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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 16:41, 29 March 2012


Name:acute lymphoblastic leukemia (T-ALL) cell line:Jurkat
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
age14
cell typet cell
cell lineJurkat
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-penis0.0902
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-lymphoma0.723
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
C110-leukemia-chronic-Eosinophils-acute-Whole-CD34-Lymphatic0
C111-medulla-lung-trachea-testis-caudate-epididymis-throat0
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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: CNhs11253

Jaspar motifP-value
MA0002.20.205
MA0003.10.396
MA0004.10.309
MA0006.10.19
MA0007.10.94
MA0009.10.619
MA0014.10.819
MA0017.10.741
MA0018.20.8
MA0019.10.349
MA0024.14.57826e-9
MA0025.10.246
MA0027.10.127
MA0028.14.11514e-6
MA0029.10.702
MA0030.10.0159
MA0031.10.621
MA0035.21.39999e-6
MA0038.10.0641
MA0039.20.581
MA0040.10.175
MA0041.10.248
MA0042.10.516
MA0043.10.0889
MA0046.10.487
MA0047.20.173
MA0048.10.414
MA0050.10.478
MA0051.10.976
MA0052.18.87316e-5
MA0055.10.0209
MA0057.10.628
MA0058.10.124
MA0059.10.0103
MA0060.14.68931e-12
MA0061.10.287
MA0062.24.38593e-12
MA0065.20.426
MA0066.10.534
MA0067.10.515
MA0068.10.185
MA0069.10.171
MA0070.10.245
MA0071.10.773
MA0072.10.0944
MA0073.10.963
MA0074.10.419
MA0076.17.63607e-9
MA0077.10.519
MA0078.10.39
MA0079.20.244
MA0080.20.0251
MA0081.10.257
MA0083.12.63299e-4
MA0084.10.798
MA0087.10.227
MA0088.12.09694e-4
MA0090.12.43653e-4
MA0091.10.254
MA0092.10.492
MA0093.10.216
MA0099.21.55652e-15
MA0100.14.92632e-5
MA0101.10.161
MA0102.20.00468
MA0103.10.141
MA0104.20.00145
MA0105.10.841
MA0106.10.943
MA0107.10.0173
MA0108.28.39728e-12
MA0111.10.719
MA0112.20.137
MA0113.10.238
MA0114.10.486
MA0115.10.00865
MA0116.10.106
MA0117.10.944
MA0119.10.313
MA0122.10.314
MA0124.10.931
MA0125.10.958
MA0131.10.0433
MA0135.10.13
MA0136.14.54656e-5
MA0137.20.166
MA0138.20.566
MA0139.10.286
MA0140.19.85368e-5
MA0141.10.965
MA0142.10.848
MA0143.10.171
MA0144.10.018
MA0145.10.0228
MA0146.10.572
MA0147.19.26516e-4
MA0148.10.103
MA0149.10.22
MA0150.10.00694
MA0152.10.209
MA0153.10.0758
MA0154.10.93
MA0155.10.317
MA0156.11.63149e-8
MA0157.10.764
MA0159.10.785
MA0160.10.534
MA0162.10.353
MA0163.10.00604
MA0164.10.953
MA0258.10.713
MA0259.10.0267



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: CNhs11253

Novel motifP-value
10.163
100.0573
1000.264
1010.641
1020.606
1030.9
1040.976
1050.716
1060.0063
1070.00787
1080.49
1090.23
110.56
1100.907
1110.0451
1120.224
1130.252
1140.881
1150.897
1160.743
1170.254
1180.895
1190.293
120.875
1200.762
1211
1220.988
1230.303
1240.147
1250.0649
1260.81
1270.22
1280.0288
1290.632
130.0732
1300.0385
1310.387
1320.878
1330.177
1340.562
1350.422
1360.146
1370.641
1380.789
1390.947
140.45
1400.551
1410.819
1420.613
1430.029
1440.906
1450.627
1460.221
1470.135
1480.706
1490.0456
150.363
1500.639
1510.266
1520.0136
1530.63
1540.528
1550.119
1560.609
1570.382
1580.721
1590.988
160.358
1600.879
1610.518
1620.3
1630.824
1640.906
1650.738
1660.843
1670.0103
1680.492
1690.0661
170.376
180.556
190.0393
20.0803
200.266
210.608
220.224
230.0143
240.222
250.292
260.348
270.924
280.557
290.228
30.676
300.123
310.474
320.00579
330.954
340.451
350.303
360.0781
370.412
380.891
390.15
40.00838
400.611
410.733
420.155
430.934
440.273
450.156
460.649
470.12
480.454
490.496
50.927
500.766
510.764
520.0164
530.651
540.325
550.0152
560.703
570.372
580.765
590.44
60.806
600.108
610.227
620.886
630.93
640.634
650.271
660.00198
670.803
680.448
690.567
70.529
700.147
710.442
720.778
730.0372
740.938
750.325
760.38
770.0848
780.567
790.232
80.549
800.944
810.706
820.753
830.781
840.834
850.0337
860.746
870.857
880.441
890.265
90.335
900.00561
910.506
920.109
930.857
940.768
950.546
960.986
970.103
980.948
990.356



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: CNhs11253


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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