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FF:10833-111D5: Difference between revisions

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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 17:28, 29 March 2012


Name:acute myeloid leukemia (FAB M4eo) cell line:EoL-3
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
ageunknown
cell typeeosinophil progenitor cell
cell lineEoL-3
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-penis0.485
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-lymphoma0.521
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: CNhs13057

Jaspar motifP-value
MA0002.20.0192
MA0003.10.771
MA0004.10.0621
MA0006.10.221
MA0007.10.609
MA0009.10.349
MA0014.10.704
MA0017.10.007
MA0018.20.00765
MA0019.10.0436
MA0024.16.47046e-5
MA0025.10.377
MA0027.10.838
MA0028.10.00569
MA0029.10.832
MA0030.10.00765
MA0031.10.0792
MA0035.20.359
MA0038.10.0111
MA0039.20.226
MA0040.10.21
MA0041.10.149
MA0042.10.475
MA0043.10.0969
MA0046.10.0713
MA0047.20.236
MA0048.10.12
MA0050.10.495
MA0051.10.0905
MA0052.10.00244
MA0055.10.0764
MA0057.10.711
MA0058.10.0492
MA0059.14.93028e-4
MA0060.10.132
MA0061.10.671
MA0062.21.94813e-5
MA0065.20.0143
MA0066.10.764
MA0067.10.939
MA0068.10.0141
MA0069.10.183
MA0070.10.359
MA0071.10.0538
MA0072.10.861
MA0073.10.901
MA0074.10.752
MA0076.10.0114
MA0077.10.801
MA0078.10.608
MA0079.20.0853
MA0080.21.62963e-7
MA0081.10.00945
MA0083.10.00648
MA0084.10.331
MA0087.10.228
MA0088.10.0444
MA0090.15.8901e-5
MA0091.10.235
MA0092.10.381
MA0093.10.0761
MA0099.22.2875e-5
MA0100.18.1775e-4
MA0101.10.373
MA0102.20.815
MA0103.10.449
MA0104.22.05626e-4
MA0105.10.00666
MA0106.10.319
MA0107.10.0588
MA0108.22.18328e-10
MA0111.10.137
MA0112.20.082
MA0113.10.964
MA0114.10.0233
MA0115.10.0033
MA0116.17.93714e-6
MA0117.10.782
MA0119.10.659
MA0122.10.506
MA0124.10.43
MA0125.10.636
MA0131.10.147
MA0135.10.175
MA0136.16.60827e-9
MA0137.20.145
MA0138.20.942
MA0139.10.705
MA0140.10.368
MA0141.10.0356
MA0142.10.386
MA0143.10.338
MA0144.10.346
MA0145.10.405
MA0146.10.102
MA0147.13.78621e-5
MA0148.10.129
MA0149.10.108
MA0150.10.293
MA0152.10.432
MA0153.10.0328
MA0154.10.0281
MA0155.10.776
MA0156.13.51635e-5
MA0157.10.411
MA0159.10.327
MA0160.10.12
MA0162.10.611
MA0163.18.10214e-16
MA0164.10.54
MA0258.10.0643
MA0259.10.0662



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: CNhs13057

Novel motifP-value
10.013
100.00696
1000.172
1010.125
1020.621
1030.145
1040.69
1050.52
1060.971
1070.471
1080.892
1090.0577
110.0704
1100.17
1110.048
1120.638
1130.997
1140.0549
1150.722
1160.221
1170.0187
1180.0198
1190.171
120.857
1200.408
1210.426
1220.633
1230.00424
1240.745
1250.235
1260.155
1270.099
1280.681
1290.45
130.0174
1300.812
1310.311
1320.626
1330.568
1340.77
1350.705
1360.343
1370.324
1380.566
1390.0763
140.888
1400.531
1410.646
1420.5
1430.906
1440.996
1450.979
1460.604
1470.236
1480.04
1490.614
150.144
1500.625
1510.658
1520.216
1530.925
1540.823
1550.0431
1560.674
1570.384
1580.835
1590.795
160.649
1600.134
1610.103
1620.672
1630.254
1640.133
1650.13
1660.392
1670.106
1680.305
1690.283
170.75
180.594
190.628
20.519
200.332
210.0318
220.858
230.273
240.133
250.207
260.0475
270.545
280.999
290.0102
30.0389
300.0797
310.753
320.675
330.48
340.751
350.145
360.0125
370.286
380.27
390.664
40.329
400.173
410.837
420.194
430.436
440.00776
450.297
460.0787
470.036
480.0505
490.143
50.993
500.962
510.591
520.407
530.384
540.751
550.844
560.963
570.0595
580.25
590.495
60.423
600.884
610.196
620.119
630.598
640.228
650.95
660.284
670.697
680.786
690.466
70.126
700.304
710.0158
720.842
730.569
740.642
750.0123
760.181
771
780.012
790.707
80.0535
800.191
810.1
820.529
830.55
840.665
850.534
860.504
870.432
880.657
890.947
90.87
900.0224
910.347
920.438
930.456
940.332
950.0761
960.674
970.347
980.172
990.386



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: CNhs13057


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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