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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 16:56, 29 March 2012


Name:biphenotypic B myelomonocytic leukemia cell line:MV-4-11
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
age10
cell typemyeloid progenitor cell
cell lineMV-4-11
companyATCC
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-penis0.0935
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-lymphoma0.411
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: CNhs11845

Jaspar motifP-value
MA0002.20.00505
MA0003.10.492
MA0004.10.093
MA0006.10.314
MA0007.10.3
MA0009.10.65
MA0014.10.274
MA0017.10.0224
MA0018.20.566
MA0019.10.0229
MA0024.10.00198
MA0025.10.704
MA0027.10.788
MA0028.17.98017e-7
MA0029.10.926
MA0030.10.0615
MA0031.10.211
MA0035.20.133
MA0038.10.0701
MA0039.20.586
MA0040.10.232
MA0041.10.239
MA0042.10.559
MA0043.10.615
MA0046.10.359
MA0047.20.353
MA0048.10.0983
MA0050.10.382
MA0051.10.673
MA0052.10.114
MA0055.10.00908
MA0057.10.703
MA0058.10.079
MA0059.10.00483
MA0060.10.00117
MA0061.10.94
MA0062.23.8666e-12
MA0065.20.0171
MA0066.10.789
MA0067.10.361
MA0068.10.934
MA0069.10.79
MA0070.10.558
MA0071.10.0186
MA0072.10.513
MA0073.10.861
MA0074.10.975
MA0076.15.68924e-7
MA0077.10.242
MA0078.10.69
MA0079.20.365
MA0080.21.68664e-10
MA0081.10.00176
MA0083.10.309
MA0084.10.312
MA0087.10.116
MA0088.10.00263
MA0090.19.25135e-5
MA0091.10.311
MA0092.10.71
MA0093.10.114
MA0099.22.04626e-4
MA0100.14.87167e-4
MA0101.10.254
MA0102.20.255
MA0103.10.606
MA0104.20.00261
MA0105.10.0715
MA0106.10.797
MA0107.10.0282
MA0108.26.83006e-6
MA0111.10.357
MA0112.20.0524
MA0113.10.953
MA0114.10.0134
MA0115.10.0236
MA0116.11.08577e-4
MA0117.10.704
MA0119.10.922
MA0122.10.965
MA0124.10.757
MA0125.10.695
MA0131.10.0257
MA0135.10.188
MA0136.18.99145e-17
MA0137.20.401
MA0138.20.969
MA0139.10.532
MA0140.10.307
MA0141.10.0455
MA0142.10.612
MA0143.10.778
MA0144.10.408
MA0145.10.617
MA0146.10.00366
MA0147.10.00108
MA0148.10.329
MA0149.10.138
MA0150.10.344
MA0152.10.0444
MA0153.10.00707
MA0154.10.197
MA0155.10.749
MA0156.15.48062e-12
MA0157.10.471
MA0159.10.306
MA0160.10.0491
MA0162.10.629
MA0163.14.65129e-12
MA0164.10.705
MA0258.10.0429
MA0259.10.08



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: CNhs11845

Novel motifP-value
10.02
100.012
1000.133
1010.179
1020.522
1030.754
1040.965
1050.828
1060.887
1070.263
1080.779
1090.064
110.0333
1100.18
1110.172
1120.98
1130.989
1140.0856
1150.718
1160.256
1170.0258
1180.169
1190.234
120.448
1200.643
1210.291
1220.93
1232.26851e-5
1240.045
1250.478
1260.221
1270.195
1280.555
1290.282
130.0036
1300.743
1310.132
1320.799
1330.823
1340.221
1350.268
1360.251
1370.569
1380.762
1390.206
140.94
1400.614
1410.526
1420.348
1430.791
1440.993
1450.416
1460.727
1470.364
1480.168
1490.813
150.527
1500.606
1510.838
1520.376
1530.912
1540.869
1550.0125
1560.685
1570.38
1580.487
1590.138
160.977
1600.616
1610.249
1620.938
1630.244
1640.201
1650.108
1660.296
1670.0269
1680.316
1690.111
170.67
180.967
190.554
20.369
200.281
210.0865
220.591
230.0777
240.399
250.227
260.0143
270.577
280.822
290.0193
30.0413
300.0446
310.553
320.451
330.421
340.984
350.343
360.00621
370.153
380.213
390.466
40.222
400.106
410.664
420.162
430.534
440.328
450.517
460.106
470.0144
480.0165
490.192
50.712
500.877
510.657
520.483
530.149
540.964
550.737
560.984
570.217
580.192
590.598
60.391
600.616
610.173
620.197
630.548
640.0885
650.732
660.0901
670.983
680.5
690.102
70.142
700.957
710.0369
720.867
730.185
740.933
750.0158
760.104
770.785
780.0696
790.35
80.0852
800.139
810.304
820.817
830.853
840.394
850.919
860.773
870.0941
880.681
890.212
90.698
900.0181
910.691
920.369
930.822
940.523
950.0246
960.655
970.391
980.337
990.523



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: CNhs11845


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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