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{{f5samples
{{f5samples
|F5samples=
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|ancestors_in_anatomy_facet=UBERON:0000061,UBERON:0000062,UBERON:0000465,UBERON:0000467,UBERON:0000468,UBERON:0000479,UBERON:0000480,UBERON:0000922,UBERON:0000923,UBERON:0000926,UBERON:0001062,UBERON:0001434,UBERON:0001474,UBERON:0002050,UBERON:0002193,UBERON:0002204,UBERON:0002371,UBERON:0002384,UBERON:0002390,UBERON:0002405,UBERON:0002532,UBERON:0004120,UBERON:0004765,UBERON:0005423
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|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000004,CL:0000012,CL:0000034,CL:0000037,CL:0000040,CL:0000048,CL:0000049,CL:0000063,CL:0000134,CL:0000144,CL:0000219,CL:0000255,CL:0000548,CL:0000557,CL:0000559,CL:0000566,CL:0000576,CL:0000723,CL:0000738,CL:0000763,CL:0000766,CL:0000837,CL:0000839,CL:0000988,CL:0001012,CL:0002009,CL:0002031,CL:0002032,CL:0002087,CL:0002194,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 16:30, 29 March 2012


Name:acute myeloid leukemia (FAB M5) cell line:THP-1 (revived)
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 stage1 year old child
sexmale
age1
cell typemonoblast
cell lineTHP-1
companyNA
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-0.0787
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-lymphoma0.675
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: CNhs10723

Jaspar motifP-value
MA0002.20.0557
MA0003.10.963
MA0004.10.194
MA0006.10.206
MA0007.10.27
MA0009.10.0733
MA0014.10.263
MA0017.16.4021e-4
MA0018.20.0241
MA0019.10.703
MA0024.11.33281e-8
MA0025.10.0498
MA0027.10.693
MA0028.17.81878e-9
MA0029.10.991
MA0030.10.023
MA0031.10.0106
MA0035.20.68
MA0038.10.213
MA0039.20.943
MA0040.10.234
MA0041.10.209
MA0042.10.244
MA0043.10.155
MA0046.10.721
MA0047.20.2
MA0048.10.16
MA0050.10.258
MA0051.10.358
MA0052.10.333
MA0055.10.0203
MA0057.10.773
MA0058.10.104
MA0059.10.00506
MA0060.11.83804e-7
MA0061.10.731
MA0062.28.24032e-17
MA0065.20.0141
MA0066.10.409
MA0067.10.461
MA0068.10.991
MA0069.10.182
MA0070.10.962
MA0071.10.0714
MA0072.10.348
MA0073.10.545
MA0074.10.393
MA0076.11.61421e-9
MA0077.10.994
MA0078.10.426
MA0079.20.403
MA0080.25.53024e-13
MA0081.13.82984e-4
MA0083.10.684
MA0084.10.209
MA0087.10.269
MA0088.10.0121
MA0090.12.56957e-4
MA0091.10.584
MA0092.10.661
MA0093.10.155
MA0099.20.00132
MA0100.12.31297e-7
MA0101.10.392
MA0102.23.20903e-5
MA0103.10.766
MA0104.23.52088e-4
MA0105.10.246
MA0106.10.544
MA0107.10.0316
MA0108.24.64126e-7
MA0111.10.209
MA0112.20.197
MA0113.10.937
MA0114.10.00161
MA0115.10.0838
MA0116.14.58999e-4
MA0117.10.795
MA0119.10.594
MA0122.10.472
MA0124.10.332
MA0125.11
MA0131.10.0234
MA0135.10.687
MA0136.19.39201e-23
MA0137.20.845
MA0138.20.26
MA0139.10.436
MA0140.10.518
MA0141.10.132
MA0142.10.634
MA0143.10.659
MA0144.10.683
MA0145.10.882
MA0146.10.12
MA0147.11.87612e-4
MA0148.10.147
MA0149.10.524
MA0150.10.227
MA0152.10.725
MA0153.10.232
MA0154.10.372
MA0155.10.184
MA0156.11.44198e-19
MA0157.10.0273
MA0159.10.954
MA0160.10.173
MA0162.10.499
MA0163.11.29563e-9
MA0164.10.837
MA0258.10.0394
MA0259.10.0469



