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{{f5samples
{{f5samples
|F5samples=
|ancestors_in_anatomy_facet=UBERON:0000061,UBERON:0000062,UBERON:0000465,UBERON:0000467,UBERON:0000468,UBERON:0000479,UBERON:0000480,UBERON:0000922,UBERON:0000923,UBERON:0000926,UBERON:0001062,UBERON:0001434,UBERON:0001474,UBERON:0002050,UBERON:0002204,UBERON:0002384,UBERON:0002532,UBERON:0004120,UBERON:0004765,UBERON:0005423
|ancestors_in_anatomy_facet=UBERON:0000061,UBERON:0000062,UBERON:0000465,UBERON:0000467,UBERON:0000468,UBERON:0000479,UBERON:0000480,UBERON:0000922,UBERON:0000923,UBERON:0000926,UBERON:0001062,UBERON:0001434,UBERON:0001474,UBERON:0002050,UBERON:0002204,UBERON:0002384,UBERON:0002532,UBERON:0004120,UBERON:0004765,UBERON:0005423
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000004,CL:0000012,CL:0000034,CL:0000035,CL:0000048,CL:0000055,CL:0000062,CL:0000063,CL:0000134,CL:0000144,CL:0000219,CL:0000255,CL:0000335,CL:0000375,CL:0000548,CL:0000723,CL:0002320,CL:0002371
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000004,CL:0000012,CL:0000034,CL:0000035,CL:0000048,CL:0000055,CL:0000062,CL:0000063,CL:0000134,CL:0000144,CL:0000219,CL:0000255,CL:0000335,CL:0000375,CL:0000548,CL:0000723,CL:0002320,CL:0002371
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|creation_date=
|creation_date=
|def=
|def=
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|fonse_cell_line=FF:0100385
|fonse_cell_line=FF:0100385
|fonse_cell_line_closure=FF:0100385
|fonse_cell_line_closure=FF:0100385

Revision as of 16:43, 29 March 2012


Name:osteosarcoma cell line:143B/TK^(-)neo^(R)
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuebone
dev stageNA
sexunknown
ageNA
cell typeosteoblast
cell line143B/TK^(-)neo^(R)
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-penis-0.0861
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-lymphoma0.351
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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: CNhs11279

Jaspar motifP-value
MA0002.20.0698
MA0003.10.255
MA0004.10.952
MA0006.10.82
MA0007.10.63
MA0009.10.966
MA0014.10.744
MA0017.10.0328
MA0018.20.759
MA0019.10.824
MA0024.17.31406e-4
MA0025.10.0864
MA0027.10.85
MA0028.10.776
MA0029.10.412
MA0030.10.014
MA0031.10.0178
MA0035.20.138
MA0038.10.0474
MA0039.20.243
MA0040.10.662
MA0041.10.167
MA0042.10.142
MA0043.10.326
MA0046.10.0806
MA0047.20.0169
MA0048.10.746
MA0050.10.0155
MA0051.10.608
MA0052.10.941
MA0055.10.706
MA0057.10.873
MA0058.10.313
MA0059.10.591
MA0060.10.00158
MA0061.10.143
MA0062.20.2
MA0065.20.00197
MA0066.10.0192
MA0067.10.841
MA0068.10.0622
MA0069.10.0916
MA0070.10.096
MA0071.10.22
MA0072.10.898
MA0073.10.78
MA0074.10.469
MA0076.10.645
MA0077.10.549
MA0078.10.364
MA0079.20.697
MA0080.20.0545
MA0081.10.304
MA0083.10.665
MA0084.10.682
MA0087.10.754
MA0088.10.164
MA0090.10.695
MA0091.10.065
MA0092.10.155
MA0093.10.854
MA0099.21.20827e-12
MA0100.10.673
MA0101.10.872
MA0102.20.761
MA0103.10.104
MA0104.20.709
MA0105.10.00115
MA0106.10.488
MA0107.10.887
MA0108.28.88636e-4
MA0111.10.374
MA0112.21.95924e-4
MA0113.10.119
MA0114.10.0381
MA0115.10.438
MA0116.10.00281
MA0117.10.809
MA0119.10.194
MA0122.10.222
MA0124.10.827
MA0125.10.937
MA0131.10.72
MA0135.10.148
MA0136.10.259
MA0137.20.122
MA0138.20.235
MA0139.10.102
MA0140.10.507
MA0141.10.255
MA0142.10.498
MA0143.10.445
MA0144.10.132
MA0145.10.192
MA0146.10.0109
MA0147.10.929
MA0148.10.0149
MA0149.10.331
MA0150.10.874
MA0152.10.357
MA0153.10.689
MA0154.10.0101
MA0155.10.201
MA0156.10.704
MA0157.10.391
MA0159.10.0423
MA0160.10.333
MA0162.10.27
MA0163.12.87642e-4
MA0164.10.71
MA0258.10.00206
MA0259.10.894



