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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 M5) cell line:NOMO-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
sexfemale
ageunknown
cell typemyeloid progenitor cell
cell lineNOMO-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-penis0.131
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-lymphoma0.493
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: CNhs13050

Jaspar motifP-value
MA0002.20.0258
MA0003.10.955
MA0004.10.127
MA0006.10.658
MA0007.10.887
MA0009.10.392
MA0014.10.292
MA0017.10.00452
MA0018.20.382
MA0019.10.0657
MA0024.13.89449e-8
MA0025.10.0954
MA0027.10.428
MA0028.16.75513e-5
MA0029.10.499
MA0030.10.0261
MA0031.10.0303
MA0035.20.227
MA0038.10.51
MA0039.20.085
MA0040.10.862
MA0041.10.539
MA0042.10.975
MA0043.10.0427
MA0046.10.523
MA0047.20.181
MA0048.10.118
MA0050.10.274
MA0051.10.807
MA0052.10.0441
MA0055.10.0358
MA0057.10.41
MA0058.10.12
MA0059.10.166
MA0060.11.69537e-6
MA0061.10.382
MA0062.22.27801e-9
MA0065.20.0538
MA0066.10.41
MA0067.10.324
MA0068.10.514
MA0069.10.174
MA0070.10.677
MA0071.10.0811
MA0072.10.451
MA0073.10.32
MA0074.10.124
MA0076.11.18128e-4
MA0077.10.921
MA0078.10.703
MA0079.20.915
MA0080.24.34734e-13
MA0081.10.00323
MA0083.10.00469
MA0084.10.323
MA0087.10.197
MA0088.10.352
MA0090.11.29364e-6
MA0091.10.275
MA0092.10.604
MA0093.10.156
MA0099.28.45454e-6
MA0100.16.42382e-4
MA0101.10.125
MA0102.20.0128
MA0103.10.638
MA0104.20.00275
MA0105.10.748
MA0106.10.971
MA0107.10.018
MA0108.20.00752
MA0111.10.127
MA0112.20.498
MA0113.10.291
MA0114.10.00301
MA0115.10.0155
MA0116.10.00593
MA0117.10.479
MA0119.10.387
MA0122.10.415
MA0124.10.342
MA0125.10.978
MA0131.10.0333
MA0135.10.767
MA0136.11.36659e-16
MA0137.20.0359
MA0138.20.417
MA0139.10.825
MA0140.10.0467
MA0141.10.0937
MA0142.10.246
MA0143.10.686
MA0144.10.23
MA0145.10.141
MA0146.10.0724
MA0147.10.00771
MA0148.10.0386
MA0149.10.227
MA0150.10.0559
MA0152.10.483
MA0153.10.1
MA0154.10.874
MA0155.10.29
MA0156.13.57645e-12
MA0157.10.152
MA0159.10.992
MA0160.10.00673
MA0162.10.24
MA0163.16.97949e-5
MA0164.10.339
MA0258.10.527
MA0259.10.132



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: CNhs13050

Novel motifP-value
10.272
100.0191
1000.327
1010.287
1020.377
1030.874
1040.777
1050.574
1060.924
1070.277
1080.539
1090.0701
110.331
1100.754
1110.35
1120.163
1130.684
1140.954
1150.164
1160.879
1170.101
1180.222
1190.762
120.489
1200.559
1210.852
1220.369
1230.0156
1240.512
1250.765
1260.672
1270.117
1280.691
1290.531
136.98667e-4
1300.927
1310.0304
1320.559
1330.673
1340.467
1350.668
1360.128
1370.264
1380.413
1390.633
140.772
1400.41
1410.401
1420.922
1430.864
1440.808
1450.356
1460.623
1470.363
1480.558
1490.304
150.707
1500.784
1510.905
1520.439
1530.901
1540.482
1550.0587
1560.933
1570.243
1580.628
1590.884
160.458
1600.591
1610.121
1620.907
1630.532
1640.587
1650.399
1660.266
1670.123
1680.424
1690.257
170.817
180.619
190.975
20.0981
200.243
210.161
220.482
230.0194
240.355
250.207
260.364
271
280.796
290.503
30.21
300.0398
310.0991
320.0472
330.491
340.766
350.803
360.102
370.702
380.386
390.341
40.0363
400.0597
410.879
420.682
430.724
440.906
450.234
460.912
470.295
480.385
490.347
50.438
500.781
510.775
520.59
530.235
540.48
550.867
560.642
570.419
580.0575
590.505
60.982
600.639
610.122
620.198
630.387
640.804
650.291
660.00398
670.822
680.605
690.863
70.0688
700.473
710.051
720.227
730.463
740.892
750.0811
760.278
770.0579
780.0591
790.18
80.579
800.608
810.489
820.132
830.234
840.513
850.149
860.665
870.0286
880.425
890.122
90.773
900.384
910.316
920.34
930.89
940.661
950.0581
960.91
970.57
980.363
990.0288



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: CNhs13050


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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