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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:0000049,CL:0000063,CL:0000134,CL:0000144,CL:0000219,CL:0000255,CL:0000548,CL:0000566,CL:0000723,CL:0000763,CL:0000837,CL:0000988,CL:0002032,CL:0002320,CL:0002371
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000004,CL:0000012,CL:0000034,CL:0000037,CL:0000048,CL:0000049,CL:0000063,CL:0000134,CL:0000144,CL:0000219,CL:0000255,CL:0000548,CL:0000566,CL:0000723,CL:0000763,CL:0000837,CL:0000988,CL:0002032,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 17:31, 29 March 2012


Name:acute myeloid leukemia (FAB M0) cell line:Kasumi-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 stageNA
sexmale
age57
cell typemyeloid progenitor cell
cell lineKasumi-3
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-penis-0.0384
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-lymphoma0.506
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
C110-leukemia-chronic-Eosinophils-acute-Whole-CD34-Lymphatic0
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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: CNhs13241

Jaspar motifP-value
MA0002.24.37189e-5
MA0003.10.259
MA0004.10.116
MA0006.10.393
MA0007.10.936
MA0009.10.126
MA0014.10.313
MA0017.10.00969
MA0018.20.093
MA0019.10.851
MA0024.12.32026e-7
MA0025.10.344
MA0027.10.167
MA0028.17.51645e-6
MA0029.10.612
MA0030.10.279
MA0031.10.96
MA0035.20.00184
MA0038.10.345
MA0039.20.553
MA0040.10.59
MA0041.10.316
MA0042.10.497
MA0043.10.941
MA0046.10.565
MA0047.20.512
MA0048.10.357
MA0050.10.0138
MA0051.10.173
MA0052.10.0987
MA0055.10.00712
MA0057.10.559
MA0058.10.00702
MA0059.10.00794
MA0060.11.42782e-9
MA0061.10.1
MA0062.23.20289e-13
MA0065.20.00463
MA0066.10.376
MA0067.10.728
MA0068.10.778
MA0069.10.04
MA0070.10.703
MA0071.10.0658
MA0072.10.447
MA0073.10.536
MA0074.10.931
MA0076.13.17153e-8
MA0077.10.658
MA0078.10.487
MA0079.20.498
MA0080.23.50931e-15
MA0081.11.40885e-4
MA0083.10.00755
MA0084.10.85
MA0087.10.76
MA0088.10.00301
MA0090.12.72378e-4
MA0091.10.771
MA0092.10.822
MA0093.10.0528
MA0099.20.00942
MA0100.14.04343e-5
MA0101.10.427
MA0102.20.105
MA0103.10.893
MA0104.20.0102
MA0105.10.00114
MA0106.10.736
MA0107.10.76
MA0108.20.00151
MA0111.10.868
MA0112.20.0838
MA0113.10.657
MA0114.10.0209
MA0115.10.0182
MA0116.11.00229e-4
MA0117.10.945
MA0119.10.811
MA0122.10.279
MA0124.10.322
MA0125.10.926
MA0131.10.221
MA0135.10.379
MA0136.12.65594e-24
MA0137.20.072
MA0138.20.406
MA0139.10.673
MA0140.14.37643e-4
MA0141.10.104
MA0142.10.489
MA0143.10.519
MA0144.10.273
MA0145.10.435
MA0146.10.0281
MA0147.10.011
MA0148.10.661
MA0149.10.193
MA0150.10.603
MA0152.10.532
MA0153.10.0183
MA0154.10.0231
MA0155.10.852
MA0156.12.26853e-21
MA0157.10.801
MA0159.10.681
MA0160.10.00226
MA0162.10.539
MA0163.15.25714e-16
MA0164.10.676
MA0258.10.182
MA0259.10.128



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: CNhs13241

Novel motifP-value
10.37
100.032
1000.993
1010.613
1020.393
1030.0127
1040.467
1050.518
1060.786
1070.304
1080.253
1090.0322
110.0374
1100.217
1110.617
1120.351
1130.674
1140.31
1150.457
1160.847
1170.0272
1180.0216
1190.653
120.463
1200.406
1210.647
1220.361
1230.524
1240.0583
1250.123
1260.115
1270.177
1280.815
1290.216
130.0014
1300.0524
1310.22
1320.468
1330.731
1340.833
1350.468
1360.119
1370.153
1380.796
1390.944
140.98
1400.416
1410.624
1420.547
1430.414
1440.246
1450.858
1460.51
1470.0112
1480.845
1490.886
150.105
1500.339
1510.878
1520.81
1530.221
1540.544
1550.257
1560.361
1570.358
1580.827
1590.487
160.913
1600.396
1610.063
1620.263
1630.534
1640.544
1650.263
1660.205
1670.447
1680.755
1690.406
170.973
180.361
190.871
20.797
200.54
210.794
220.419
230.00686
240.0207
250.0242
260.152
270.25
280.97
290.0573
30.0201
300.309
310.33
320.0288
330.0939
340.528
350.29
360.0446
370.115
380.458
390.225
40.0966
400.0273
410.718
420.0581
430.452
440.611
450.921
460.17
470.0153
480.0202
490.322
50.831
500.897
510.729
520.344
530.305
540.538
550.813
560.828
570.538
580.188
590.229
60.816
600.606
610.136
620.228
630.953
640.191
650.47
660.00443
670.913
680.526
690.755
70.00176
700.215
710.0142
720.465
730.276
740.704
750.0112
760.276
770.686
780.00401
790.0233
80.264
800.358
810.974
820.883
830.0358
840.8
850.399
860.497
870.0259
880.324
890.81
90.141
900.283
910.863
920.0791
930.178
940.763
957.02915e-5
960.608
970.56
980.39
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: CNhs13241


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)
0000049 (common myeloid progenitor)
0000134 (mesenchymal cell)
0000219 (motile cell)
0000255 (eukaryotic cell)
0000548 (animal cell)
0000566 (angioblastic mesenchymal cell)
0000723 (somatic stem cell)
0000763 (myeloid cell)
0000837 (hematopoietic multipotent progenitor cell)
0000988 (hematopoietic cell)
0002032 (hematopoietic oligopotent progenitor cell)
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)
8692 (myeloid leukemia)

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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