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{{f5samples
{{f5samples
|F5samples=
|ancestors_in_anatomy_facet=UBERON:0000061,UBERON:0000465,UBERON:0000479,UBERON:0001062,UBERON:0002384
|ancestors_in_anatomy_facet=UBERON:0000061,UBERON:0000465,UBERON:0000479,UBERON:0001062,UBERON:0002384
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000004,CL:0000012,CL:0000034,CL:0000037,CL:0000048,CL:0000051,CL:0000063,CL:0000134,CL:0000144,CL:0000219,CL:0000255,CL:0000542,CL:0000548,CL:0000566,CL:0000723,CL:0000738,CL:0000826,CL:0000837,CL:0000838,CL:0000945,CL:0000988,CL:0002031,CL:0002032,CL:0002087,CL:0002320,CL:0002371
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000004,CL:0000012,CL:0000034,CL:0000037,CL:0000048,CL:0000051,CL:0000063,CL:0000134,CL:0000144,CL:0000219,CL:0000255,CL:0000542,CL:0000548,CL:0000566,CL:0000723,CL:0000738,CL:0000826,CL:0000837,CL:0000838,CL:0000945,CL:0000988,CL:0002031,CL:0002032,CL:0002087,CL:0002320,CL:0002371
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|creation_date=
|creation_date=
|def=
|def=
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|fonse_cell_line=FF:0100104
|fonse_cell_line=FF:0100104
|fonse_cell_line_closure=FF:0100104
|fonse_cell_line_closure=FF:0100104

Revision as of 16:42, 29 March 2012


Name:Burkitt's lymphoma cell line:RAJI
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
age11
cell typeb cell
cell lineRAJI
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-penis0.254
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-lymphoma0.606
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
C110-leukemia-chronic-Eosinophils-acute-Whole-CD34-Lymphatic0
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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: CNhs11268

Jaspar motifP-value
MA0002.20.309
MA0003.10.384
MA0004.10.0879
MA0006.10.201
MA0007.10.457
MA0009.10.854
MA0014.10.959
MA0017.10.323
MA0018.20.941
MA0019.10.0168
MA0024.19.04595e-6
MA0025.10.0781
MA0027.10.655
MA0028.10.00114
MA0029.10.405
MA0030.10.229
MA0031.10.951
MA0035.20.896
MA0038.10.492
MA0039.20.558
MA0040.10.192
MA0041.10.217
MA0042.10.477
MA0043.10.789
MA0046.10.206
MA0047.20.69
MA0048.10.446
MA0050.10.575
MA0051.10.891
MA0052.10.0501
MA0055.10.0821
MA0057.10.705
MA0058.10.0667
MA0059.10.00751
MA0060.19.3843e-5
MA0061.10.0213
MA0062.25.67889e-5
MA0065.20.0821
MA0066.10.721
MA0067.10.76
MA0068.10.114
MA0069.10.41
MA0070.10.904
MA0071.10.363
MA0072.10.515
MA0073.10.968
MA0074.10.437
MA0076.12.89382e-4
MA0077.10.255
MA0078.10.185
MA0079.20.216
MA0080.20.128
MA0081.10.0626
MA0083.11.81935e-4
MA0084.10.196
MA0087.10.177
MA0088.10.00381
MA0090.18.27396e-4
MA0091.10.884
MA0092.10.896
MA0093.10.0987
MA0099.24.30573e-5
MA0100.10.0339
MA0101.10.0914
MA0102.20.16
MA0103.10.0362
MA0104.23.09706e-4
MA0105.14.1117e-4
MA0106.10.214
MA0107.10.203
MA0108.21.03402e-13
MA0111.10.156
MA0112.20.407
MA0113.10.205
MA0114.10.0974
MA0115.10.0275
MA0116.13.17348e-4
MA0117.10.58
MA0119.10.745
MA0122.10.424
MA0124.10.6
MA0125.10.631
MA0131.10.103
MA0135.10.0359
MA0136.10.0109
MA0137.20.00167
MA0138.20.58
MA0139.10.363
MA0140.10.129
MA0141.10.155
MA0142.10.0567
MA0143.10.797
MA0144.10.00746
MA0145.10.106
MA0146.10.606
MA0147.17.5519e-5
MA0148.10.873
MA0149.10.0586
MA0150.10.506
MA0152.10.599
MA0153.10.00968
MA0154.10.0754
MA0155.10.391
MA0156.10.0672
MA0157.10.507
MA0159.10.279
MA0160.10.266
MA0162.10.801
MA0163.11.50872e-7
MA0164.10.555
MA0258.10.173
MA0259.10.0406



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: CNhs11268

Novel motifP-value
10.0119
100.013
1000.123
1010.0699
1020.434
1030.515
1040.81
1050.876
1060.427
1070.351
1080.984
1090.244
110.0847
1100.179
1110.02
1120.512
1130.715
1140.383
1150.857
1160.786
1170.0117
1180.216
1190.101
120.957
1200.691
1210.683
1220.817
1231.0331e-4
1240.189
1250.032
1260.339
1270.765
1280.201
1290.901
130.0917
1300.774
1310.159
1320.41
1330.524
1340.708
1350.966
1360.493
1370.345
1380.744
1390.342
140.7
1400.402
1410.301
1420.171
1430.411
1440.729
1450.116
1460.961
1470.499
1480.38
1490.36
150.239
1500.844
1510.78
1520.0148
1530.713
1540.703
1550.0245
1560.735
1570.155
1580.3
1590.676
160.904
1600.483
1610.0588
1620.798
1630.499
1640.226
1650.755
1660.583
1670.0458
1680.461
1690.786
170.718
180.572
190.819
20.38
200.295
210.137
220.594
230.158
240.815
250.158
260.0405
270.983
280.443
290.0202
30.148
300.0625
310.874
320.57
330.987
340.39
350.174
360.048
370.554
380.729
390.52
40.426
400.284
410.743
420.146
430.456
440.473
450.236
460.126
470.0733
480.16
490.0579
50.999
500.962
510.837
520.219
530.357
540.705
550.812
560.991
570.0487
580.285
590.74
60.575
600.699
610.137
620.277
630.56
640.286
650.573
660.0852
670.835
680.18
690.943
70.18
700.911
710.0118
720.879
730.449
740.328
750.00865
760.103
770.503
780.408
790.396
80.225
800.932
810.0481
820.725
830.774
840.446
850.453
860.518
870.521
880.923
890.29
90.409
900.00191
910.725
920.902
930.877
940.235
950.259
960.624
970.069
980.516
990.318



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: CNhs11268


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)
0000051 (common lymphoid progenitor)
0000134 (mesenchymal cell)
0000219 (motile cell)
0000255 (eukaryotic cell)
0000542 (lymphocyte)
0000548 (animal cell)
0000566 (angioblastic mesenchymal cell)
0000723 (somatic stem cell)
0000738 (leukocyte)
0000826 (pro-B cell)
0000837 (hematopoietic multipotent progenitor cell)
0000838 (lymphoid lineage restricted progenitor cell)
0000945 (lymphocyte of B lineage)
0000988 (hematopoietic cell)
0002031 (hematopoietic lineage restricted progenitor cell)
0002032 (hematopoietic oligopotent progenitor cell)
0002087 (nongranular leukocyte)
0002320 (connective tissue cell)
0002371 (somatic cell)

DOID: Disease
0050686 (organ system cancer)
0060058 (lymphoma)
0060083 (immune system cancer)
14566 (disease of cellular proliferation)
162 (cancer)
2531 (hematologic cancer)
4 (disease)

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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