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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=
|ancestors_in_cell_lineage_facet=
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|creation_date=
|creation_date=
|def=
|def=
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|fonse_cell_line=FF:0100400
|fonse_cell_line=FF:0100400
|fonse_cell_line_closure=FF:0100400
|fonse_cell_line_closure=FF:0100400

Revision as of 16:55, 29 March 2012


Name:Ewing's sarcoma cell line:Hs 863.T
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
sexfemale
age5
cell typeosteoblast
cell lineHs 863.T
companyATCC
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
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-penis0.0965
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-lymphoma-0.31
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: CNhs11836

Jaspar motifP-value
MA0002.20.619
MA0003.10.896
MA0004.10.0644
MA0006.10.184
MA0007.10.468
MA0009.10.313
MA0014.10.13
MA0017.10.547
MA0018.22.28951e-4
MA0019.10.338
MA0024.19.92329e-6
MA0025.10.00214
MA0027.10.358
MA0028.12.62666e-5
MA0029.10.29
MA0030.10.0496
MA0031.10.0855
MA0035.20.0697
MA0038.12.04187e-4
MA0039.20.00237
MA0040.10.744
MA0041.10.315
MA0042.10.606
MA0043.12.29919e-5
MA0046.10.238
MA0047.20.193
MA0048.10.0229
MA0050.10.206
MA0051.10.193
MA0052.10.195
MA0055.10.768
MA0057.10.879
MA0058.10.00431
MA0059.10.726
MA0060.17.70217e-17
MA0061.10.171
MA0062.21.07912e-11
MA0065.20.856
MA0066.10.483
MA0067.10.013
MA0068.10.627
MA0069.10.135
MA0070.10.898
MA0071.10.817
MA0072.10.428
MA0073.10.852
MA0074.10.334
MA0076.14.99962e-6
MA0077.10.741
MA0078.10.704
MA0079.20.469
MA0080.25.51223e-8
MA0081.10.00154
MA0083.10.0749
MA0084.10.735
MA0087.10.888
MA0088.10.436
MA0090.12.06017e-5
MA0091.10.217
MA0092.10.0562
MA0093.10.0318
MA0099.28.48667e-4
MA0100.10.316
MA0101.10.00748
MA0102.20.00935
MA0103.10.0596
MA0104.20.00193
MA0105.10.567
MA0106.10.0773
MA0107.10.016
MA0108.20.386
MA0111.10.534
MA0112.20.00297
MA0113.10.256
MA0114.10.492
MA0115.10.12
MA0116.10.249
MA0117.10.201
MA0119.10.0207
MA0122.10.186
MA0124.10.158
MA0125.10.187
MA0131.10.204
MA0135.10.248
MA0136.12.93504e-12
MA0137.20.125
MA0138.20.316
MA0139.10.67
MA0140.10.322
MA0141.10.762
MA0142.10.13
MA0143.10.885
MA0144.10.574
MA0145.10.4
MA0146.10.774
MA0147.10.0412
MA0148.10.488
MA0149.10.893
MA0150.10.113
MA0152.10.0268
MA0153.10.519
MA0154.10.355
MA0155.10.491
MA0156.11.27473e-8
MA0157.10.514
MA0159.10.134
MA0160.10.178
MA0162.10.073
MA0163.10.00268
MA0164.10.625
MA0258.10.0584
MA0259.10.496



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: CNhs11836

Novel motifP-value
10.316
100.384
1000.921
1010.902
1020.618
1030.302
1040.602
1050.198
1060.0324
1070.0155
1080.195
1090.683
110.365
1100.76
1110.345
1120.222
1130.146
1140.107
1150.155
1160.0458
1170.951
1180.893
1190.149
120.221
1200.788
1210.895
1220.0968
1230.375
1240.612
1250.55
1260.978
1270.897
1280.0886
1290.864
130.909
1300.193
1310.821
1320.24
1330.956
1340.813
1350.744
1360.447
1370.462
1380.776
1390.0382
140.309
1400.412
1410.78
1420.809
1430.685
1440.339
1450.467
1460.42
1470.151
1480.353
1490.00485
150.729
1500.174
1510.659
1520.0218
1530.242
1540.207
1550.229
1560.443
1570.365
1580.0524
1590.305
160.0178
1600.87
1610.495
1620.326
1630.851
1640.0159
1650.695
1660.0433
1670.615
1680.236
1690.0203
170.164
180.0449
190.0039
20.432
200.974
210.266
220.405
230.0899
240.345
250.517
260.272
270.872
280.647
290.375
30.373
300.966
310.448
322.42994e-17
330.965
340.925
350.844
360.0697
370.126
380.591
390.301
40.74
400.212
410.973
420.709
430.23
440.312
450.952
460.15
470.971
480.936
490.384
50.21
500.57
510.848
520.578
530.548
540.545
550.0313
560.852
570.287
580.791
590.12
60.522
600.506
610.342
620.397
630.131
640.906
650.394
660.183
670.565
680.968
690.397
70.437
700.062
710.185
720.934
730.0115
740.383
750.466
760.726
770.0454
780.977
790.00188
80.0321
800.548
810.36
820.0601
830.888
840.643
850.0257
860.725
870.643
880.568
890.211
90.746
900.331
910.541
920.031
930.963
940.334
950.54
960.333
970.475
980.613
990.0735



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: CNhs11836


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

DOID: Disease
0050686 (organ system cancer)
0050687 (cell type cancer)
1115 (sarcoma)
1192 (peripheral nervous system neoplasm)
14566 (disease of cellular proliferation)
162 (cancer)
3093 (nervous system cancer)
3369 (peripheral primitive neuroectodermal tumor)
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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