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{{f5samples
{{f5samples
|F5samples=
|ancestors_in_anatomy_facet=UBERON:0000061,UBERON:0000062,UBERON:0000063,UBERON:0000064,UBERON:0000065,UBERON:0000072,UBERON:0000077,UBERON:0000078,UBERON:0000119,UBERON:0000465,UBERON:0000467,UBERON:0000468,UBERON:0000475,UBERON:0000479,UBERON:0000480,UBERON:0000481,UBERON:0000483,UBERON:0000490,UBERON:0000922,UBERON:0000923,UBERON:0000924,UBERON:0000925,UBERON:0000926,UBERON:0000949,UBERON:0000974,UBERON:0001004,UBERON:0001007,UBERON:0001041,UBERON:0001042,UBERON:0001048,UBERON:0001062,UBERON:0001555,UBERON:0001557,UBERON:0002050,UBERON:0002193,UBERON:0002342,UBERON:0002346,UBERON:0002368,UBERON:0002370,UBERON:0002384,UBERON:0002390,UBERON:0002405,UBERON:0002530,UBERON:0002532,UBERON:0003075,UBERON:0003104,UBERON:0003295,UBERON:0003351,UBERON:0003408,UBERON:0003929,UBERON:0004119,UBERON:0004120,UBERON:0004121,UBERON:0004177,UBERON:0004185,UBERON:0004807,UBERON:0004921,UBERON:0005057,UBERON:0005058,UBERON:0005291,UBERON:0005423,UBERON:0005428,UBERON:0005434,UBERON:0005562,UBERON:0005911,UBERON:0006562,UBERON:0006598,UBERON:0007026,UBERON:0007284,UBERON:0007690,UBERON:0009113,UBERON:0009142,UBERON:0009145
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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 16:57, 29 March 2012


Name:NK T cell leukemia cell line:KHYG-1
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
sexfemale
age45
cell typet cell, nk, immature
cell lineKHYG-1
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-penis0.385
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-lymphoma0.599
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
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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-Whole0.126
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: CNhs11867

Jaspar motifP-value
MA0002.20.00125
MA0003.10.53
MA0004.10.304
MA0006.10.347
MA0007.10.543
MA0009.10.914
MA0014.10.539
MA0017.10.282
MA0018.20.249
MA0019.10.0787
MA0024.11.50297e-6
MA0025.10.273
MA0027.10.369
MA0028.11.36227e-5
MA0029.10.328
MA0030.10.104
MA0031.10.272
MA0035.20.00158
MA0038.10.229
MA0039.20.476
MA0040.10.207
MA0041.10.29
MA0042.10.297
MA0043.10.176
MA0046.10.249
MA0047.20.966
MA0048.10.492
MA0050.11.0389e-4
MA0051.10.0818
MA0052.10.0535
MA0055.10.391
MA0057.10.934
MA0058.10.224
MA0059.10.0147
MA0060.15.38374e-13
MA0061.10.724
MA0062.21.022e-11
MA0065.20.0422
MA0066.10.878
MA0067.10.45
MA0068.10.0285
MA0069.10.939
MA0070.10.543
MA0071.10.445
MA0072.10.023
MA0073.10.626
MA0074.10.426
MA0076.19.32635e-8
MA0077.10.508
MA0078.10.718
MA0079.20.331
MA0080.22.07486e-5
MA0081.10.128
MA0083.10.298
MA0084.10.859
MA0087.10.32
MA0088.10.0689
MA0090.14.22347e-4
MA0091.10.928
MA0092.10.872
MA0093.10.272
MA0099.20.0195
MA0100.10.0403
MA0101.10.31
MA0102.20.625
MA0103.10.241
MA0104.20.00442
MA0105.10.0147
MA0106.10.966
MA0107.10.123
MA0108.20.00359
MA0111.10.348
MA0112.20.607
MA0113.10.997
MA0114.10.168
MA0115.10.29
MA0116.12.19174e-4
MA0117.10.993
MA0119.10.856
MA0122.10.371
MA0124.10.978
MA0125.10.696
MA0131.10.0627
MA0135.10.0244
MA0136.14.29368e-8
MA0137.20.77
MA0138.20.571
MA0139.10.0297
MA0140.11.15012e-4
MA0141.10.224
MA0142.10.494
MA0143.10.283
MA0144.10.593
MA0145.10.529
MA0146.10.141
MA0147.10.00215
MA0148.10.937
MA0149.10.0372
MA0150.10.899
MA0152.10.175
MA0153.10.309
MA0154.10.607
MA0155.10.369
MA0156.14.90849e-11
MA0157.10.0234
MA0159.10.312
MA0160.10.662
MA0162.10.935
MA0163.12.66529e-9
MA0164.10.988
MA0258.10.244
MA0259.10.103



