255,CL:0000548,CL:0000566,CL:0000723,CL:0000763,CL:0000837,CL:0000988,CL:0002032,CL:0002320,CL:0002371
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|creation_date=
|creation_date=
|def=
|def=
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|fonse_cell_line=FF:0101035
|fonse_cell_line=FF:0101035
|fonse_cell_line_closure=FF:0101035
|fonse_cell_line_closure=FF:0101035

Revision as of 16:30, 29 March 2012


Name:chronic myelogenous leukemia cell line:KU812
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueblood
dev stageNA
sexmale
ageunknown
cell typebasophil progenitor cell
cell lineKU812
companyRIKEN Bioresource centre
collaborationYukio Nakamura (RIKEN BRC)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberNA
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0
Download raw sequence, BAM & CTSS
Hg19
BAMCTSS
[{{{hg19bam}}} download][{{{hg19ctss}}} donwload]
Hg38
BAMCTSS
[{{{hg38bam}}} download][{{{hg38ctss}}} 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

Coexpression clusterscore
C0-CD14-Eosinophils-Neutrophils-Basophils-CD34-immature-Peripheral0
C1-testis-epididymis-embryonic-medulla-pituitary-trachea-caudate0
C10-occipital-temporal-parietal-brain-duodenum-Neurons-Neural0
C100-rhabdomyosarcoma-gastric-pineal-Wilms-cervical-mesodermal-endometrial0
C101-small-cerebellum-maxillary-colon-parietal-epididymis-merkel0
C102-neuroblastoma-testicular-pituitary-carcinosarcoma-rectum-acantholytic-iPS0
C103-CD4-CD8-Natural-Peripheral-Whole-Neutrophils-Basophils0
C104-Mast-Basophils-immature-CD14-CD34-eye-Natural0
C105-heart-skeletal-occipital-hippocampus-acute-Sebocyte-penis-0.0485
C106-Hep2-epitheloid-placenta-cervical-rectal-anaplastic-glassy0
C107-Neutrophils-CD14-Eosinophils-Monocytederived-Whole-Peripheral-blood0
C108-breast-hepatoblastoma-MCF7-parotid-salivary-submaxillary-prostate0
C109-Reticulocytes-non-acute-Hodgkin-Burkitt-retinoblastoma-lymphoma0.616
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C91-Fibroblast-Smooth-mesenchymal-Mesothelial-Small-Preadipocyte-Hair0
C92-CD14CD16-CD14-Eosinophils-Basophils-Neutrophils-Macrophage-Whole0
C93-chronic-acute-leukemia-acantholytic-medulloblastoma-testis-papillotubular0.145
C94-smallcell-adrenal-lung-nonsmall-small-somatostatinoma-teratocarcinoma0
C95-lung-aorta-trachea-penis-Alveolar-throat-endometrioid0
C96-non-acute-tonsil-spleen-Burkitt-lymphoma-appendix0
C97-small-smallcell-gastrointestinal-argyrophil-putamen-duodenum-brain0
C98-CD8-Natural-Basophils-blood-CD4-Peripheral-Whole0
C99-hairy-mycosis-submaxillary-salivary-cord-kidney-parotid0



