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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 16:32, 29 March 2012


Name:Burkitt's lymphoma cell line:DAUDI
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 stage16 year old adolescent
sexmale
age16
cell typeb cell
cell lineDAUDI
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-penis0.0374
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-lymphoma0.751
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
C110-leukemia-chronic-Eosinophils-acute-Whole-CD34-Lymphatic0
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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: CNhs10739

Jaspar motifP-value
MA0002.20.213
MA0003.10.367
MA0004.10.039
MA0006.10.204
MA0007.10.382
MA0009.10.26
MA0014.10.943
MA0017.10.567
MA0018.20.825
MA0019.10.0899
MA0024.13.0985e-9
MA0025.10.476
MA0027.10.236
MA0028.12.19411e-5
MA0029.10.605
MA0030.10.446
MA0031.10.636
MA0035.20.467
MA0038.10.0234
MA0039.20.721
MA0040.10.178
MA0041.10.174
MA0042.10.674
MA0043.10.915
MA0046.10.138
MA0047.20.342
MA0048.10.431
MA0050.10.125
MA0051.10.251
MA0052.10.0235
MA0055.10.205
MA0057.10.693
MA0058.10.0122
MA0059.10.00401
MA0060.11.70947e-11
MA0061.10.26
MA0062.22.1172e-8
MA0065.20.154
MA0066.10.724
MA0067.10.914
MA0068.10.0776
MA0069.10.26
MA0070.10.524
MA0071.10.659
MA0072.10.428
MA0073.10.826
MA0074.10.324
MA0076.14.69977e-7
MA0077.10.163
MA0078.10.141
MA0079.20.273
MA0080.22.58402e-4
MA0081.10.00333
MA0083.11.10363e-5
MA0084.10.319
MA0087.10.0578
MA0088.10.00144
MA0090.17.62011e-5
MA0091.10.986
MA0092.10.945
MA0093.10.0248
MA0099.22.16419e-8
MA0100.10.00404
MA0101.10.987
MA0102.20.115
MA0103.10.00765
MA0104.21.9197e-4
MA0105.10.0145
MA0106.10.282
MA0107.10.779
MA0108.22.86828e-10
MA0111.10.21
MA0112.20.71
MA0113.10.131
MA0114.10.215
MA0115.10.02
MA0116.15.6412e-4
MA0117.10.63
MA0119.10.74
MA0122.10.595
MA0124.10.692
MA0125.10.82
MA0131.10.0628
MA0135.10.005
MA0136.19.30656e-7
MA0137.20.00838
MA0138.20.238
MA0139.10.222
MA0140.10.0227
MA0141.10.4
MA0142.10.011
MA0143.10.305
MA0144.10.00481
MA0145.10.114
MA0146.10.724
MA0147.15.52207e-5
MA0148.10.567
MA0149.10.0795
MA0150.10.0357
MA0152.10.194
MA0153.10.0304
MA0154.10.258
MA0155.10.351
MA0156.11.93776e-5
MA0157.10.242
MA0159.10.343
MA0160.10.529
MA0162.10.521
MA0163.12.23662e-5
MA0164.10.61
MA0258.10.512
MA0259.10.0467



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: CNhs10739

Novel motifP-value
10.0248
100.0137
1000.197
1010.097
1020.316
1030.279
1040.589
1050.997
1060.0837
1070.0301
1080.342
1090.226
110.14
1100.188
1110.0603
1120.82
1130.906
1140.43
1150.762
1160.857
1170.0173
1180.36
1190.259
120.789
1200.696
1210.558
1220.474
1230.0011
1240.171
1250.224
1260.473
1270.471
1280.0234
1290.963
130.192
1300.928
1310.0365
1320.127
1330.385
1340.351
1350.428
1360.149
1370.0601
1380.367
1390.486
140.637
1400.617
1410.404
1420.218
1430.293
1440.308
1450.238
1460.664
1470.316
1480.964
1490.228
150.135
1500.796
1510.345
1520.00534
1530.681
1540.779
1550.0486
1560.778
1570.298
1580.3
1590.854
160.974
1600.907
1610.15
1620.989
1630.547
1640.405
1650.795
1660.236
1670.0364
1680.524
1690.535
170.596
180.605
190.521
20.25
200.395
210.208
220.607
230.0295
240.399
250.096
260.0459
270.982
280.379
290.0247
30.294
300.0973
310.996
320.195
330.595
340.318
350.294
360.0408
370.884
380.675
390.163
40.146
400.261
410.708
420.148
430.715
440.566
450.249
460.212
470.0294
480.146
490.144
50.87
500.697
510.933
520.0779
530.808
540.65
550.757
560.864
570.197
580.29
590.588
60.683
600.296
610.179
620.299
630.923
640.321
650.351
660.0147
670.684
680.189
690.861
70.188
700.861
710.0342
720.849
730.269
740.622
750.0132
760.0859
770.211
780.524
790.212
80.203
800.828
810.0636
820.757
830.718
840.853
850.161
860.412
870.375
880.781
890.696
90.48
900.00361
910.19
920.263
930.864
940.264
950.337
960.733
970.173
980.715
990.272



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: CNhs10739


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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