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{{f5samples
{{f5samples
|F5samples=
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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 (fresh)
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-0.0265
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-lymphoma0.699
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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: CNhs10722

Jaspar motifP-value
MA0002.20.118
MA0003.10.998
MA0004.10.198
MA0006.10.171
MA0007.10.352
MA0009.10.0797
MA0014.10.71
MA0017.10.00114
MA0018.20.105
MA0019.10.313
MA0024.19.71378e-10
MA0025.10.0455
MA0027.10.898
MA0028.18.17334e-8
MA0029.10.722
MA0030.10.0217
MA0031.10.00409
MA0035.20.979
MA0038.10.242
MA0039.20.448
MA0040.10.126
MA0041.10.94
MA0042.10.436
MA0043.10.0315
MA0046.10.579
MA0047.20.183
MA0048.10.0591
MA0050.10.455
MA0051.10.78
MA0052.10.414
MA0055.10.011
MA0057.10.796
MA0058.10.103
MA0059.10.00242
MA0060.19.63103e-6
MA0061.10.639
MA0062.26.08435e-14
MA0065.20.0387
MA0066.10.473
MA0067.10.373
MA0068.10.727
MA0069.10.354
MA0070.10.482
MA0071.10.0878
MA0072.10.529
MA0073.10.641
MA0074.10.201
MA0076.14.96973e-8
MA0077.10.666
MA0078.10.581
MA0079.20.17
MA0080.22.5022e-12
MA0081.10.0012
MA0083.10.517
MA0084.10.0497
MA0087.10.131
MA0088.10.0104
MA0090.12.61034e-5
MA0091.10.431
MA0092.10.478
MA0093.10.145
MA0099.21.28074e-5
MA0100.14.59036e-6
MA0101.10.224
MA0102.25.54225e-5
MA0103.10.951
MA0104.23.15206e-4
MA0105.10.201
MA0106.10.752
MA0107.10.00853
MA0108.25.11052e-7
MA0111.10.154
MA0112.20.213
MA0113.10.957
MA0114.10.0033
MA0115.10.106
MA0116.10.00106
MA0117.10.661
MA0119.10.934
MA0122.10.327
MA0124.10.523
MA0125.10.475
MA0131.10.00672
MA0135.10.524
MA0136.19.30278e-21
MA0137.20.627
MA0138.20.275
MA0139.10.735
MA0140.10.648
MA0141.10.104
MA0142.10.795
MA0143.10.785
MA0144.10.804
MA0145.10.718
MA0146.10.201
MA0147.12.07178e-4
MA0148.10.0796
MA0149.10.48
MA0150.10.0843
MA0152.10.471
MA0153.10.168
MA0154.10.46
MA0155.10.171
MA0156.17.10863e-17
MA0157.10.0156
MA0159.10.909
MA0160.10.288
MA0162.10.565
MA0163.11.0312e-9
MA0164.10.779
MA0258.10.0743
MA0259.10.0607



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: CNhs10722

Novel motifP-value
10.041
100.0156
1000.158
1010.264
1020.803
1030.719
1040.697
1050.781
1060.0874
1070.146
1080.426
1090.0228
110.122
1100.251
1110.477
1120.65
1130.152
1140.223
1150.359
1160.626
1170.0555
1180.176
1190.878
120.802
1200.514
1210.899
1220.0751
1230.953
1240.227
1250.485
1260.533
1270.0855
1280.101
1290.899
130.00104
1300.516
1310.00929
1320.921
1330.345
1340.456
1350.222
1360.197
1370.448
1380.909
1390.675
140.726
1400.192
1410.825
1420.795
1430.333
1440.717
1450.596
1460.753
1470.143
1480.0258
1490.188
150.251
1500.533
1510.484
1520.0569
1530.462
1540.863
1550.0714
1560.791
1570.595
1580.431
1590.505
160.747
1600.765
1610.111
1620.538
1630.561
1640.473
1650.0451
1660.293
1670.401
1680.976
1690.98
170.576
180.909
190.846
20.261
200.296
210.284
220.826
230.00888
240.0299
250.412
260.608
270.527
280.873
290.0141
30.0355
300.0849
310.487
320.102
330.36
340.534
350.494
360.0474
370.4
380.229
390.247
40.115
400.333
410.861
420.131
430.863
440.446
450.284
460.169
470.0746
480.0505
490.809
50.68
500.801
510.847
520.0977
530.395
540.504
550.564
560.771
570.239
580.24
590.752
60.559
600.293
610.0996
620.351
630.95
640.314
650.79
660.00684
670.376
680.171
690.361
70.174
700.261
710.0732
720.741
730.761
740.756
750.038
760.237
770.486
780.034
790.232
80.558
800.249
810.408
820.651
830.817
840.857
850.0248
860.967
870.0361
880.397
890.394
90.621
900.0681
910.18
920.0885
930.648
940.884
950.00392
960.635
970.556
980.546
990.439



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: CNhs10722


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)

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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