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 no result for this sample


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: CNhs10727

Jaspar motifP-value
MA0002.20.377
MA0003.10.784
MA0004.10.12
MA0006.10.165
MA0007.10.608
MA0009.10.509
MA0014.10.594
MA0017.10.361
MA0018.20.0234
MA0019.10.534
MA0024.13.48453e-6
MA0025.10.442
MA0027.10.3
MA0028.11.50806e-7
MA0029.13.31368e-5
MA0030.10.361
MA0031.10.0481
MA0035.26.88529e-24
MA0038.10.8
MA0039.20.415
MA0040.10.0682
MA0041.10.286
MA0042.10.792
MA0043.10.107
MA0046.10.8
MA0047.20.647
MA0048.10.265
MA0050.10.694
MA0051.10.56
MA0052.10.00502
MA0055.10.0103
MA0057.10.744
MA0058.10.156
MA0059.10.00641
MA0060.14.94666e-17
MA0061.10.803
MA0062.29.24967e-13
MA0065.20.124
MA0066.10.812
MA0067.10.897
MA0068.10.141
MA0069.10.523
MA0070.10.247
MA0071.10.625
MA0072.10.00621
MA0073.10.692
MA0074.10.528
MA0076.14.2937e-9
MA0077.10.414
MA0078.10.601
MA0079.20.633
MA0080.23.2434e-7
MA0081.10.0109
MA0083.10.468
MA0084.10.528
MA0087.10.0889
MA0088.17.84851e-4
MA0090.10.0118
MA0091.10.84
MA0092.10.544
MA0093.10.118
MA0099.20.00139
MA0100.14.10559e-4
MA0101.10.487
MA0102.20.209
MA0103.10.749
MA0104.29.02252e-6
MA0105.10.0303
MA0106.10.918
MA0107.10.0498
MA0108.20.359
MA0111.10.415
MA0112.20.69
MA0113.10.387
MA0114.10.204
MA0115.10.383
MA0116.10.00285
MA0117.10.784
MA0119.10.287
MA0122.10.757
MA0124.10.659
MA0125.10.931
MA0131.10.27
MA0135.10.934
MA0136.11.69741e-6
MA0137.20.0345
MA0138.20.643
MA0139.10.459
MA0140.11.44004e-42
MA0141.10.796
MA0142.10.757
MA0143.10.651
MA0144.10.487
MA0145.10.508
MA0146.10.329
MA0147.11.02022e-6
MA0148.10.582
MA0149.10.118
MA0150.10.639
MA0152.10.495
MA0153.10.234
MA0154.10.271
MA0155.10.616
MA0156.13.4264e-9
MA0157.10.0028
MA0159.10.674
MA0160.10.445
MA0162.10.964
MA0163.15.42934e-10
MA0164.10.978
MA0258.10.677
MA0259.10.00512



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: CNhs10727

Novel motifP-value
10.165
100.0148
1000.704
1010.236
1020.528
1030.721
1040.559
1050.492
1060.217
1070.502
1080.374
1090.0433
110.155
1100.157
1110.0557
1120.0705
1130.694
1140.49
1150.0834
1160.974
1170.0672
1180.961
1190.307
120.933
1200.676
1210.566
1220.911
1230.655
1240.0181
1250.567
1260.32
1270.494
1280.25
1290.865
130.00505
1300.00929
1310.423
1320.407
1330.18
1340.841
1350.514
1360.0478
1370.694
1380.626
1390.537
140.298
1400.828
1410.308
1420.458
1430.208
1440.609
1450.537
1460.358
1470.101
1480.848
1490.141
150.484
1500.978
1510.524
1520.0466
1530.847
1540.989
1550.0894
1560.64
1570.741
1580.88
1590.364
160.312
1600.343
1610.403
1620.907
1630.238
1640.12
1650.797
1660.336
1670.433
1680.779
1690.674
170.741
180.269
190.801
20.225
200.164
210.927
220.845
230.0146
240.554
250.185
260.504
270.499
280.492
290.0438
30.303
300.0201
310.175
320.0119
330.116
340.607
350.632
360.0225
370.479
380.863
390.489
40.0214
400.182
410.899
420.373
430.481
440.575
450.74
460.553
470.0966
480.191
490.084
50.57
500.998
510.638
520.265
530.164
540.586
550.351
560.98
570.487
580.169
590.878
60.959
600.753
610.342
620.29
630.981
640.427
650.328
662.6691e-9
670.802
680.257
690.866
70.0267
700.383
710.0707
720.865
730.453
740.542
750.0456
760.235
770.187
780.0323
790.0851
80.89
800.435
810.943
820.819
830.401
840.893
850.183
860.987
870.199
880.503
890.391
90.873
900.304
910.12
920.261
930.89
940.568
950.0322
960.941
970.341
980.322
990.471



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: CNhs10727


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)
0000037 (hematopoietic stem cell)
0000048 (multi fate stem cell)
0000049 (common myeloid progenitor)
0000134 (mesenchymal cell)
0000219 (motile cell)
0000255 (eukaryotic cell)
0000548 (animal cell)
0000566 (angioblastic mesenchymal cell)
0000723 (somatic stem cell)
0000763 (myeloid cell)
0000837 (hematopoietic multipotent progenitor cell)
0000988 (hematopoietic cell)
0002032 (hematopoietic oligopotent progenitor cell)
0002320 (connective tissue cell)
0002371 (somatic cell)

DOID: Disease
0050686 (organ system cancer)
0060083 (immune system cancer)
1036 (chronic leukemia)
1240 (leukemia)
14566 (disease of cellular proliferation)
162 (cancer)
2531 (hematologic cancer)
4 (disease)
8692 (myeloid leukemia)

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

FF: FANTOM5
NA

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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