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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 17:27, 29 March 2012


Name:acute myeloid leukemia (FAB M2) cell line:Kasumi-6
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
age64
cell typemyeloid progenitor cell
cell lineKasumi-6
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-penis0.244
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-lymphoma0.438
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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: CNhs13052

Jaspar motifP-value
MA0002.20.00563
MA0003.10.725
MA0004.10.0574
MA0006.10.248
MA0007.10.969
MA0009.10.0888
MA0014.10.607
MA0017.10.0225
MA0018.24.60786e-4
MA0019.10.0392
MA0024.10.00141
MA0025.10.154
MA0027.10.00101
MA0028.12.47552e-4
MA0029.10.414
MA0030.10.0694
MA0031.10.623
MA0035.20.0279
MA0038.11.20242e-5
MA0039.20.148
MA0040.10.461
MA0041.10.301
MA0042.10.373
MA0043.10.0984
MA0046.10.192
MA0047.20.208
MA0048.10.387
MA0050.10.0187
MA0051.10.0967
MA0052.12.3291e-4
MA0055.10.191
MA0057.10.612
MA0058.10.0213
MA0059.10.00444
MA0060.10.169
MA0061.10.288
MA0062.21.86671e-8
MA0065.20.0158
MA0066.10.583
MA0067.10.943
MA0068.10.0584
MA0069.10.476
MA0070.10.883
MA0071.10.111
MA0072.10.64
MA0073.10.718
MA0074.10.879
MA0076.12.7898e-5
MA0077.10.382
MA0078.10.4
MA0079.20.211
MA0080.22.10615e-13
MA0081.10.00292
MA0083.14.21553e-5
MA0084.10.919
MA0087.10.182
MA0088.10.0376
MA0090.13.68006e-5
MA0091.10.456
MA0092.10.984
MA0093.10.0627
MA0099.22.74275e-7
MA0100.12.58654e-5
MA0101.10.504
MA0102.20.468
MA0103.10.183
MA0104.20.00103
MA0105.17.71254e-4
MA0106.10.973
MA0107.10.0413
MA0108.21.75524e-16
MA0111.10.181
MA0112.20.0653
MA0113.10.574
MA0114.10.051
MA0115.10.219
MA0116.11.14718e-4
MA0117.10.856
MA0119.10.387
MA0122.10.622
MA0124.10.562
MA0125.10.669
MA0131.10.278
MA0135.10.18
MA0136.17.11515e-21
MA0137.20.942
MA0138.20.493
MA0139.10.325
MA0140.10.00204
MA0141.10.043
MA0142.10.943
MA0143.10.876
MA0144.10.649
MA0145.10.61
MA0146.10.173
MA0147.16.27488e-4
MA0148.10.0876
MA0149.10.182
MA0150.10.598
MA0152.10.365
MA0153.10.0659
MA0154.10.0643
MA0155.10.95
MA0156.11.75421e-15
MA0157.10.976
MA0159.10.354
MA0160.10.0514
MA0162.10.728
MA0163.13.89635e-16
MA0164.10.992
MA0258.10.0514
MA0259.10.0849



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: CNhs13052

Novel motifP-value
10.0362
100.00982
1000.32
1010.088
1020.882
1030.0678
1040.663
1050.559
1060.871
1070.405
1080.439
1090.0526
110.069
1100.182
1110.0226
1120.21
1130.688
1140.0566
1150.65
1160.277
1170.0103
1180.0429
1190.996
120.954
1200.402
1210.554
1220.507
1230.0619
1240.045
1250.0437
1260.286
1270.325
1280.711
1290.802
130.013
1300.897
1310.268
1320.565
1330.466
1340.238
1350.279
1360.351
1370.185
1380.542
1390.122
140.868
1400.456
1410.272
1420.106
1430.99
1440.529
1450.64
1460.845
1470.0511
1480.159
1490.237
150.131
1500.795
1510.746
1520.279
1530.859
1540.916
1550.00823
1560.729
1570.35
1580.376
1590.615
160.739
1600.229
1610.0178
1620.726
1630.856
1640.094
1650.663
1660.959
1670.0415
1680.279
1690.5
170.873
180.758
190.573
20.574
200.566
210.257
220.837
230.0798
240.199
250.162
260.0247
270.389
280.71
290.0311
30.0108
300.147
310.637
320.311
330.268
340.727
350.0903
360.0432
370.142
380.564
390.449
40.185
400.199
410.765
420.161
430.541
440.353
450.5
460.0677
470.0343
480.0796
490.224
50.976
500.81
510.748
520.277
530.404
540.668
550.719
560.9
570.154
580.146
590.748
60.359
600.889
610.0591
620.147
630.446
640.189
650.715
660.134
670.696
680.683
690.941
70.067
700.99
710.00648
720.731
730.501
740.251
750.00638
760.0887
770.881
780.0269
790.851
80.121
800.112
810.371
820.403
830.29
840.521
850.801
860.709
870.601
880.622
890.662
90.82
900.0376
910.371
920.995
930.673
940.522
950.0212
960.813
970.404
980.201
990.492



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: CNhs13052


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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