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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:0000051,CL:0000063,CL:0000134,CL:0000144,CL:0000219,CL:0000255,CL:0000542,CL:0000548,CL:0000566,CL:0000723,CL:0000738,CL:0000837,CL:0000988,CL:0002032,CL:0002087,CL:0002320,CL:0002371
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000004,CL:0000012,CL:0000034,CL:0000037,CL:0000048,CL:0000051,CL:0000063,CL:0000134,CL:0000144,CL:0000219,CL:0000255,CL:0000542,CL:0000548,CL:0000566,CL:0000723,CL:0000738,CL:0000837,CL:0000988,CL:0002032,CL:0002087,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 16:40, 29 March 2012


Name:acute lymphoblastic leukemia (B-ALL) cell line:BALL-1
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
sexunknown
ageunknown
cell typeb cell
cell lineBALL-1
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-penis0.242
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-lymphoma0.709
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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
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: CNhs11251

Jaspar motifP-value
MA0002.20.547
MA0003.10.448
MA0004.10.0851
MA0006.10.311
MA0007.10.48
MA0009.10.462
MA0014.10.889
MA0017.10.117
MA0018.20.355
MA0019.10.158
MA0024.11.23037e-8
MA0025.10.117
MA0027.10.228
MA0028.12.35556e-6
MA0029.10.317
MA0030.10.111
MA0031.10.268
MA0035.20.693
MA0038.10.693
MA0039.20.538
MA0040.10.046
MA0041.10.0586
MA0042.10.177
MA0043.10.618
MA0046.10.0742
MA0047.20.375
MA0048.10.45
MA0050.10.00794
MA0051.10.0442
MA0052.10.506
MA0055.10.0565
MA0057.10.836
MA0058.10.0445
MA0059.10.00126
MA0060.10.00266
MA0061.10.00337
MA0062.22.1856e-9
MA0065.20.0217
MA0066.10.63
MA0067.10.659
MA0068.10.521
MA0069.10.682
MA0070.10.606
MA0071.10.322
MA0072.10.916
MA0073.10.803
MA0074.10.723
MA0076.11.71369e-9
MA0077.10.473
MA0078.10.234
MA0079.20.124
MA0080.26.60993e-4
MA0081.10.012
MA0083.11.91265e-7
MA0084.10.118
MA0087.10.232
MA0088.10.00835
MA0090.11.47504e-5
MA0091.10.677
MA0092.10.854
MA0093.10.076
MA0099.27.11817e-12
MA0100.10.00439
MA0101.10.273
MA0102.20.283
MA0103.10.0118
MA0104.21.79074e-4
MA0105.17.84933e-6
MA0106.10.566
MA0107.10.284
MA0108.21.11002e-9
MA0111.10.167
MA0112.20.408
MA0113.10.486
MA0114.10.0463
MA0115.10.0498
MA0116.17.73228e-6
MA0117.10.922
MA0119.10.698
MA0122.10.854
MA0124.10.782
MA0125.10.606
MA0131.10.202
MA0135.10.022
MA0136.15.84944e-6
MA0137.20.00353
MA0138.20.637
MA0139.10.687
MA0140.10.856
MA0141.10.392
MA0142.10.0794
MA0143.10.657
MA0144.10.00938
MA0145.10.114
MA0146.10.227
MA0147.17.04303e-5
MA0148.10.257
MA0149.10.134
MA0150.10.1
MA0152.10.795
MA0153.10.00158
MA0154.10.0241
MA0155.10.525
MA0156.15.49827e-6
MA0157.10.968
MA0159.10.206
MA0160.10.753
MA0162.10.951
MA0163.12.58504e-11
MA0164.10.82
MA0258.10.312
MA0259.10.107



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: CNhs11251

Novel motifP-value
10.024
100.0186
1000.0787
1010.403
1020.992
1030.672
1040.987
1050.614
1060.706
1070.415
1080.762
1090.139
110.0746
1100.162
1110.0402
1120.465
1130.813
1140.967
1150.609
1160.394
1170.0044
1180.333
1190.255
120.527
1200.084
1210.574
1220.892
1230.00124
1240.0683
1250.0401
1260.418
1270.864
1280.113
1290.4
130.0389
1300.762
1310.242
1320.887
1330.601
1340.464
1350.283
1360.206
1370.155
1380.731
1390.486
140.824
1400.684
1410.00765
1420.353
1430.943
1440.722
1450.289
1460.53
1470.084
1480.32
1490.785
150.181
1500.782
1510.584
1520.0467
1530.917
1540.616
1550.00937
1560.813
1570.507
1580.879
1590.386
160.875
1600.354
1610.239
1620.663
1630.385
1640.131
1650.428
1660.313
1670.111
1680.409
1690.955
170.975
180.57
190.7
20.15
200.308
210.199
220.742
230.15
240.514
250.148
260.0526
270.956
280.447
290.0205
30.128
300.0511
310.845
320.305
330.587
340.7
350.222
360.0349
370.29
380.785
390.244
40.435
400.151
410.831
420.136
430.465
440.0161
450.303
460.231
470.0447
480.0898
490.16
50.823
500.977
510.806
520.088
530.715
540.83
550.346
560.723
570.0489
580.169
590.828
60.626
600.655
610.0718
620.162
630.785
640.317
650.718
660.16
670.397
680.375
690.954
70.204
700.924
710.0296
720.497
730.869
740.543
750.00244
760.118
770.533
780.201
790.483
80.239
800.559
810.123
820.918
830.882
840.558
850.213
860.389
870.26
880.768
890.62
90.489
900.0152
910.68
920.507
930.853
940.39
950.168
960.903
970.203
980.607
990.409



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: CNhs11251


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)
0000051 (common lymphoid progenitor)
0000134 (mesenchymal cell)
0000219 (motile cell)
0000255 (eukaryotic cell)
0000542 (lymphocyte)
0000548 (animal cell)
0000566 (angioblastic mesenchymal cell)
0000723 (somatic stem cell)
0000738 (leukocyte)
0000837 (hematopoietic multipotent progenitor cell)
0000988 (hematopoietic cell)
0002032 (hematopoietic oligopotent progenitor cell)
0002087 (nongranular leukocyte)
0002320 (connective tissue cell)
0002371 (somatic cell)

DOID: Disease
0050686 (organ system cancer)
0060083 (immune system cancer)
1240 (leukemia)
12603 (acute leukemia)
14566 (disease of cellular proliferation)
162 (cancer)
2531 (hematologic cancer)
4 (disease)

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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