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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:0000084,CL:0000134,CL:0000144,CL:0000219,CL:0000255,CL:0000542,CL:0000548,CL:0000566,CL:0000723,CL:0000738,CL:0000827,CL:0000837,CL:0000838,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:0000084,CL:0000134,CL:0000144,CL:0000219,CL:0000255,CL:0000542,CL:0000548,CL:0000566,CL:0000723,CL:0000738,CL:0000827,CL:0000837,CL:0000838,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 16:32, 29 March 2012


Name:acute lymphoblastic leukemia (T-ALL) cell line:HPB-ALL
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 typet cell
cell lineHPB-ALL
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-0.0249
C106-Hep2-epitheloid-placenta-cervical-rectal-anaplastic-glassy0
C107-Neutrophils-CD14-Eosinophils-Monocytederived-Whole-Peripheral-blood0
C108-breast-hepatoblastoma-MCF7-parotid-salivary-submaxillary-prostate0
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C90-neuroectodermal-peripheral-neuroepithelioma-neuroblastoma-carcinoid-parietal-putamen0
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: CNhs10746

Jaspar motifP-value
MA0002.20.0324
MA0003.10.459
MA0004.10.281
MA0006.10.264
MA0007.10.488
MA0009.10.695
MA0014.10.469
MA0017.10.533
MA0018.20.567
MA0019.10.147
MA0024.11.80814e-11
MA0025.10.481
MA0027.10.135
MA0028.11.42389e-6
MA0029.10.793
MA0030.10.227
MA0031.10.503
MA0035.20.0319
MA0038.10.888
MA0039.20.173
MA0040.10.182
MA0041.10.39
MA0042.10.614
MA0043.10.37
MA0046.10.262
MA0047.20.527
MA0048.10.762
MA0050.10.172
MA0051.10.401
MA0052.10.022
MA0055.10.34
MA0057.10.406
MA0058.10.151
MA0059.10.0385
MA0060.19.25153e-13
MA0061.10.607
MA0062.22.28702e-11
MA0065.20.644
MA0066.10.414
MA0067.10.672
MA0068.10.168
MA0069.10.445
MA0070.10.0484
MA0071.10.251
MA0072.10.217
MA0073.10.792
MA0074.10.152
MA0076.19.48402e-11
MA0077.10.939
MA0078.10.951
MA0079.20.237
MA0080.20.103
MA0081.10.327
MA0083.10.00426
MA0084.10.803
MA0087.10.275
MA0088.10.0125
MA0090.13.30941e-5
MA0091.10.8
MA0092.10.485
MA0093.10.25
MA0099.22.93595e-10
MA0100.11.01965e-5
MA0101.10.157
MA0102.20.00321
MA0103.10.0451
MA0104.20.00638
MA0105.10.244
MA0106.10.69
MA0107.10.0476
MA0108.23.38841e-11
MA0111.10.209
MA0112.20.156
MA0113.10.359
MA0114.10.655
MA0115.10.308
MA0116.10.0783
MA0117.10.695
MA0119.10.691
MA0122.10.542
MA0124.10.268
MA0125.10.828
MA0131.10.0384
MA0135.10.0596
MA0136.18.50481e-4
MA0137.20.0437
MA0138.20.408
MA0139.10.304
MA0140.10.0438
MA0141.10.901
MA0142.10.745
MA0143.10.232
MA0144.10.00428
MA0145.10.0809
MA0146.10.594
MA0147.10.00159
MA0148.10.338
MA0149.10.635
MA0150.10.0277
MA0152.10.633
MA0153.10.0435
MA0154.10.897
MA0155.10.57
MA0156.11.92325e-8
MA0157.10.424
MA0159.10.797
MA0160.10.857
MA0162.10.244
MA0163.10.0409
MA0164.10.983
MA0258.10.82
MA0259.10.0223



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: CNhs10746

Novel motifP-value
10.114
100.0214
1000.642
1010.245
1020.586
1030.987
1040.756
1050.517
1060.0624
1070.0119
1080.272
1090.633
110.305
1100.899
1110.14
1120.301
1130.8
1140.797
1150.256
1160.598
1170.042
1180.509
1190.969
120.856
1200.896
1210.477
1220.882
1234.66501e-4
1240.0773
1250.342
1260.413
1270.981
1280.187
1290.443
130.285
1300.335
1310.29
1320.532
1330.281
1340.769
1350.861
1360.334
1370.469
1380.816
1390.853
140.763
1400.679
1410.324
1420.147
1430.123
1440.524
1450.569
1460.73
1470.0358
1480.726
1490.047
150.0797
1500.994
1510.762
1520.00446
1530.906
1540.766
1550.0213
1560.86
1570.467
1580.0361
1590.635
160.513
1600.816
1610.0526
1620.69
1630.447
1640.823
1650.465
1660.73
1670.0979
1680.947
1690.157
170.706
180.785
190.0734
20.39
200.473
210.124
220.376
230.0461
240.95
250.212
260.544
270.906
280.265
290.124
30.422
300.216
310.393
320.00136
330.802
340.402
350.0899
360.243
370.83
380.879
390.0738
40.337
400.468
410.926
420.117
430.939
440.994
450.324
460.435
470.091
480.334
490.0984
50.984
500.719
510.642
520.066
530.473
540.626
550.144
560.744
570.419
580.268
590.366
60.372
600.464
610.166
620.28
630.805
640.404
650.337
660.0075
670.922
680.0586
690.784
70.264
700.962
710.396
720.615
730.0156
740.133
750.0333
760.692
770.0133
780.257
790.193
80.908
800.229
810.94
820.228
830.665
840.675
850.0105
860.674
870.733
880.601
890.243
90.573
900.0485
910.38
920.328
930.911
940.167
950.7
960.262
970.357
980.807
990.138



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: CNhs10746


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)
0000084 (T cell)
0000134 (mesenchymal cell)
0000219 (motile cell)
0000255 (eukaryotic cell)
0000542 (lymphocyte)
0000548 (animal cell)
0000566 (angioblastic mesenchymal cell)
0000723 (somatic stem cell)
0000738 (leukocyte)
0000827 (pro-T cell)
0000837 (hematopoietic multipotent progenitor cell)
0000838 (lymphoid lineage restricted progenitor cell)
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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