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{{f5samples
{{f5samples
|F5samples=
|ancestors_in_anatomy_facet=
|ancestors_in_anatomy_facet=
|ancestors_in_cell_lineage_facet=
|ancestors_in_cell_lineage_facet=
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|creation_date=
|creation_date=
|def=
|def=
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|fonse_cell_line=FF:10430-106D7
|fonse_cell_line=FF:10430-106D7
|fonse_cell_line_closure=FF:10430-106D7
|fonse_cell_line_closure=FF:10430-106D7

Revision as of 16:32, 29 March 2012


Name:non T non B acute lymphoblastic leukemia (ALL) cell line:P30/OHK
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 stage11 year old child
sexfemale
age11
cell typelymphocyte
cell lineP30/OHK
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
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C87-retinoblastoma-left-nonsmall-heart-small-diaphragm-bronchogenic0
C88-Melanocyte-melanoma-Macrophage-Mesenchymal-migratory-Dendritic-Monocytederived0
C89-small-retinoblastoma-medulloblastoma-iPS-acantholytic-eye-bronchogenic0
C9-skeletal-diaphragm-tongue-throat-penis-heart-left0
C90-neuroectodermal-peripheral-neuroepithelioma-neuroblastoma-carcinoid-parietal-putamen0
C91-Fibroblast-Smooth-mesenchymal-Mesothelial-Small-Preadipocyte-Hair0
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-appendix0.857
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: CNhs10747

Jaspar motifP-value
MA0002.20.131
MA0003.10.288
MA0004.10.384
MA0006.10.368
MA0007.10.187
MA0009.10.543
MA0014.10.66
MA0017.10.229
MA0018.20.067
MA0019.10.539
MA0024.14.28524e-10
MA0025.10.559
MA0027.18.08763e-4
MA0028.18.31201e-4
MA0029.10.881
MA0030.10.035
MA0031.10.11
MA0035.20.278
MA0038.10.00979
MA0039.20.97
MA0040.10.192
MA0041.10.461
MA0042.10.899
MA0043.10.489
MA0046.10.702
MA0047.20.35
MA0048.10.537
MA0050.10.133
MA0051.10.257
MA0052.10.438
MA0055.10.494
MA0057.10.171
MA0058.10.397
MA0059.10.359
MA0060.15.85462e-26
MA0061.10.24
MA0062.28.9537e-7
MA0065.20.209
MA0066.10.211
MA0067.10.428
MA0068.10.351
MA0069.10.785
MA0070.10.00585
MA0071.10.474
MA0072.10.109
MA0073.10.679
MA0074.10.206
MA0076.17.72608e-5
MA0077.10.16
MA0078.10.844
MA0079.20.974
MA0080.20.765
MA0081.10.0974
MA0083.14.44626e-5
MA0084.10.927
MA0087.10.502
MA0088.10.497
MA0090.11.53843e-4
MA0091.10.357
MA0092.10.0491
MA0093.10.365
MA0099.27.22156e-15
MA0100.12.95869e-6
MA0101.10.31
MA0102.20.346
MA0103.10.826
MA0104.20.0691
MA0105.10.366
MA0106.10.245
MA0107.10.0898
MA0108.20.00485
MA0111.10.771
MA0112.20.00152
MA0113.10.267
MA0114.10.484
MA0115.10.139
MA0116.10.302
MA0117.10.692
MA0119.10.248
MA0122.10.89
MA0124.10.652
MA0125.10.754
MA0131.10.0129
MA0135.10.539
MA0136.10.123
MA0137.20.123
MA0138.20.166
MA0139.10.796
MA0140.10.381
MA0141.10.4
MA0142.10.289
MA0143.10.48
MA0144.10.0117
MA0145.10.0219
MA0146.10.301
MA0147.10.109
MA0148.10.399
MA0149.10.785
MA0150.10.00143
MA0152.10.436
MA0153.10.072
MA0154.10.33
MA0155.10.202
MA0156.10.0348
MA0157.10.329
MA0159.10.513
MA0160.10.726
MA0162.10.132
MA0163.10.477
MA0164.10.358
MA0258.10.0765
MA0259.10.143



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: CNhs10747

Novel motifP-value
10.495
100.555
1000.775
1010.839
1020.779
1030.303
1040.689
1050.229
1060.0922
1070.04
1080.27
1090.438
110.438
1100.372
1110.459
1120.095
1130.682
1140.124
1150.337
1160.159
1170.392
1180.588
1190.11
120.452
1200.868
1210.487
1220.823
1230.141
1240.503
1250.565
1260.986
1270.704
1280.147
1290.423
130.541
1300.386
1310.0199
1320.344
1330.282
1340.701
1350.365
1360.375
1370.512
1380.823
1390.0161
140.907
1400.98
1410.723
1420.795
1430.489
1440.655
1450.328
1460.761
1470.251
1480.0649
1490.0413
150.607
1500.927
1510.227
1520.024
1530.992
1540.769
1550.0476
1560.646
1570.484
1580.585
1590.229
160.12
1600.224
1610.934
1620.624
1630.786
1640.672
1650.448
1660.488
1670.531
1680.865
1690.0211
170.106
180.13
190.0643
20.163
200.289
210.876
220.106
230.00167
240.317
250.666
260.978
270.417
280.544
290.436
30.44
300.197
310.147
320.00752
330.735
340.241
350.651
360.365
370.177
380.226
390.101
40.281
400.669
410.506
420.949
430.187
440.409
450.17
460.635
470.869
480.54
490.614
50.473
500.88
510.386
520.0857
530.922
540.286
550.0369
560.519
570.911
580.917
590.0758
60.663
600.0627
610.56
620.658
630.371
640.74
650.0221
660.00326
670.817
680.519
690.751
70.828
700.00834
710.386
720.554
730.0327
740.543
750.601
760.869
770.00651
780.682
790.276
80.291
800.788
810.504
820.0273
830.118
840.9
850.00125
860.624
870.5
880.582
890.0248
90.205
900.614
910.142
920.0107
930.672
940.412
950.774
960.614
970.181
980.587
990.274



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: CNhs10747


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

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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