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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 M7) cell line:M-MOK
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 typemegakaryoblast
cell lineM-MOK
companyRIKEN Bioresource centre
collaborationYukio Nakamura (RIKEN BRC)
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-0.0256
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-lymphoma0.59
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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: CNhs13049

Jaspar motifP-value
MA0002.25.61925e-4
MA0003.10.948
MA0004.10.222
MA0006.10.135
MA0007.10.512
MA0009.10.9
MA0014.10.289
MA0017.10.117
MA0018.20.025
MA0019.10.117
MA0024.12.2164e-13
MA0025.10.387
MA0027.10.0104
MA0028.13.70786e-6
MA0029.10.0585
MA0030.10.396
MA0031.10.761
MA0035.27.17388e-12
MA0038.10.0907
MA0039.20.11
MA0040.10.373
MA0041.10.0949
MA0042.10.0606
MA0043.10.129
MA0046.10.816
MA0047.20.205
MA0048.10.334
MA0050.10.00496
MA0051.10.0189
MA0052.10.0665
MA0055.10.0831
MA0057.10.51
MA0058.10.193
MA0059.10.044
MA0060.15.55923e-11
MA0061.10.678
MA0062.26.24957e-12
MA0065.20.0373
MA0066.10.846
MA0067.10.637
MA0068.10.136
MA0069.10.04
MA0070.10.902
MA0071.10.0736
MA0072.10.279
MA0073.10.756
MA0074.10.856
MA0076.11.24528e-6
MA0077.10.904
MA0078.10.562
MA0079.20.482
MA0080.24.64202e-9
MA0081.10.0224
MA0083.17.6801e-5
MA0084.10.713
MA0087.10.137
MA0088.10.00473
MA0090.12.1855e-5
MA0091.10.512
MA0092.10.471
MA0093.10.243
MA0099.26.21296e-9
MA0100.19.16993e-7
MA0101.10.839
MA0102.20.126
MA0103.10.598
MA0104.20.00815
MA0105.10.0379
MA0106.10.315
MA0107.10.318
MA0108.22.99456e-11
MA0111.10.331
MA0112.20.69
MA0113.10.756
MA0114.10.104
MA0115.10.297
MA0116.10.0233
MA0117.10.665
MA0119.10.806
MA0122.10.364
MA0124.10.582
MA0125.10.774
MA0131.10.152
MA0135.10.149
MA0136.12.73039e-12
MA0137.20.848
MA0138.20.288
MA0139.10.293
MA0140.13.09209e-15
MA0141.10.112
MA0142.10.924
MA0143.10.502
MA0144.10.985
MA0145.10.207
MA0146.10.527
MA0147.10.00122
MA0148.10.34
MA0149.10.368
MA0150.10.0209
MA0152.10.399
MA0153.10.176
MA0154.10.273
MA0155.10.663
MA0156.13.01276e-13
MA0157.10.545
MA0159.10.463
MA0160.10.0231
MA0162.10.555
MA0163.12.89768e-5
MA0164.10.215
MA0258.10.974
MA0259.10.00856



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: CNhs13049

Novel motifP-value
10.146
100.0705
1000.733
1010.308
1020.143
1030.295
1040.476
1050.781
1060.204
1070.225
1080.458
1090.183
110.161
1100.322
1110.654
1120.795
1130.197
1140.624
1150.339
1160.511
1170.0355
1180.397
1190.556
120.966
1200.271
1210.962
1220.59
1230.00283
1240.0461
1250.718
1260.291
1270.491
1280.594
1290.332
130.00639
1300.0244
1310.991
1320.303
1330.974
1340.434
1350.897
1360.263
1370.364
1380.613
1390.53
140.86
1400.154
1410.668
1420.707
1430.383
1440.51
1450.763
1460.332
1470.209
1480.897
1490.296
150.145
1500.84
1510.941
1520.101
1530.48
1540.119
1550.0761
1560.79
1570.578
1580.952
1590.464
160.279
1600.679
1610.192
1620.765
1630.172
1640.897
1650.572
1660.162
1670.152
1680.179
1690.645
170.41
180.431
190.821
20.543
200.436
210.919
220.71
230.0398
240.139
250.102
260.495
270.949
280.905
290.0266
30.321
300.182
310.311
320.0113
330.541
340.952
350.39
360.0513
370.77
380.459
390.0891
40.00295
400.615
410.766
420.164
430.677
440.798
450.769
460.276
470.0381
480.215
490.27
50.639
500.47
510.722
520.191
530.754
540.677
550.336
560.879
570.0599
580.136
590.839
60.634
600.88
610.202
620.106
630.424
640.206
650.243
662.30523e-5
670.225
680.441
690.59
70.0169
700.184
710.0476
720.602
730.198
740.911
750.014
760.958
770.333
780.00245
790.00279
80.476
800.52
810.785
820.804
830.211
840.75
850.0793
860.605
870.276
880.257
890.302
90.646
900.224
910.855
920.079
930.959
940.742
950.249
960.609
970.689
980.0251
990.209



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: CNhs13049


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)
9119 (acute 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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