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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:0000236,CL:0000255,CL:0000542,CL:0000548,CL:0000566,CL:0000723,CL:0000738,CL:0000785,CL:0000816,CL:0000817,CL:0000818,CL:0000819,CL:0000826,CL:0000837,CL:0000838,CL:0000945,CL:0000954,CL:0000955,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:0000236,CL:0000255,CL:0000542,CL:0000548,CL:0000566,CL:0000723,CL:0000738,CL:0000785,CL:0000816,CL:0000817,CL:0000818,CL:0000819,CL:0000826,CL:0000837,CL:0000838,CL:0000945,CL:0000954,CL:0000955,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 16:50, 29 March 2012


Name:diffuse large B-cell lymphoma cell line:CTB-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
age70
cell typeb cell
cell lineCTB-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-penis0.521
C106-Hep2-epitheloid-placenta-cervical-rectal-anaplastic-glassy0
C107-Neutrophils-CD14-Eosinophils-Monocytederived-Whole-Peripheral-blood0
C108-breast-hepatoblastoma-MCF7-parotid-salivary-submaxillary-prostate0
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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
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: CNhs11741

Jaspar motifP-value
MA0002.20.681
MA0003.10.437
MA0004.10.161
MA0006.10.171
MA0007.10.514
MA0009.10.875
MA0014.10.662
MA0017.10.246
MA0018.20.119
MA0019.10.0343
MA0024.19.91734e-10
MA0025.10.17
MA0027.10.036
MA0028.10.00341
MA0029.10.408
MA0030.10.226
MA0031.10.772
MA0035.20.754
MA0038.10.777
MA0039.20.19
MA0040.10.146
MA0041.10.0576
MA0042.10.318
MA0043.10.424
MA0046.10.167
MA0047.20.934
MA0048.10.27
MA0050.10.905
MA0051.10.94
MA0052.10.0372
MA0055.10.152
MA0057.10.723
MA0058.10.204
MA0059.10.00732
MA0060.10.00254
MA0061.10.26
MA0062.26.60593e-4
MA0065.20.0789
MA0066.10.662
MA0067.10.402
MA0068.10.112
MA0069.10.246
MA0070.10.795
MA0071.10.778
MA0072.10.58
MA0073.10.95
MA0074.10.576
MA0076.10.0019
MA0077.10.842
MA0078.10.724
MA0079.20.104
MA0080.20.788
MA0081.10.505
MA0083.11.77164e-6
MA0084.10.766
MA0087.10.2
MA0088.10.0103
MA0090.11.45204e-4
MA0091.10.782
MA0092.10.51
MA0093.10.197
MA0099.21.34197e-13
MA0100.10.0173
MA0101.10.721
MA0102.20.0988
MA0103.10.0309
MA0104.27.98674e-4
MA0105.10.00421
MA0106.10.371
MA0107.10.435
MA0108.23.66216e-10
MA0111.10.187
MA0112.20.564
MA0113.10.208
MA0114.10.0883
MA0115.10.00363
MA0116.12.26361e-4
MA0117.10.994
MA0119.10.768
MA0122.10.306
MA0124.10.235
MA0125.10.746
MA0131.10.0386
MA0135.10.0497
MA0136.10.186
MA0137.22.60706e-5
MA0138.20.909
MA0139.10.861
MA0140.10.549
MA0141.10.208
MA0142.10.0224
MA0143.10.933
MA0144.17.39177e-4
MA0145.10.0643
MA0146.10.807
MA0147.12.36815e-4
MA0148.10.671
MA0149.10.174
MA0150.10.0128
MA0152.10.607
MA0153.10.00439
MA0154.10.215
MA0155.10.543
MA0156.10.238
MA0157.10.868
MA0159.10.518
MA0160.10.76
MA0162.10.821
MA0163.11.25874e-7
MA0164.10.33
MA0258.10.564
MA0259.10.0299



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: CNhs11741

Novel motifP-value
10.0527
100.00685
1000.103
1010.211
1020.71
1030.542
1040.772
1050.747
1060.704
1070.568
1080.741
1090.404
110.0968
1100.151
1110.0356
1120.721
1130.782
1140.491
1150.35
1160.598
1170.0224
1180.164
1190.19
120.458
1200.354
1210.976
1220.839
1231.01965e-4
1240.283
1250.139
1260.752
1270.999
1280.355
1290.822
130.213
1300.446
1310.632
1320.694
1330.577
1340.764
1350.533
1360.0823
1370.856
1380.506
1390.281
140.847
1400.289
1410.0588
1420.395
1430.761
1440.589
1450.38
1460.987
1470.433
1480.115
1490.706
150.288
1500.856
1510.944
1520.0119
1530.869
1540.747
1550.017
1560.7
1570.246
1580.853
1590.316
160.647
1600.322
1610.0309
1620.626
1630.497
1640.0565
1650.882
1660.979
1670.0389
1680.968
1690.596
170.871
180.669
190.881
20.25
200.364
210.0453
220.433
230.073
240.818
250.0993
260.0326
270.99
280.939
290.0152
30.184
300.0749
310.839
320.651
330.599
340.338
350.179
360.052
370.657
380.651
390.268
40.529
400.298
410.817
420.205
430.615
440.0272
450.205
460.105
470.0429
480.123
490.132
50.66
500.835
510.671
520.183
530.65
540.837
550.442
560.95
570.0974
580.256
590.727
60.767
600.585
610.217
620.246
630.68
640.203
650.626
660.205
670.965
680.391
690.823
70.316
700.823
710.0215
720.726
730.356
740.854
750.00878
760.0382
770.293
780.221
790.563
80.133
800.283
810.11
820.96
830.966
840.911
850.14
860.583
870.431
880.861
890.691
90.295
908.97078e-4
910.569
920.25
930.919
940.427
950.456
960.876
970.0538
980.33
990.323



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: CNhs11741


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)
0000236 (B cell)
0000255 (eukaryotic cell)
0000542 (lymphocyte)
0000548 (animal cell)
0000566 (angioblastic mesenchymal cell)
0000723 (somatic stem cell)
0000738 (leukocyte)
0000785 (mature B cell)
0000816 (immature B cell)
0000817 (precursor B cell)
0000818 (transitional stage B cell)
0000819 (B-1 B cell)
0000826 (pro-B cell)
0000837 (hematopoietic multipotent progenitor cell)
0000838 (lymphoid lineage restricted progenitor cell)
0000945 (lymphocyte of B lineage)
0000954 (small pre-B-II cell)
0000955 (pre-B-II cell)
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)
0060073 (lymphatic system cancer)
0060083 (immune system cancer)
14566 (disease of cellular proliferation)
162 (cancer)
2531 (hematologic cancer)
4 (disease)
8675 (lymphosarcoma)

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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