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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 16:57, 29 March 2012


Name:acute myeloid leukemia (FAB M2) cell line:NKM-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
age33
cell typemyeloid progenitor cell
cell lineNKM-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-penis0.386
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-lymphoma0.452
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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: CNhs11864

Jaspar motifP-value
MA0002.20.00995
MA0003.10.658
MA0004.10.0116
MA0006.10.453
MA0007.10.671
MA0009.10.898
MA0014.10.986
MA0017.10.0886
MA0018.20.0373
MA0019.10.0137
MA0024.15.68956e-4
MA0025.10.124
MA0027.10.0313
MA0028.10.00216
MA0029.10.945
MA0030.10.211
MA0031.10.225
MA0035.20.457
MA0038.10.0246
MA0039.20.243
MA0040.10.375
MA0041.10.324
MA0042.10.486
MA0043.10.0437
MA0046.10.203
MA0047.20.286
MA0048.10.141
MA0050.10.0199
MA0051.10.281
MA0052.10.579
MA0055.10.211
MA0057.10.944
MA0058.10.00723
MA0059.10.00103
MA0060.10.12
MA0061.10.93
MA0062.22.07004e-7
MA0065.20.102
MA0066.10.614
MA0067.10.938
MA0068.10.851
MA0069.10.372
MA0070.10.695
MA0071.10.263
MA0072.10.86
MA0073.10.791
MA0074.10.641
MA0076.10.00526
MA0077.10.964
MA0078.10.751
MA0079.20.468
MA0080.24.62369e-10
MA0081.10.00162
MA0083.10.0134
MA0084.10.675
MA0087.10.574
MA0088.10.0217
MA0090.13.50269e-4
MA0091.10.349
MA0092.10.482
MA0093.10.0162
MA0099.23.65868e-5
MA0100.10.00195
MA0101.10.156
MA0102.20.342
MA0103.10.622
MA0104.28.00642e-5
MA0105.10.0247
MA0106.10.485
MA0107.10.0189
MA0108.27.08617e-7
MA0111.10.429
MA0112.20.142
MA0113.10.762
MA0114.10.0723
MA0115.10.078
MA0116.15.75159e-4
MA0117.10.843
MA0119.10.324
MA0122.10.619
MA0124.10.872
MA0125.10.631
MA0131.10.0773
MA0135.10.0324
MA0136.12.01829e-15
MA0137.20.0124
MA0138.20.614
MA0139.10.583
MA0140.10.432
MA0141.10.16
MA0142.10.917
MA0143.10.831
MA0144.10.12
MA0145.10.399
MA0146.10.0079
MA0147.12.4977e-5
MA0148.10.295
MA0149.10.156
MA0150.10.188
MA0152.10.115
MA0153.10.0734
MA0154.10.00561
MA0155.10.732
MA0156.16.34431e-8
MA0157.10.636
MA0159.10.66
MA0160.10.282
MA0162.10.77
MA0163.11.20809e-11
MA0164.10.721
MA0258.10.0517
MA0259.10.044



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: CNhs11864

Novel motifP-value
10.0304
100.0141
1000.178
1010.0622
1020.738
1030.689
1040.876
1050.93
1060.627
1070.903
1080.738
1090.141
110.0423
1100.127
1110.273
1120.589
1130.522
1140.261
1150.34
1160.216
1170.00442
1180.186
1190.173
120.78
1200.203
1210.936
1220.907
1232.72946e-5
1240.108
1250.362
1260.631
1270.343
1280.671
1290.296
130.0254
1300.938
1310.533
1320.967
1330.94
1340.541
1350.343
1360.358
1370.894
1380.551
1390.239
140.526
1400.38
1410.478
1420.307
1430.235
1440.947
1450.297
1460.98
1470.406
1480.0376
1490.832
150.196
1500.583
1510.411
1520.27
1530.961
1540.666
1550.111
1560.437
1570.397
1580.96
1590.521
160.956
1600.285
1610.12
1620.436
1630.221
1640.327
1650.569
1660.746
1670.179
1680.441
1690.102
170.705
180.751
190.574
20.545
200.523
210.0882
220.69
230.133
240.597
250.223
260.0176
270.453
280.842
290.0515
30.0824
300.136
310.84
320.399
330.647
340.776
350.127
360.0376
370.18
380.488
390.603
40.053
400.466
410.988
420.142
430.369
440.392
450.345
460.0572
470.0263
480.041
490.0533
50.988
500.916
510.739
520.617
530.0815
540.988
550.916
560.659
570.101
580.254
590.645
60.299
600.713
610.0966
620.208
630.318
640.201
650.988
660.167
670.82
680.844
690.155
70.114
700.288
710.0866
720.827
730.474
740.98
750.0182
760.0898
770.827
780.031
790.553
80.0731
800.361
810.208
820.4
830.86
840.621
850.528
860.117
870.0961
880.468
890.191
90.862
900.181
910.651
920.655
930.576
940.498
950.0795
960.604
970.357
980.299
990.675



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: CNhs11864


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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