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FF:10828-111C9: 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 M1) cell line:HYT-1
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
age62
cell typemyeloid progenitor cell
cell lineHYT-1
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-penis0.248
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-lymphoma0.419
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: CNhs13054

Jaspar motifP-value
MA0002.20.00631
MA0003.10.352
MA0004.10.00793
MA0006.10.203
MA0007.10.953
MA0009.10.151
MA0014.10.744
MA0017.10.284
MA0018.23.5987e-4
MA0019.10.0508
MA0024.10.00104
MA0025.10.305
MA0027.10.252
MA0028.10.00108
MA0029.10.75
MA0030.10.0423
MA0031.10.279
MA0035.20.00957
MA0038.10.0362
MA0039.20.735
MA0040.10.589
MA0041.10.244
MA0042.10.362
MA0043.10.0609
MA0046.10.0675
MA0047.20.84
MA0048.10.336
MA0050.10.202
MA0051.10.274
MA0052.10.202
MA0055.10.197
MA0057.10.769
MA0058.10.00472
MA0059.10.00313
MA0060.14.97754e-4
MA0061.10.195
MA0062.21.65337e-8
MA0065.20.0266
MA0066.10.618
MA0067.10.763
MA0068.10.275
MA0069.10.296
MA0070.10.758
MA0071.10.17
MA0072.10.966
MA0073.10.63
MA0074.10.443
MA0076.15.39346e-4
MA0077.10.642
MA0078.10.68
MA0079.20.476
MA0080.21.19108e-14
MA0081.10.00165
MA0083.10.021
MA0084.10.462
MA0087.10.321
MA0088.10.039
MA0090.11.248e-4
MA0091.10.754
MA0092.10.169
MA0093.10.00674
MA0099.20.00857
MA0100.10.0567
MA0101.10.79
MA0102.20.386
MA0103.10.295
MA0104.27.99816e-4
MA0105.15.24086e-4
MA0106.10.986
MA0107.10.103
MA0108.23.96895e-9
MA0111.10.206
MA0112.20.13
MA0113.10.565
MA0114.10.396
MA0115.10.187
MA0116.16.79367e-5
MA0117.10.722
MA0119.10.336
MA0122.10.497
MA0124.10.726
MA0125.10.594
MA0131.10.136
MA0135.10.0224
MA0136.13.70528e-16
MA0137.20.0949
MA0138.20.804
MA0139.10.0786
MA0140.10.0139
MA0141.10.766
MA0142.10.576
MA0143.10.647
MA0144.10.589
MA0145.10.369
MA0146.10.00775
MA0147.12.60369e-4
MA0148.10.991
MA0149.10.456
MA0150.10.864
MA0152.10.0039
MA0153.10.005
MA0154.10.0267
MA0155.10.853
MA0156.12.50701e-11
MA0157.10.332
MA0159.10.552
MA0160.10.106
MA0162.10.495
MA0163.11.04112e-15
MA0164.10.742
MA0258.10.0749
MA0259.10.011



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: CNhs13054

Novel motifP-value
10.11
100.0252
1000.554
1010.193
1020.433
1030.347
1040.93
1050.854
1060.825
1070.159
1080.856
1090.0889
110.171
1100.26
1110.243
1120.827
1130.997
1140.137
1150.907
1160.119
1170.0144
1180.0486
1190.673
120.633
1200.12
1210.862
1220.52
1232.08652e-5
1240.132
1250.211
1260.271
1270.684
1280.748
1290.933
130.0116
1300.755
1310.762
1320.765
1330.906
1340.623
1350.628
1360.237
1370.329
1380.963
1390.307
140.751
1400.538
1410.294
1420.208
1430.743
1440.321
1450.896
1460.549
1470.106
1480.482
1490.452
150.567
1500.954
1510.646
1520.623
1530.597
1540.496
1550.0442
1560.755
1570.139
1580.0543
1590.107
160.823
1600.214
1610.0687
1620.994
1630.499
1640.229
1650.643
1660.556
1670.145
1680.216
1690.0935
170.744
180.604
190.986
20.843
200.704
210.196
220.602
230.151
240.255
250.134
260.214
270.547
280.675
290.0375
30.125
300.0808
310.277
320.0583
330.473
340.962
350.15
360.105
370.123
380.619
390.317
40.226
400.162
410.554
420.403
430.481
440.721
450.778
460.18
470.0676
480.0434
490.214
50.721
500.768
510.588
520.358
530.037
540.848
550.256
560.753
570.144
580.0487
590.525
60.97
600.935
610.0423
620.0544
630.296
640.265
650.83
660.0348
670.849
680.722
690.617
70.04
700.604
710.0234
720.446
730.277
740.346
750.0182
760.617
770.282
780.0208
790.147
80.66
800.155
810.889
820.924
830.214
840.136
850.613
860.461
870.887
880.178
890.52
90.671
900.139
910.325
920.413
930.871
940.763
950.0467
960.526
970.457
980.124
990.466



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: CNhs13054


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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