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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 16:59, 29 March 2012


Name:acute myeloid leukemia (FAB M7) cell line:MKPL-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
age66
cell typemyeloid progenitor cell
cell lineMKPL-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
C106-Hep2-epitheloid-placenta-cervical-rectal-anaplastic-glassy0
C107-Neutrophils-CD14-Eosinophils-Monocytederived-Whole-Peripheral-blood0
C108-breast-hepatoblastoma-MCF7-parotid-salivary-submaxillary-prostate0
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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: CNhs11888

Jaspar motifP-value
MA0002.20.044
MA0003.10.941
MA0004.10.0804
MA0006.10.239
MA0007.10.801
MA0009.10.972
MA0014.10.766
MA0017.10.0697
MA0018.20.0215
MA0019.10.191
MA0024.12.02439e-4
MA0025.10.0332
MA0027.10.694
MA0028.18.75986e-9
MA0029.10.00329
MA0030.10.0969
MA0031.10.86
MA0035.21.60159e-18
MA0038.10.7
MA0039.20.387
MA0040.10.233
MA0041.10.667
MA0042.10.591
MA0043.10.00501
MA0046.10.625
MA0047.20.531
MA0048.10.973
MA0050.10.068
MA0051.10.272
MA0052.10.00266
MA0055.10.0417
MA0057.10.316
MA0058.10.0741
MA0059.10.00477
MA0060.16.67712e-6
MA0061.10.393
MA0062.21.33867e-12
MA0065.20.0105
MA0066.10.875
MA0067.10.966
MA0068.10.0359
MA0069.10.0717
MA0070.10.466
MA0071.10.269
MA0072.10.572
MA0073.10.65
MA0074.10.865
MA0076.12.82527e-8
MA0077.10.814
MA0078.10.666
MA0079.20.464
MA0080.28.36494e-5
MA0081.10.0139
MA0083.10.528
MA0084.10.0649
MA0087.10.183
MA0088.10.0109
MA0090.10.0135
MA0091.10.214
MA0092.10.547
MA0093.10.155
MA0099.20.00262
MA0100.16.50057e-4
MA0101.10.393
MA0102.20.0509
MA0103.10.998
MA0104.22.74812e-4
MA0105.10.0893
MA0106.10.538
MA0107.10.0528
MA0108.25.05994e-8
MA0111.10.0536
MA0112.20.321
MA0113.10.688
MA0114.10.0565
MA0115.10.0117
MA0116.10.00437
MA0117.10.788
MA0119.10.78
MA0122.10.753
MA0124.10.301
MA0125.10.481
MA0131.10.379
MA0135.10.523
MA0136.12.10739e-7
MA0137.20.0924
MA0138.20.691
MA0139.10.557
MA0140.11.84307e-18
MA0141.10.303
MA0142.10.837
MA0143.10.145
MA0144.10.646
MA0145.10.521
MA0146.10.0846
MA0147.11.03213e-4
MA0148.10.859
MA0149.10.0169
MA0150.10.714
MA0152.10.323
MA0153.10.972
MA0154.10.191
MA0155.10.819
MA0156.11.47635e-6
MA0157.10.964
MA0159.10.438
MA0160.10.0279
MA0162.10.662
MA0163.17.22236e-8
MA0164.10.776
MA0258.10.0632
MA0259.10.0575



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: CNhs11888

Novel motifP-value
10.0102
100.0462
1000.618
1010.416
1020.34
1030.381
1040.847
1050.341
1060.335
1070.465
1080.744
1090.0389
110.097
1100.541
1110.00271
1120.322
1130.394
1140.0456
1150.073
1160.149
1170.0651
1180.697
1190.282
120.414
1200.788
1210.484
1220.358
1231.2231e-4
1240.0163
1250.812
1260.322
1270.288
1280.392
1290.186
130.0216
1300.447
1310.604
1320.121
1330.641
1340.579
1350.467
1360.164
1370.648
1380.908
1390.36
140.638
1400.9
1410.274
1420.44
1430.781
1440.947
1450.515
1460.69
1470.0562
1480.572
1490.266
150.125
1500.827
1510.732
1520.102
1530.727
1540.659
1550.241
1560.365
1570.705
1580.187
1590.682
160.639
1600.588
1610.133
1620.587
1630.157
1640.972
1650.526
1660.227
1670.195
1680.868
1690.75
170.928
180.483
190.576
20.628
200.766
210.788
220.63
230.102
240.699
250.185
260.473
270.614
280.818
290.259
30.435
300.118
310.35
320.028
330.634
340.949
350.142
360.014
370.58
380.493
390.328
40.0848
400.139
410.79
420.275
430.86
440.722
450.809
460.263
470.116
480.139
490.0694
50.632
500.861
510.461
520.918
530.104
540.778
550.391
560.564
570.126
580.0706
590.983
60.372
600.711
610.291
620.0959
630.962
640.0685
650.942
660.0385
670.759
680.201
690.605
70.161
700.807
710.48
720.826
730.546
740.779
750.152
760.404
770.42
780.00318
790.154
80.38
800.884
810.562
820.487
830.493
840.935
850.377
860.877
870.306
880.756
890.868
90.806
900.273
910.411
920.337
930.979
940.709
950.175
960.0661
970.663
980.114
990.155



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: CNhs11888


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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