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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 17:35, 29 March 2012


Name:acute myeloid leukemia (FAB M2) cell line:Kasumi-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
sexmale
age7
cell typemyeloid progenitor cell
cell lineKasumi-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-penis0.232
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-lymphoma0.43
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
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: CNhs13502

Jaspar motifP-value
MA0002.20.75
MA0003.10.748
MA0004.10.0137
MA0006.10.136
MA0007.10.912
MA0009.10.45
MA0014.10.927
MA0017.10.556
MA0018.23.40149e-4
MA0019.10.127
MA0024.11.93484e-4
MA0025.10.545
MA0027.10.298
MA0028.10.0549
MA0029.10.929
MA0030.10.0179
MA0031.10.13
MA0035.20.122
MA0038.12.97851e-4
MA0039.20.252
MA0040.10.244
MA0041.10.0958
MA0042.10.415
MA0043.10.0495
MA0046.10.241
MA0047.20.36
MA0048.10.336
MA0050.11.41319e-4
MA0051.10.0214
MA0052.10.00815
MA0055.10.0547
MA0057.10.658
MA0058.10.0179
MA0059.14.03294e-6
MA0060.10.633
MA0061.10.843
MA0062.20.0205
MA0065.20.00994
MA0066.10.453
MA0067.10.166
MA0068.10.0333
MA0069.10.946
MA0070.10.31
MA0071.10.0455
MA0072.10.899
MA0073.10.933
MA0074.10.734
MA0076.10.328
MA0077.10.41
MA0078.10.652
MA0079.20.326
MA0080.21.99916e-7
MA0081.10.00885
MA0083.11.87274e-6
MA0084.10.828
MA0087.10.246
MA0088.10.107
MA0090.17.69899e-4
MA0091.10.571
MA0092.10.741
MA0093.10.0217
MA0099.28.99667e-8
MA0100.13.7026e-4
MA0101.10.111
MA0102.20.679
MA0103.10.349
MA0104.23.28335e-6
MA0105.10.0067
MA0106.10.411
MA0107.10.012
MA0108.22.90596e-12
MA0111.10.343
MA0112.20.122
MA0113.10.811
MA0114.10.0379
MA0115.10.223
MA0116.10.00264
MA0117.10.899
MA0119.10.367
MA0122.10.949
MA0124.10.629
MA0125.10.182
MA0131.10.261
MA0135.10.319
MA0136.17.34982e-8
MA0137.20.00206
MA0138.20.758
MA0139.10.331
MA0140.10.0667
MA0141.10.0528
MA0142.10.779
MA0143.10.849
MA0144.10.0819
MA0145.10.377
MA0146.10.206
MA0147.17.72786e-8
MA0148.10.306
MA0149.10.0254
MA0150.10.0158
MA0152.10.0879
MA0153.10.0357
MA0154.10.108
MA0155.10.632
MA0156.17.29062e-4
MA0157.10.586
MA0159.10.768
MA0160.10.0444
MA0162.10.686
MA0163.14.71222e-14
MA0164.10.84
MA0258.10.145
MA0259.10.00445



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: CNhs13502

Novel motifP-value
10.0884
100.0163
1000.342
1010.19
1020.455
1030.605
1040.702
1050.232
1060.474
1070.165
1080.863
1090.0702
110.0508
1100.138
1110.0101
1120.261
1130.715
1140.0055
1150.435
1160.201
1170.0342
1180.027
1190.772
120.586
1200.134
1210.833
1220.662
1230.00617
1240.169
1250.259
1260.0871
1270.0421
1280.992
1290.29
130.0076
1300.613
1310.298
1320.824
1330.814
1340.548
1350.92
1360.102
1370.251
1380.651
1390.12
140.592
1400.193
1410.215
1420.0706
1430.67
1440.859
1450.735
1460.948
1470.192
1480.0404
1490.454
150.273
1500.97
1510.566
1520.135
1530.977
1540.918
1550.0336
1560.981
1570.301
1580.478
1590.674
160.673
1600.0896
1610.0993
1620.13
1630.344
1640.0348
1650.516
1660.199
1670.00919
1680.164
1690.468
170.801
180.734
190.781
20.568
200.335
210.0363
220.979
230.149
240.226
250.279
260.0209
270.532
280.978
290.0431
30.169
300.0787
310.379
320.349
330.737
340.706
350.158
360.0388
370.389
380.826
390.579
40.065
400.334
410.702
420.246
430.496
440.115
450.575
460.0985
470.0417
480.0499
490.272
50.982
500.952
510.856
520.189
530.512
540.51
550.369
560.969
570.00562
580.255
590.517
60.328
600.975
610.121
620.151
630.485
640.231
650.491
660.0813
670.744
680.413
690.325
70.0587
700.424
710.0357
720.858
730.987
740.552
750.0163
760.0882
770.725
780.0147
790.166
80.048
800.204
810.121
820.267
830.521
840.299
850.605
860.609
870.504
880.471
890.606
90.825
900.00348
910.784
920.857
930.726
940.583
950.129
960.593
970.366
980.175
990.508



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: CNhs13502


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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