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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 (thawed)
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-0.0746
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-lymphoma0.693
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: CNhs10724

Jaspar motifP-value
MA0002.20.0907
MA0003.10.879
MA0004.10.2
MA0006.10.176
MA0007.10.505
MA0009.10.0451
MA0014.10.483
MA0017.10.00634
MA0018.20.852
MA0019.10.357
MA0024.12.59928e-9
MA0025.10.00191
MA0027.10.672
MA0028.14.02925e-8
MA0029.10.86
MA0030.10.204
MA0031.10.0275
MA0035.20.924
MA0038.10.212
MA0039.20.662
MA0040.10.206
MA0041.10.358
MA0042.10.145
MA0043.11.11995e-4
MA0046.10.747
MA0047.20.45
MA0048.10.135
MA0050.10.401
MA0051.10.23
MA0052.10.443
MA0055.10.0253
MA0057.10.686
MA0058.10.112
MA0059.10.00645
MA0060.12.35813e-7
MA0061.10.347
MA0062.27.68189e-15
MA0065.20.0368
MA0066.10.691
MA0067.10.166
MA0068.10.866
MA0069.10.298
MA0070.10.894
MA0071.10.14
MA0072.10.434
MA0073.10.621
MA0074.10.222
MA0076.19.5122e-9
MA0077.10.974
MA0078.10.777
MA0079.20.306
MA0080.23.51646e-13
MA0081.11.92152e-4
MA0083.10.793
MA0084.10.268
MA0087.10.169
MA0088.10.00648
MA0090.11.59405e-4
MA0091.10.562
MA0092.10.548
MA0093.10.158
MA0099.28.277e-4
MA0100.11.49792e-7
MA0101.10.247
MA0102.28.95306e-6
MA0103.10.411
MA0104.28.42149e-5
MA0105.10.552
MA0106.10.375
MA0107.10.0137
MA0108.23.37056e-5
MA0111.10.136
MA0112.20.396
MA0113.10.584
MA0114.10.0033
MA0115.10.192
MA0116.10.0029
MA0117.10.533
MA0119.10.644
MA0122.10.714
MA0124.10.592
MA0125.10.995
MA0131.10.00935
MA0135.10.986
MA0136.19.8968e-24
MA0137.20.88
MA0138.20.311
MA0139.10.822
MA0140.10.543
MA0141.10.128
MA0142.10.685
MA0143.10.704
MA0144.10.635
MA0145.10.738
MA0146.10.316
MA0147.17.65313e-5
MA0148.10.345
MA0149.10.58
MA0150.10.125
MA0152.10.442
MA0153.10.323
MA0154.10.781
MA0155.10.0823
MA0156.12.95371e-19
MA0157.10.0748
MA0159.10.73
MA0160.10.289
MA0162.10.395
MA0163.15.42695e-7
MA0164.10.78
MA0258.10.186
MA0259.10.028



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: CNhs10724

Novel motifP-value
10.129
100.0336
1000.177
1010.292
1020.982
1030.357
1040.655
1050.808
1060.0423
1070.0337
1080.216
1090.0313
110.271
1100.375
1110.635
1120.746
1130.164
1140.496
1150.757
1160.865
1170.0546
1180.128
1190.141
120.695
1200.502
1210.667
1220.161
1230.241
1240.277
1250.624
1260.583
1270.0698
1280.0644
1290.826
130.00159
1300.489
1310.00307
1320.655
1330.332
1340.466
1350.0594
1360.101
1370.182
1380.89
1390.697
140.835
1400.0774
1410.973
1420.584
1430.15
1440.611
1450.427
1460.82
1470.0568
1480.0174
1490.0845
150.467
1500.594
1510.446
1520.0509
1530.47
1540.64
1550.0689
1560.968
1570.449
1580.479
1590.385
160.577
1600.792
1610.134
1620.351
1630.518
1640.502
1650.0138
1660.256
1670.389
1680.873
1690.712
170.391
180.514
190.986
20.112
200.375
210.597
220.866
230.00478
240.0573
250.238
260.941
270.849
280.928
290.0217
30.0625
300.108
310.252
320.0377
330.279
340.406
350.699
360.0463
370.477
380.527
390.123
40.344
400.376
410.745
420.116
430.996
440.821
450.256
460.404
470.0821
480.146
490.973
50.845
500.955
510.88
520.118
530.906
540.418
550.396
560.586
570.497
580.303
590.982
60.248
600.431
610.121
620.498
630.616
640.503
650.411
660.0145
670.856
680.322
690.738
70.111
700.0781
710.153
720.995
730.846
740.93
750.0436
760.337
770.245
780.609
790.198
80.394
800.439
810.65
820.517
830.501
840.538
850.0337
860.763
870.0322
880.406
890.325
90.557
900.0814
910.222
920.0339
930.802
940.95
950.0042
960.758
970.67
980.758
990.146



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: CNhs10724


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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