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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,FF:0101035
|fonse_cell_line=FF:0100104,FF:0101035
|fonse_cell_line_closure=FF:0100104,FF:0101035
|fonse_cell_line_closure=FF:0100104,FF:0101035

Revision as of 16:31, 29 March 2012


Name:adult T-cell leukemia cell line:ATN-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 stage47 year old adult
sexmale
age47
cell typet cell
cell lineATN-1
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-0.0188
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-lymphoma0.636
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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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: CNhs10738

Jaspar motifP-value
MA0002.20.11
MA0003.10.827
MA0004.10.672
MA0006.10.995
MA0007.10.803
MA0009.10.776
MA0014.10.452
MA0017.10.153
MA0018.20.381
MA0019.10.937
MA0024.12.805e-4
MA0025.10.4
MA0027.10.248
MA0028.15.39683e-7
MA0029.10.0506
MA0030.10.31
MA0031.10.076
MA0035.20.00243
MA0038.11.03722e-4
MA0039.20.00858
MA0040.10.206
MA0041.10.126
MA0042.10.294
MA0043.10.832
MA0046.10.696
MA0047.20.885
MA0048.10.371
MA0050.10.0126
MA0051.10.161
MA0052.10.0718
MA0055.10.0354
MA0057.10.999
MA0058.10.474
MA0059.10.0649
MA0060.12.11829e-42
MA0061.10.00282
MA0062.22.84062e-13
MA0065.20.0622
MA0066.10.841
MA0067.10.668
MA0068.10.408
MA0069.10.377
MA0070.10.288
MA0071.10.555
MA0072.10.0224
MA0073.10.809
MA0074.10.712
MA0076.11.54739e-10
MA0077.10.441
MA0078.10.151
MA0079.20.842
MA0080.22.31901e-5
MA0081.10.038
MA0083.10.705
MA0084.10.395
MA0087.10.417
MA0088.10.00468
MA0090.10.00436
MA0091.10.319
MA0092.10.543
MA0093.10.537
MA0099.20.996
MA0100.10.00741
MA0101.10.0174
MA0102.20.0894
MA0103.10.37
MA0104.20.0231
MA0105.13.91712e-6
MA0106.10.797
MA0107.10.0356
MA0108.20.00659
MA0111.10.332
MA0112.20.206
MA0113.10.571
MA0114.10.115
MA0115.10.298
MA0116.16.36526e-4
MA0117.10.6
MA0119.10.443
MA0122.10.652
MA0124.10.364
MA0125.10.655
MA0131.10.197
MA0135.10.0888
MA0136.19.43551e-9
MA0137.20.279
MA0138.20.399
MA0139.10.149
MA0140.13.11977e-6
MA0141.10.315
MA0142.10.448
MA0143.10.601
MA0144.10.615
MA0145.10.7
MA0146.10.0685
MA0147.10.0236
MA0148.10.717
MA0149.10.0843
MA0150.10.58
MA0152.10.0594
MA0153.10.0184
MA0154.10.0565
MA0155.10.454
MA0156.17.29101e-10
MA0157.10.00129
MA0159.10.281
MA0160.10.243
MA0162.10.623
MA0163.11.05727e-6
MA0164.10.847
MA0258.10.352
MA0259.10.206



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: CNhs10738

Novel motifP-value
10.0189
100.0206
1000.52
1010.0431
1020.35
1030.33
1040.609
1050.349
1060.677
1070.584
1080.749
1090.00216
110.0158
1100.108
1110.454
1120.248
1130.768
1140.598
1150.237
1160.95
1170.0095
1180.873
1190.332
120.815
1200.422
1210.361
1220.43
1230.0474
1240.0118
1250.405
1260.235
1270.464
1280.504
1290.577
130.0574
1300.258
1310.491
1320.3
1330.275
1340.721
1350.96
1360.178
1370.784
1380.888
1390.413
140.653
1400.233
1410.711
1420.739
1430.039
1440.854
1450.425
1460.283
1470.156
1480.271
1490.592
150.106
1500.31
1510.832
1520.223
1530.436
1540.888
1550.205
1560.446
1570.935
1580.299
1590.583
160.862
1600.747
1610.401
1620.715
1630.901
1640.0391
1650.786
1660.211
1670.188
1680.765
1690.281
170.537
180.543
190.891
20.629
200.622
210.555
220.911
230.545
240.315
250.205
260.0392
270.64
280.317
290.0476
30.0822
300.193
310.736
320.432
330.351
340.515
350.464
360.0236
370.29
380.454
390.909
40.0128
400.0514
410.784
420.0221
430.202
440.561
450.982
460.199
470.0132
480.062
490.0141
50.506
500.609
510.784
520.0585
530.154
540.904
550.751
560.394
570.343
580.164
590.864
60.753
600.987
610.21
620.162
630.744
640.197
650.672
661.20976e-9
670.46
680.415
690.718
70.0941
700.617
710.0364
720.763
730.735
740.761
750.0219
760.764
770.903
780.276
790.34
80.519
800.661
810.764
820.849
830.00519
840.666
850.847
860.0957
870.04
880.82
890.233
90.992
900.129
910.104
920.96
930.812
940.193
950.0102
960.191
970.263
980.674
990.638



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: CNhs10738


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)
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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