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FF:10836-111D8: 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:F-36E
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 typeerythroblast
cell lineF-36E
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-penis0.184
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-lymphoma0.554
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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: CNhs13060

Jaspar motifP-value
MA0002.20.324
MA0003.10.829
MA0004.10.157
MA0006.10.325
MA0007.10.679
MA0009.10.269
MA0014.10.345
MA0017.10.0242
MA0018.24.53685e-4
MA0019.10.375
MA0024.14.66494e-5
MA0025.10.209
MA0027.10.432
MA0028.10.0801
MA0029.10.0581
MA0030.10.438
MA0031.10.903
MA0035.22.41967e-18
MA0038.10.388
MA0039.20.239
MA0040.10.402
MA0041.10.605
MA0042.10.949
MA0043.10.0109
MA0046.10.834
MA0047.20.251
MA0048.10.697
MA0050.10.081
MA0051.10.0862
MA0052.11.40205e-4
MA0055.10.131
MA0057.10.374
MA0058.10.138
MA0059.10.0024
MA0060.17.18234e-7
MA0061.10.659
MA0062.20.0584
MA0065.28.13813e-4
MA0066.10.367
MA0067.10.46
MA0068.10.00296
MA0069.10.195
MA0070.10.426
MA0071.10.152
MA0072.10.228
MA0073.10.998
MA0074.10.285
MA0076.10.121
MA0077.10.932
MA0078.10.779
MA0079.20.423
MA0080.20.875
MA0081.10.587
MA0083.12.80973e-4
MA0084.10.719
MA0087.10.184
MA0088.10.00284
MA0090.10.0348
MA0091.10.504
MA0092.10.336
MA0093.10.193
MA0099.20.174
MA0100.10.00434
MA0101.10.851
MA0102.20.138
MA0103.10.306
MA0104.28.56882e-4
MA0105.18.12442e-4
MA0106.10.493
MA0107.10.409
MA0108.22.55158e-8
MA0111.10.208
MA0112.20.144
MA0113.10.651
MA0114.10.00494
MA0115.10.00584
MA0116.17.66743e-4
MA0117.10.654
MA0119.10.144
MA0122.10.513
MA0124.10.468
MA0125.10.734
MA0131.10.678
MA0135.10.0896
MA0136.10.199
MA0137.20.102
MA0138.20.479
MA0139.10.349
MA0140.14.4466e-28
MA0141.10.00866
MA0142.10.0936
MA0143.10.499
MA0144.10.993
MA0145.10.728
MA0146.10.29
MA0147.17.08098e-5
MA0148.10.201
MA0149.10.00364
MA0150.10.636
MA0152.10.809
MA0153.10.436
MA0154.10.0773
MA0155.10.38
MA0156.10.273
MA0157.10.373
MA0159.10.901
MA0160.10.00299
MA0162.10.687
MA0163.11.10789e-6
MA0164.10.817
MA0258.10.149
MA0259.10.133



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: CNhs13060

Novel motifP-value
10.00577
100.0606
1000.642
1010.637
1020.286
1030.0201
1040.992
1050.305
1060.612
1070.554
1080.723
1090.0537
110.0928
1100.156
1110.0447
1120.837
1130.63
1140.0176
1150.0189
1160.344
1170.0599
1180.835
1190.74
120.836
1200.793
1210.724
1220.351
1230.0617
1240.0375
1250.724
1260.195
1270.15
1280.66
1290.117
130.0753
1300.171
1310.972
1320.163
1330.0024
1340.885
1350.742
1360.757
1370.834
1380.899
1390.039
140.945
1400.151
1410.0265
1420.819
1430.818
1440.951
1450.943
1460.922
1470.225
1480.102
1490.182
150.0655
1500.889
1510.721
1520.152
1530.276
1540.872
1550.0778
1560.575
1570.601
1580.0683
1590.479
160.594
1600.102
1610.0508
1620.968
1630.663
1640.78
1650.583
1660.312
1670.0272
1680.972
1690.834
170.144
180.152
190.78
20.432
200.818
210.548
220.674
230.679
240.609
250.27
260.0575
270.989
280.539
290.0881
30.288
300.204
310.797
320.335
330.872
340.958
350.0942
360.0304
370.465
380.662
390.622
40.202
400.379
410.441
420.235
430.256
440.844
450.743
460.0623
470.0513
480.468
490.0338
50.154
500.666
510.304
520.659
530.709
540.85
550.762
560.493
570.0937
580.219
590.637
60.976
600.746
610.439
620.064
630.841
640.134
650.851
660.0202
670.844
680.352
690.328
70.101
700.66
710.091
720.934
730.575
740.0947
750.0237
760.704
770.876
780.0196
790.0973
80.0865
800.698
810.463
820.551
830.221
840.198
850.933
860.89
870.93
880.949
890.459
90.695
900.0127
910.5
920.832
930.263
940.049
950.288
960.369
970.923
980.0629
990.426



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: CNhs13060


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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