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: CNhs11279

Novel motifP-value
10.00934
100.099
1000.527
1010.93
1020.964
1030.0778
1040.896
1050.897
1060.365
1070.542
1080.536
1090.106
110.0122
1100.0918
1110.398
1120.00901
1130.574
1140.0108
1150.204
1160.0792
1170.0681
1180.0481
1190.0381
120.834
1200.744
1210.94
1220.583
1230.436
1240.448
1250.319
1260.607
1270.283
1280.578
1290.346
130.164
1300.103
1310.104
1320.345
1330.87
1340.459
1350.838
1360.721
1370.692
1380.629
1390.0119
140.381
1400.253
1410.278
1420.653
1430.96
1440.391
1450.888
1460.886
1470.957
1480.0278
1490.044
150.623
1500.84
1510.47
1520.639
1530.602
1540.926
1550.0303
1560.861
1570.229
1580.814
1590.784
160.0776
1600.352
1610.439
1620.881
1630.753
1640.148
1650.589
1660.064
1670.28
1680.686
1690.0158
170.244
180.787
190.188
20.626
200.728
210.556
220.091
230.981
240.598
250.56
260.25
270.164
280.967
290.0808
30.0449
300.829
310.389
323.3313e-5
330.16
340.937
350.623
360.0285
370.0618
380.201
390.633
40.288
400.0243
410.533
420.724
430.117
440.00151
450.993
460.146
470.0335
480.104
490.184
50.609
500.861
510.551
520.666
530.54
540.681
550.974
560.305
570.624
580.361
590.124
60.549
600.269
610.588
620.365
630.219
640.0898
650.207
660.0565
670.794
680.577
690.471
70.384
703.30304e-4
710.0246
720.111
730.171
740.608
750.13
760.378
770.0442
780.655
790.0264
80.126
800.899
810.314
820.00322
830.404
840.275
850.0141
860.641
870.85
880.926
890.00808
90.77
900.966
910.443
920.0778
930.971
940.34
950.053
960.0695
970.316
980.234
990.579



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: CNhs11279


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)
0000035 (single fate stem cell)
0000048 (multi fate stem cell)
0000055 (non-terminally differentiated cell)
0000062 (osteoblast)
0000134 (mesenchymal cell)
0000219 (motile cell)
0000255 (eukaryotic cell)
0000335 (mesenchyme condensation cell)
0000375 (osteoprogenitor cell)
0000548 (animal cell)
0000723 (somatic stem cell)
0002320 (connective tissue cell)
0002371 (somatic cell)

DOID: Disease
0050686 (organ system cancer)
0060100 (musculoskeletal system cancer)
14566 (disease of cellular proliferation)
162 (cancer)
201 (connective tissue cancer)
3347 (osteosarcoma)
4 (disease)

UBERON: Anatomy
0000061 (anatomical structure)
0000062 (organ)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000479 (tissue)
0000480 (anatomical group)
0000922 (embryo)
0000923 (germ layer)
0000926 (mesoderm)
0001062 (anatomical entity)
0001434 (skeletal system)
0001474 (bone element)
0002050 (embryonic structure)
0002204 (musculoskeletal system)
0002384 (connective tissue)
0002532 (epiblast (generic))
0004120 (mesoderm-derived structure)
0004765 (skeletal element)
0005423 (developing anatomical structure)

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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