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: CNhs11867

Novel motifP-value
10.0626
100.00474
1000.299
1010.0264
1020.46
1030.477
1040.581
1050.888
1060.4
1070.324
1080.992
1090.0463
110.041
1100.307
1110.126
1120.479
1130.466
1140.314
1150.489
1160.809
1170.0176
1180.597
1190.505
120.875
1200.958
1210.976
1220.666
1232.6626e-4
1240.0067
1250.644
1260.484
1270.295
1280.478
1290.625
130.162
1300.286
1310.491
1320.913
1330.608
1340.776
1350.7
1360.116
1370.584
1380.324
1390.501
140.756
1400.534
1410.526
1420.665
1433.44943e-4
1440.661
1450.589
1460.944
1470.194
1480.23
1490.193
150.281
1500.23
1510.983
1520.0492
1530.57
1540.87
1550.0771
1560.84
1570.63
1580.958
1590.404
160.541
1600.812
1610.232
1620.863
1630.462
1640.76
1650.754
1660.441
1670.0362
1680.642
1690.856
170.621
180.315
190.677
20.545
200.405
210.265
220.619
230.663
240.582
250.0551
260.121
270.576
280.431
290.0261
30.134
300.135
310.797
320.363
330.418
340.691
350.305
360.0348
370.371
380.569
390.669
40.0126
400.0825
410.467
420.146
430.326
440.317
450.477
460.197
470.0369
480.135
490.0105
50.826
500.677
510.931
520.0664
530.201
540.997
550.522
560.677
570.199
580.102
590.889
60.826
600.923
610.1
620.0909
630.644
640.121
650.783
663.55465e-7
670.623
680.643
690.735
70.105
700.324
710.0387
720.549
730.921
740.817
750.00855
760.518
770.214
780.305
790.265
80.381
800.862
810.41
820.83
830.7
840.523
850.174
860.279
870.176
880.996
890.185
90.772
900.177
910.346
920.495
930.627
940.358
950.0164
960.415
970.0967
980.321
990.384



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: CNhs11867


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)
0000789 (alpha-beta T cell)
0000790 (immature alpha-beta T cell)
0000791 (mature alpha-beta T cell)
0000805 (immature single positive thymocyte)
0000806 (DN2 thymocyte)
0000807 (DN3 thymocyte)
0000808 (DN4 thymocyte)
0000809 (double-positive, alpha-beta thymocyte)
0000814 (mature NK T cell)
0000827 (pro-T cell)
0000837 (hematopoietic multipotent progenitor cell)
0000838 (lymphoid lineage restricted progenitor cell)
0000893 (thymocyte)
0000894 (DN1 thymic pro-T cell)
0000911 (effector T cell)
0000914 (immature NK T cell)
0000988 (hematopoietic cell)
0002031 (hematopoietic lineage restricted progenitor cell)
0002032 (hematopoietic oligopotent progenitor cell)
0002039 (immature NK T cell stage I)
0002040 (immature NK T cell stage II)
0002041 (immature NK T cell stage III)
0002042 (immature NK T cell stage IV)
0002087 (nongranular leukocyte)
0002127 (innate effector T cell)
0002320 (connective tissue cell)
0002371 (somatic cell)
0002419 (mature T cell)
0002420 (immature T cell)
0002425 (early T lineage precursor)
0002489 (double negative thymocyte)

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)
0000062 (organ)
0000063 (organ segment)
0000064 (organ part)
0000065 (respiratory tract)
0000072 (segment of respiratory tract)
0000077 (mixed endoderm/mesoderm-derived structure)
0000078 (mixed ectoderm/mesoderm/endoderm-derived structure)
0000119 (cell layer)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000475 (organism subdivision)
0000479 (tissue)
0000480 (anatomical group)
0000481 (multi-tissue structure)
0000483 (epithelium)
0000490 (unilaminar epithelium)
0000922 (embryo)
0000923 (germ layer)
0000924 (ectoderm)
0000925 (endoderm)
0000926 (mesoderm)
0000949 (endocrine system)
0000974 (neck)
0001004 (respiratory system)
0001007 (digestive system)
0001041 (foregut)
0001042 (chordate pharynx)
0001048 (primordium)
0001062 (anatomical entity)
0001555 (digestive tract)
0001557 (upper respiratory tract)
0002050 (embryonic structure)
0002193 (hemolymphoid system)
0002342 (neural crest)
0002346 (neurectoderm)
0002368 (endocrine gland)
0002370 (thymus)
0002384 (connective tissue)
0002390 (hematopoietic system)
0002405 (immune system)
0002530 (gland)
0002532 (epiblast (generic))
0003075 (neural plate)
0003104 (mesenchyme)
0003295 (pharyngeal gland)
0003351 (pharyngeal epithelium)
0003408 (gland of gut)
0003929 (gut epithelium)
0004119 (endoderm-derived structure)
0004120 (mesoderm-derived structure)
0004121 (ectoderm-derived structure)
0004177 (hemopoietic organ)
0004185 (endodermal part of digestive tract)
0004807 (respiratory system epithelium)
0004921 (subdivision of digestive tract)
0005057 (immune organ)
0005058 (hemolymphoid system gland)
0005291 (embryonic tissue)
0005423 (developing anatomical structure)
0005428 (vagal neural crest)
0005562 (thymus primordium)
0005911 (endo-epithelium)
0006562 (pharynx)
0006598 (presumptive structure)
0007026 (primitive gut)
0007284 (presumptive neural plate)
0007690 (early pharyngeal endoderm)
0009113 (thymic region)
0009142 (entire embryonic mesenchyme)
0009145 (pharyngeal region of foregut)

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