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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:0100104
|fonse_cell_line=FF:0100104
|fonse_cell_line_closure=FF:0100104
|fonse_cell_line_closure=FF:0100104

Revision as of 16:58, 29 March 2012


Name:anaplastic large cell lymphoma cell line:Ki-JK
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
age15
cell typelymphoid cell
cell lineKi-JK
companyJAPAN HEALTH SCIENCES FOUNDATION - Health Science Research Resources Bank
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
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-penis0.282
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-lymphoma0.479
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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: CNhs11881

Jaspar motifP-value
MA0002.20.00765
MA0003.10.706
MA0004.10.0699
MA0006.10.178
MA0007.10.887
MA0009.10.661
MA0014.10.811
MA0017.10.597
MA0018.20.454
MA0019.10.113
MA0024.10.00231
MA0025.10.294
MA0027.10.786
MA0028.16.6802e-5
MA0029.10.827
MA0030.10.00859
MA0031.10.00438
MA0035.20.626
MA0038.10.914
MA0039.20.824
MA0040.10.0748
MA0041.10.267
MA0042.10.441
MA0043.10.162
MA0046.10.75
MA0047.20.123
MA0048.10.0962
MA0050.11.27002e-6
MA0051.10.00144
MA0052.10.0337
MA0055.10.016
MA0057.10.877
MA0058.10.101
MA0059.11.37079e-4
MA0060.10.281
MA0061.10.551
MA0062.26.76937e-7
MA0065.20.044
MA0066.10.515
MA0067.10.432
MA0068.10.268
MA0069.10.278
MA0070.10.271
MA0071.10.0715
MA0072.10.214
MA0073.10.943
MA0074.10.648
MA0076.12.23231e-5
MA0077.10.221
MA0078.10.552
MA0079.20.117
MA0080.20.142
MA0081.10.249
MA0083.10.0152
MA0084.10.346
MA0087.10.285
MA0088.10.00155
MA0090.10.0115
MA0091.10.503
MA0092.10.548
MA0093.10.0689
MA0099.21.89598e-6
MA0100.10.132
MA0101.10.763
MA0102.20.249
MA0103.10.504
MA0104.28.0745e-5
MA0105.10.00336
MA0106.10.55
MA0107.10.235
MA0108.22.11641e-7
MA0111.10.343
MA0112.20.273
MA0113.10.722
MA0114.10.134
MA0115.10.488
MA0116.10.00702
MA0117.10.716
MA0119.10.372
MA0122.10.715
MA0124.10.257
MA0125.10.658
MA0131.10.125
MA0135.10.0848
MA0136.15.03159e-5
MA0137.21.98013e-6
MA0138.20.393
MA0139.10.208
MA0140.10.823
MA0141.10.00436
MA0142.10.516
MA0143.10.602
MA0144.10.00126
MA0145.10.44
MA0146.10.0493
MA0147.13.56026e-6
MA0148.10.552
MA0149.10.0255
MA0150.10.00175
MA0152.10.462
MA0153.10.0664
MA0154.10.543
MA0155.10.127
MA0156.11.6652e-7
MA0157.10.0429
MA0159.10.116
MA0160.10.0281
MA0162.10.576
MA0163.11.56241e-13
MA0164.10.79
MA0258.10.182
MA0259.10.0159



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: CNhs11881

Novel motifP-value
10.018
100.014
1000.0229
1010.534
1020.371
1030.308
1040.793
1050.631
1060.594
1070.275
1080.719
1090.00369
110.0352
1100.138
1110.327
1120.617
1130.932
1140.24
1150.656
1160.125
1170.00433
1180.0619
1190.266
120.749
1200.354
1210.154
1220.467
1232.56098e-4
1240.629
1250.599
1260.528
1270.655
1280.263
1290.32
130.0296
1300.754
1310.9
1320.668
1330.293
1340.811
1350.314
1360.0724
1370.656
1380.147
1390.303
140.875
1400.198
1410.96
1420.361
1430.011
1440.821
1450.781
1460.708
1470.328
1480.0868
1490.255
150.0835
1500.941
1510.767
1520.291
1530.922
1540.804
1550.134
1560.48
1570.618
1580.657
1590.812
160.955
1600.299
1610.572
1620.141
1630.722
1640.0137
1650.643
1660.264
1670.0377
1680.374
1690.118
170.726
180.225
190.739
20.407
200.107
210.102
220.92
230.463
240.257
250.15
260.0125
270.812
280.898
290.0434
30.154
300.0625
310.488
320.542
330.332
340.452
350.424
360.0292
370.241
380.578
390.537
40.89
400.141
410.879
420.156
430.642
440.0298
450.313
460.526
470.0219
480.0357
490.354
50.768
500.954
510.808
520.0835
530.408
540.716
550.695
560.945
570.149
580.292
590.937
60.432
600.971
610.206
620.0754
630.438
640.127
650.998
660.249
670.957
680.379
690.538
70.294
700.097
710.0784
720.418
730.386
740.592
750.00767
760.0501
770.736
780.113
790.345
80.153
800.157
810.397
820.363
830.836
840.658
850.706
860.335
870.237
880.754
890.934
90.45
900.00892
910.85
920.591
930.851
940.287
950.00261
960.191
970.168
980.214
990.594



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: CNhs11881


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)
0060058 (lymphoma)
0060083 (immune system cancer)
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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