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FF:10835-111D7: 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 M6) cell line:EEB
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
age49
cell typeerythroblast
cell lineEEB
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-penis0.16
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-lymphoma0.643
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
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C93-chronic-acute-leukemia-acantholytic-medulloblastoma-testis-papillotubular0.107
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: CNhs13059

Jaspar motifP-value
MA0002.20.06
MA0003.10.813
MA0004.10.181
MA0006.10.254
MA0007.10.999
MA0009.10.98
MA0014.10.866
MA0017.10.1
MA0018.20.613
MA0019.10.719
MA0024.14.75225e-9
MA0025.10.37
MA0027.10.895
MA0028.11.01886e-11
MA0029.10.00674
MA0030.10.85
MA0031.10.82
MA0035.22.03638e-19
MA0038.10.797
MA0039.20.743
MA0040.10.0481
MA0041.10.846
MA0042.10.546
MA0043.10.207
MA0046.10.535
MA0047.20.592
MA0048.10.791
MA0050.10.0236
MA0051.10.13
MA0052.10.504
MA0055.10.00388
MA0057.10.921
MA0058.10.051
MA0059.10.00864
MA0060.14.8696e-12
MA0061.10.739
MA0062.23.03952e-17
MA0065.20.0122
MA0066.10.751
MA0067.10.39
MA0068.10.0024
MA0069.10.159
MA0070.10.0386
MA0071.10.00774
MA0072.10.251
MA0073.10.838
MA0074.10.101
MA0076.11.31641e-16
MA0077.10.0458
MA0078.10.173
MA0079.20.323
MA0080.20.572
MA0081.10.148
MA0083.10.633
MA0084.10.141
MA0087.10.259
MA0088.15.09398e-4
MA0090.10.00172
MA0091.10.646
MA0092.10.854
MA0093.10.107
MA0099.20.00197
MA0100.10.0208
MA0101.10.989
MA0102.25.48705e-5
MA0103.10.965
MA0104.20.00256
MA0105.10.127
MA0106.10.201
MA0107.10.21
MA0108.20.448
MA0111.10.447
MA0112.20.394
MA0113.10.362
MA0114.10.0211
MA0115.10.00536
MA0116.10.0191
MA0117.10.808
MA0119.10.942
MA0122.10.387
MA0124.10.812
MA0125.10.921
MA0131.10.256
MA0135.10.459
MA0136.10.00204
MA0137.20.397
MA0138.20.715
MA0139.10.0805
MA0140.11.98708e-25
MA0141.11.2981e-7
MA0142.10.539
MA0143.10.0169
MA0144.10.443
MA0145.10.636
MA0146.10.281
MA0147.12.82759e-4
MA0148.10.665
MA0149.10.0162
MA0150.10.00296
MA0152.10.463
MA0153.10.265
MA0154.10.477
MA0155.10.795
MA0156.12.72907e-7
MA0157.10.835
MA0159.10.883
MA0160.19.53322e-4
MA0162.10.0417
MA0163.11.27875e-5
MA0164.10.706
MA0258.10.416
MA0259.10.0139



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: CNhs13059

Novel motifP-value
10.0588
100.0243
1000.518
1010.735
1020.332
1030.584
1040.829
1050.722
1060.0585
1070.0367
1080.405
1090.0322
110.178
1100.338
1110.123
1120.995
1130.0858
1140.15
1150.452
1160.139
1170.0174
1180.309
1190.352
120.324
1200.514
1210.769
1220.114
1230.142
1240.389
1250.326
1260.756
1270.24
1280.139
1290.227
130.0621
1300.17
1310.522
1320.138
1330.958
1340.689
1350.821
1360.0972
1370.23
1380.905
1390.222
140.922
1400.773
1410.204
1420.878
1430.78
1440.552
1450.807
1460.954
1470.117
1480.26
1490.0632
150.0374
1500.906
1510.628
1520.0196
1530.499
1540.42
1550.054
1560.119
1570.685
1580.658
1590.141
160.995
1600.947
1610.122
1620.671
1630.632
1640.85
1650.829
1660.0727
1670.335
1680.216
1690.913
170.838
180.966
190.743
20.261
200.221
210.415
220.894
230.0816
240.0269
250.0908
260.0505
270.588
280.411
290.0705
30.537
300.0817
310.626
320.166
330.0429
340.741
350.273
360.0214
370.618
380.299
390.116
40.067
400.411
410.924
420.325
430.819
440.514
450.358
460.518
470.0442
480.267
490.391
50.922
500.375
510.769
520.048
530.923
540.441
550.477
560.658
570.253
580.275
590.811
60.254
600.561
610.242
620.315
630.537
640.622
650.551
661.16577e-5
670.651
680.501
690.658
70.0394
700.34
710.222
720.573
730.726
740.701
750.0086
760.215
770.17
780.0161
790.0685
80.422
800.181
810.47
820.77
830.155
840.22
850.0556
860.605
870.076
880.575
890.467
90.615
900.176
910.15
920.438
930.551
940.902
950.0255
960.438
970.962
980.146
990.288



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: CNhs13059


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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