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: CNhs10723

Novel motifP-value
10.0677
100.0245
1000.281
1010.399
1020.633
1030.182
1040.533
1050.817
1060.0318
1070.0735
1080.211
1090.0201
110.161
1100.272
1110.628
1120.682
1130.248
1140.539
1150.334
1160.87
1170.0653
1180.116
1190.782
120.724
1200.469
1210.763
1220.0708
1230.404
1240.287
1250.497
1260.437
1270.0458
1280.0793
1290.292
139.13312e-4
1300.262
1310.0167
1320.867
1330.438
1340.496
1350.227
1360.124
1370.353
1380.965
1390.669
140.812
1400.0446
1410.706
1420.553
1430.445
1440.787
1450.711
1460.806
1470.0927
1480.05
1490.0894
150.303
1500.741
1510.429
1520.0417
1530.764
1540.547
1550.204
1560.823
1570.64
1580.512
1590.43
160.828
1600.848
1610.0525
1620.625
1630.668
1640.503
1650.013
1660.382
1670.564
1680.904
1690.932
170.504
180.738
190.752
20.218
200.386
210.484
220.672
230.0104
240.0272
250.294
260.707
270.402
280.913
290.0233
30.0241
300.2
310.408
320.0807
330.502
340.718
350.651
360.0573
370.342
380.271
390.23
40.239
400.278
410.956
420.1
430.831
440.606
450.348
460.293
470.0603
480.0508
490.735
50.919
500.795
510.775
520.0907
530.656
540.609
550.717
560.609
570.307
580.204
590.562
60.491
600.454
610.199
620.409
630.984
640.311
650.577
660.00289
670.401
680.0883
690.623
70.0754
700.188
710.106
720.943
730.844
740.775
750.0524
760.184
770.65
780.0206
790.241
80.563
800.499
810.422
820.824
830.396
840.831
850.0324
860.67
870.0226
880.387
890.617
90.407
900.0502
910.0439
920.101
930.765
940.708
950.00312
960.764
970.614
980.685
990.33



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: CNhs10723


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)
0000040 (monoblast)
0000048 (multi fate stem cell)
0000049 (common myeloid progenitor)
0000134 (mesenchymal cell)
0000219 (motile cell)
0000255 (eukaryotic cell)
0000548 (animal cell)
0000557 (granulocyte monocyte progenitor cell)
0000559 (promonocyte)
0000566 (angioblastic mesenchymal cell)
0000576 (monocyte)
0000723 (somatic stem cell)
0000738 (leukocyte)
0000763 (myeloid cell)
0000766 (myeloid leukocyte)
0000837 (hematopoietic multipotent progenitor cell)
0000839 (myeloid lineage restricted progenitor cell)
0000988 (hematopoietic cell)
0001012 (CD7-negative lymphoid progenitor OR granulocyte monocyte progenitor)
0002009 (macrophage dendritic cell progenitor)
0002031 (hematopoietic lineage restricted progenitor cell)
0002032 (hematopoietic oligopotent progenitor cell)
0002087 (nongranular leukocyte)
0002194 (monopoietic 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)
0000062 (organ)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000479 (tissue)
0000480 (anatomical group)
0000922 (embryo)
0000923 (germ layer)
0000926 (mesoderm)
0001062 (anatomical entity)
0001434 (skeletal system)
0001474 (bone element)
0002050 (embryonic structure)
0002193 (hemolymphoid system)
0002204 (musculoskeletal system)
0002371 (bone marrow)
0002384 (connective tissue)
0002390 (hematopoietic system)
0002405 (immune system)
0002532 (epiblast (generic))
0004120 (mesoderm-derived structure)
0004765 (skeletal element)
0005423 (developing anatomical structure)

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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