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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:0000236,CL:0000255,CL:0000542,CL:0000548,CL:0000566,CL:0000723,CL:0000738,CL:0000817,CL:0000826,CL:0000837,CL:0000838,CL:0000945,CL:0000988,CL:0002031,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:0000236,CL:0000255,CL:0000542,CL:0000548,CL:0000566,CL:0000723,CL:0000738,CL:0000817,CL:0000826,CL:0000837,CL:0000838,CL:0000945,CL:0000988,CL:0002031,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 16:43, 29 March 2012


Name:acute lymphoblastic leukemia (B-ALL) cell line:NALM-6
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
ageNA
cell typeb cell
cell lineNALM-6
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-penis0.102
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-lymphoma0.774
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
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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: CNhs11282

Jaspar motifP-value
MA0002.20.936
MA0003.10.549
MA0004.10.0179
MA0006.10.129
MA0007.10.575
MA0009.10.463
MA0014.10.968
MA0017.10.186
MA0018.20.65
MA0019.10.159
MA0024.11.35506e-14
MA0025.10.36
MA0027.15.02718e-4
MA0028.17.62186e-4
MA0029.10.408
MA0030.10.573
MA0031.10.918
MA0035.20.0717
MA0038.10.112
MA0039.20.322
MA0040.10.0288
MA0041.10.336
MA0042.10.871
MA0043.10.255
MA0046.10.384
MA0047.20.863
MA0048.10.412
MA0050.10.0238
MA0051.10.0825
MA0052.10.083
MA0055.10.0686
MA0057.10.991
MA0058.10.0148
MA0059.12.08616e-4
MA0060.13.39946e-13
MA0061.10.929
MA0062.26.12314e-6
MA0065.20.0453
MA0066.10.87
MA0067.10.848
MA0068.10.62
MA0069.10.395
MA0070.10.0284
MA0071.10.415
MA0072.10.438
MA0073.10.861
MA0074.10.456
MA0076.15.40344e-5
MA0077.10.656
MA0078.10.953
MA0079.20.162
MA0080.20.0707
MA0081.10.0522
MA0083.14.44839e-10
MA0084.10.852
MA0087.10.39
MA0088.10.00182
MA0090.11.33431e-5
MA0091.10.264
MA0092.10.845
MA0093.10.0218
MA0099.22.10158e-11
MA0100.13.0566e-4
MA0101.10.24
MA0102.20.0287
MA0103.10.341
MA0104.21.48542e-5
MA0105.10.169
MA0106.10.554
MA0107.10.0521
MA0108.21.47455e-7
MA0111.10.332
MA0112.20.75
MA0113.10.272
MA0114.10.0404
MA0115.10.00788
MA0116.10.00604
MA0117.10.98
MA0119.10.657
MA0122.10.515
MA0124.10.252
MA0125.10.916
MA0131.10.0485
MA0135.10.1
MA0136.18.97159e-4
MA0137.20.0661
MA0138.20.829
MA0139.10.467
MA0140.10.0131
MA0141.10.541
MA0142.10.112
MA0143.10.703
MA0144.10.0394
MA0145.10.0391
MA0146.10.852
MA0147.13.32456e-6
MA0148.10.784
MA0149.10.147
MA0150.10.00508
MA0152.10.799
MA0153.10.0218
MA0154.10.174
MA0155.10.312
MA0156.10.0022
MA0157.10.384
MA0159.10.434
MA0160.10.496
MA0162.10.971
MA0163.14.47274e-6
MA0164.10.938
MA0258.10.795
MA0259.10.0112



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: CNhs11282

Novel motifP-value
10.0536
100.0321
1000.115
1010.602
1020.966
1030.581
1040.769
1050.871
1060.595
1070.172
1080.375
1090.172
110.168
1100.231
1110.192
1120.35
1130.648
1140.801
1150.53
1160.895
1170.0366
1180.494
1190.913
120.372
1200.395
1210.957
1220.932
1230.00638
1240.136
1250.306
1260.834
1270.159
1280.314
1290.597
130.0415
1300.184
1310.0535
1320.503
1330.319
1340.981
1350.212
1360.438
1370.541
1380.227
1390.273
140.897
1400.742
1410.117
1420.442
1430.709
1440.709
1450.733
1460.729
1470.291
1480.425
1490.243
150.24
1500.54
1510.398
1520.0162
1530.931
1540.656
1550.0102
1560.817
1570.224
1580.202
1590.535
160.477
1600.327
1610.183
1620.97
1630.911
1640.464
1650.836
1660.371
1670.0365
1680.47
1690.335
170.532
180.958
190.351
20.127
200.283
210.306
220.52
230.00989
240.81
250.131
260.0825
270.838
280.865
290.0296
30.434
300.0625
310.607
320.0125
330.689
340.367
350.158
360.0431
370.844
380.964
390.101
40.13
400.155
410.792
420.28
430.825
440.51
450.182
460.0998
470.0709
480.25
490.197
50.919
500.729
510.907
520.139
530.861
540.504
550.133
560.703
570.0907
580.57
590.488
60.987
600.491
610.0933
620.499
630.475
640.425
650.279
660.0133
670.957
680.0309
690.613
70.149
700.17
710.0523
720.685
730.18
740.763
750.0311
760.408
770.367
780.0601
790.173
80.328
800.716
810.499
820.402
830.59
840.459
850.0127
860.523
870.604
880.629
890.358
90.379
900.0231
910.405
920.0567
930.705
940.525
950.165
960.714
970.359
980.504
990.171



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: CNhs11282


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)
0000236 (B cell)
0000255 (eukaryotic cell)
0000542 (lymphocyte)
0000548 (animal cell)
0000566 (angioblastic mesenchymal cell)
0000723 (somatic stem cell)
0000738 (leukocyte)
0000817 (precursor B cell)
0000826 (pro-B cell)
0000837 (hematopoietic multipotent progenitor cell)
0000838 (lymphoid lineage restricted progenitor cell)
0000945 (lymphocyte of B lineage)
0000988 (hematopoietic cell)
0002031 (hematopoietic lineage restricted progenitor 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)
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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