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FF:10829-111D1: 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 M3) cell line:HL60
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 typemyeloid progenitor cell
cell lineHL60
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-penis0.237
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-lymphoma0.56
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: CNhs13055

Jaspar motifP-value
MA0002.20.0085
MA0003.10.943
MA0004.10.0106
MA0006.10.152
MA0007.10.927
MA0009.10.279
MA0014.10.676
MA0017.10.0319
MA0018.20.0178
MA0019.10.109
MA0024.10.0013
MA0025.10.996
MA0027.10.1
MA0028.10.00102
MA0029.10.396
MA0030.10.0176
MA0031.10.129
MA0035.20.231
MA0038.12.83812e-4
MA0039.20.0997
MA0040.10.21
MA0041.10.247
MA0042.10.482
MA0043.10.95
MA0046.10.0866
MA0047.20.992
MA0048.10.299
MA0050.14.34603e-4
MA0051.10.00239
MA0052.13.28593e-4
MA0055.10.112
MA0057.10.694
MA0058.10.00374
MA0059.15.10875e-6
MA0060.10.4
MA0061.10.592
MA0062.27.45034e-7
MA0065.20.00716
MA0066.10.156
MA0067.10.549
MA0068.10.00442
MA0069.10.979
MA0070.10.53
MA0071.10.0232
MA0072.10.647
MA0073.10.782
MA0074.10.921
MA0076.11.33856e-4
MA0077.10.419
MA0078.10.861
MA0079.20.075
MA0080.28.04026e-8
MA0081.10.00825
MA0083.16.45001e-4
MA0084.10.536
MA0087.10.169
MA0088.10.00302
MA0090.14.2372e-4
MA0091.10.445
MA0092.10.419
MA0093.10.00821
MA0099.20.00444
MA0100.10.0128
MA0101.10.486
MA0102.20.988
MA0103.10.114
MA0104.27.36815e-6
MA0105.10.00404
MA0106.10.349
MA0107.10.11
MA0108.24.73348e-14
MA0111.10.34
MA0112.20.0197
MA0113.10.777
MA0114.10.038
MA0115.10.0191
MA0116.11.02551e-5
MA0117.10.742
MA0119.10.34
MA0122.10.323
MA0124.10.876
MA0125.10.522
MA0131.10.528
MA0135.10.15
MA0136.16.9421e-12
MA0137.20.0291
MA0138.20.494
MA0139.10.3
MA0140.10.115
MA0141.10.00936
MA0142.10.0815
MA0143.10.926
MA0144.10.334
MA0145.10.663
MA0146.10.611
MA0147.19.8639e-7
MA0148.10.84
MA0149.10.0818
MA0150.10.827
MA0152.10.298
MA0153.10.0483
MA0154.10.0271
MA0155.10.868
MA0156.11.0531e-7
MA0157.10.521
MA0159.10.0964
MA0160.10.12
MA0162.10.828
MA0163.12.08836e-14
MA0164.10.901
MA0258.10.0516
MA0259.10.0127



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: CNhs13055

Novel motifP-value
10.0139
100.00841
1000.262
1010.219
1020.69
1030.0643
1040.902
1050.387
1060.921
1070.497
1080.912
1090.0308
110.0644
1100.229
1110.00928
1120.574
1130.512
1140.00895
1150.826
1160.229
1170.0439
1180.0488
1190.692
120.94
1200.0418
1210.814
1220.845
1230.0192
1240.181
1250.0417
1260.592
1270.107
1280.93
1290.164
130.0437
1300.987
1310.424
1320.97
1330.219
1340.873
1350.758
1360.357
1370.423
1380.548
1390.00463
140.75
1400.0169
1410.0605
1420.42
1430.98
1440.634
1450.672
1460.728
1470.433
1480.0104
1490.402
150.0787
1500.934
1510.677
1520.156
1530.634
1540.835
1550.0181
1560.766
1570.711
1580.815
1590.507
160.475
1600.289
1610.0907
1620.541
1630.378
1640.0248
1650.663
1660.275
1670.021
1680.908
1690.396
170.716
180.286
190.719
20.669
200.449
210.122
220.877
230.299
240.184
250.182
260.052
270.526
280.904
290.0147
30.0784
300.0972
310.732
320.926
330.293
340.741
350.0819
360.0218
370.316
380.323
390.645
40.322
400.348
410.536
420.174
430.379
440.0461
450.51
460.0738
470.0317
480.0637
490.15
50.579
500.846
510.864
520.332
530.805
540.916
550.569
560.756
570.0478
580.227
590.521
60.501
600.699
610.176
620.0965
630.428
640.108
650.97
660.526
670.823
680.665
690.422
70.0978
700.179
710.0155
720.943
730.741
740.368
750.0102
760.318
770.69
780.0466
790.847
80.0475
800.437
810.181
820.418
830.436
840.378
850.94
860.44
870.645
880.644
890.473
90.941
900.0154
910.939
920.719
930.345
940.208
950.112
960.43
970.38
980.112
990.587



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: CNhs13055


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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