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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 16:48, 29 March 2012


Name:chronic lymphocytic leukemia (T-CLL) cell line:SKW-3
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 stage27 year old adult
sexmale
age27
cell typet cell
cell lineSKW-3
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-penis0.066
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-lymphoma0.658
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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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: CNhs11714

Jaspar motifP-value
MA0002.29.59318e-4
MA0003.10.982
MA0004.10.395
MA0006.10.493
MA0007.10.667
MA0009.10.9
MA0014.10.691
MA0017.10.114
MA0018.29.84657e-4
MA0019.10.192
MA0024.12.82884e-7
MA0025.10.32
MA0027.10.399
MA0028.10.00979
MA0029.10.687
MA0030.10.0071
MA0031.10.138
MA0035.25.0818e-4
MA0038.10.783
MA0039.20.312
MA0040.10.142
MA0041.10.113
MA0042.10.265
MA0043.10.00187
MA0046.10.0342
MA0047.20.595
MA0048.10.956
MA0050.10.756
MA0051.10.756
MA0052.10.0285
MA0055.10.509
MA0057.10.747
MA0058.10.506
MA0059.10.00354
MA0060.17.88823e-4
MA0061.10.564
MA0062.22.9811e-5
MA0065.20.00788
MA0066.10.132
MA0067.10.04
MA0068.10.432
MA0069.10.472
MA0070.10.868
MA0071.10.188
MA0072.10.28
MA0073.10.766
MA0074.10.901
MA0076.10.00146
MA0077.10.541
MA0078.10.759
MA0079.20.177
MA0080.27.95428e-4
MA0081.10.133
MA0083.17.1531e-5
MA0084.10.969
MA0087.10.285
MA0088.10.00757
MA0090.14.06942e-4
MA0091.10.342
MA0092.10.375
MA0093.10.485
MA0099.22.37246e-6
MA0100.10.0181
MA0101.10.167
MA0102.20.0191
MA0103.10.0196
MA0104.20.00228
MA0105.10.00313
MA0106.10.352
MA0107.10.0457
MA0108.21.55921e-8
MA0111.10.188
MA0112.20.0523
MA0113.10.902
MA0114.10.124
MA0115.10.18
MA0116.15.63041e-5
MA0117.10.686
MA0119.10.445
MA0122.10.879
MA0124.10.369
MA0125.10.364
MA0131.10.403
MA0135.10.0883
MA0136.18.9519e-5
MA0137.20.0217
MA0138.20.702
MA0139.10.172
MA0140.14.67122e-4
MA0141.10.0637
MA0142.10.623
MA0143.10.375
MA0144.10.187
MA0145.10.574
MA0146.10.73
MA0147.13.32843e-4
MA0148.10.357
MA0149.10.0351
MA0150.10.499
MA0152.10.278
MA0153.10.0422
MA0154.10.0294
MA0155.10.948
MA0156.16.38343e-5
MA0157.10.95
MA0159.10.0973
MA0160.10.381
MA0162.10.454
MA0163.12.19565e-14
MA0164.10.864
MA0258.10.0439
MA0259.10.0504



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: CNhs11714

Novel motifP-value
10.0365
100.0182
1000.25
1010.499
1020.467
1030.056
1040.442
1050.946
1060.844
1070.853
1080.837
1090.0164
110.0369
1100.222
1110.108
1120.515
1130.803
1140.0892
1150.196
1160.231
1170.0281
1180.982
1190.318
120.597
1200.246
1210.458
1220.769
1230.0215
1240.0779
1250.00422
1260.618
1270.363
1280.756
1290.226
130.126
1300.235
1310.654
1320.813
1330.203
1340.483
1350.885
1360.547
1370.942
1380.429
1390.308
140.874
1400.181
1410.101
1420.219
1433.53499e-5
1440.934
1450.317
1460.432
1470.503
1480.281
1490.497
150.0885
1500.558
1510.964
1520.0506
1530.882
1540.754
1550.109
1560.874
1570.237
1580.969
1590.205
160.36
1600.0747
1610.0901
1620.979
1630.397
1640.208
1650.431
1660.957
1670.0501
1680.821
1690.84
170.74
180.551
190.964
20.95
200.79
210.107
220.81
230.378
240.305
250.17
260.0222
270.248
280.861
290.00763
30.211
300.326
310.835
320.35
330.485
340.587
350.0857
360.0204
370.4
380.499
390.735
40.226
400.228
410.444
420.18
430.249
440.0807
450.508
460.0672
470.00606
480.071
490.0597
50.322
500.759
510.732
520.193
530.676
540.688
550.912
560.653
570.332
580.266
590.499
60.446
600.973
610.393
620.108
630.344
640.116
650.631
660.0252
670.715
680.534
690.37
70.223
700.218
710.00993
720.934
730.691
740.284
750.0196
760.389
770.77
780.243
790.478
80.104
800.33
810.196
820.372
830.646
840.958
850.743
860.487
870.271
880.689
890.232
90.954
900.135
910.983
920.714
930.107
940.172
950.124
960.0839
970.36
980.224
990.561



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: CNhs11714


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)
1036 (chronic leukemia)
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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