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{{f5samples
{{f5samples
|F5samples=
|ancestors_in_anatomy_facet=UBERON:0000061,UBERON:0000465,UBERON:0000468,UBERON:0000922,UBERON:0000923,UBERON:0000924,UBERON:0001062,UBERON:0002050,UBERON:0002346,UBERON:0002532,UBERON:0005423
|ancestors_in_anatomy_facet=UBERON:0000061,UBERON:0000465,UBERON:0000468,UBERON:0000922,UBERON:0000923,UBERON:0000924,UBERON:0001062,UBERON:0002050,UBERON:0002346,UBERON:0002532,UBERON:0005423
|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:10697-109G4
|fonse_cell_line=FF:10697-109G4
|fonse_cell_line_closure=FF:10697-109G4
|fonse_cell_line_closure=FF:10697-109G4

Revision as of 16:55, 29 March 2012


Name:peripheral neuroectodermal tumor cell line:KU-SN
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueperipheral nervous system
dev stageNA
sexfemale
age4
cell typeunclassifiable
cell lineKU-SN
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-penis0.389
C106-Hep2-epitheloid-placenta-cervical-rectal-anaplastic-glassy0
C107-Neutrophils-CD14-Eosinophils-Monocytederived-Whole-Peripheral-blood0
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C9-skeletal-diaphragm-tongue-throat-penis-heart-left0
C90-neuroectodermal-peripheral-neuroepithelioma-neuroblastoma-carcinoid-parietal-putamen0.184
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: CNhs11830

Jaspar motifP-value
MA0002.26.01137e-4
MA0003.10.152
MA0004.10.00535
MA0006.10.0788
MA0007.10.197
MA0009.10.636
MA0014.10.926
MA0017.12.11012e-4
MA0018.20.00349
MA0019.10.154
MA0024.10.0214
MA0025.10.843
MA0027.10.453
MA0028.10.121
MA0029.10.697
MA0030.10.355
MA0031.10.2
MA0035.20.629
MA0038.10.117
MA0039.20.037
MA0040.10.0211
MA0041.10.141
MA0042.10.193
MA0043.10.0709
MA0046.10.008
MA0047.20.577
MA0048.10.0822
MA0050.13.74768e-11
MA0051.14.99184e-7
MA0052.10.392
MA0055.10.209
MA0057.10.155
MA0058.10.00138
MA0059.10.0274
MA0060.10.037
MA0061.10.224
MA0062.20.203
MA0065.20.0107
MA0066.10.247
MA0067.10.074
MA0068.10.162
MA0069.10.76
MA0070.10.433
MA0071.10.334
MA0072.10.661
MA0073.10.239
MA0074.10.624
MA0076.10.0175
MA0077.10.315
MA0078.10.368
MA0079.20.0523
MA0080.23.36862e-12
MA0081.10.0332
MA0083.10.0548
MA0084.10.337
MA0087.10.101
MA0088.10.0364
MA0090.10.117
MA0091.10.0557
MA0092.10.188
MA0093.10.00501
MA0099.22.81495e-14
MA0100.10.248
MA0101.10.144
MA0102.20.0152
MA0103.10.949
MA0104.24.07209e-4
MA0105.10.21
MA0106.10.352
MA0107.10.0499
MA0108.20.00936
MA0111.10.955
MA0112.20.00791
MA0113.10.4
MA0114.10.00426
MA0115.10.064
MA0116.10.404
MA0117.10.536
MA0119.10.737
MA0122.10.136
MA0124.10.143
MA0125.10.835
MA0131.10.0607
MA0135.10.0465
MA0136.12.51424e-6
MA0137.20.00219
MA0138.20.293
MA0139.10.566
MA0140.10.386
MA0141.10.0912
MA0142.10.264
MA0143.10.202
MA0144.10.00119
MA0145.10.0221
MA0146.10.111
MA0147.11.02031e-4
MA0148.10.832
MA0149.10.00686
MA0150.17.00069e-4
MA0152.10.0332
MA0153.10.0935
MA0154.10.334
MA0155.10.181
MA0156.10.00645
MA0157.10.543
MA0159.10.17
MA0160.10.0067
MA0162.10.663
MA0163.10.149
MA0164.10.655
MA0258.10.076
MA0259.10.00632



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: CNhs11830

Novel motifP-value
10.412
100.396
1000.168
1010.921
1020.948
1030.0492
1040.456
1050.26
1060.00265
1070.00518
1080.613
1090.0867
110.66
1100.798
1110.762
1120.298
1130.28
1140.301
1150.792
1160.923
1170.808
1180.887
1190.741
120.118
1200.405
1210.0359
1220.0968
1230.0208
1240.396
1250.829
1260.466
1270.315
1280.105
1290.208
130.876
1300.934
1310.389
1320.397
1330.882
1340.814
1350.0332
1360.1
1370.319
1380.898
1390.591
140.544
1400.575
1410.373
1420.514
1430.364
1440.813
1450.798
1460.746
1470.741
1480.0972
1490.186
150.958
1500.334
1510.658
1520.00175
1530.36
1540.331
1550.949
1560.78
1570.462
1580.318
1590.143
160.275
1600.535
1610.902
1620.436
1630.696
1640.462
1650.646
1660.832
1670.147
1680.0988
1690.0355
170.499
180.429
190.123
20.0888
200.48
210.95
220.0582
230.0657
240.521
250.613
260.356
270.68
280.933
290.564
30.837
300.0587
310.342
320.015
330.899
340.143
350.351
360.134
370.548
380.513
390.267
40.788
400.34
410.066
420.285
430.74
440.831
450.131
460.825
470.568
480.987
490.912
50.582
500.297
510.846
520.129
530.799
540.32
550.572
560.996
570.146
580.666
590.0549
60.673
600.141
610.915
620.475
630.71
640.705
650.214
660.414
670.0328
680.526
690.289
70.702
700.529
710.934
720.872
730.00684
740.303
750.538
760.429
770.0528
780.334
790.467
80.973
800.0103
810.553
820.514
830.627
840.732
850.0548
860.855
870.0742
880.25
890.229
90.119
900.198
910.155
920.572
930.153
940.892
950.882
960.672
970.811
980.31
990.61



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: CNhs11830


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
0050687 (cell type cancer)
14566 (disease of cellular proliferation)
162 (cancer)
171 (neuroectodermal tumor)
2994 (germ cell cancer)
3095 (germ cell and embryonal cancer)
4 (disease)

UBERON: Anatomy
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000468 (multi-cellular organism)
0000922 (embryo)
0000923 (germ layer)
0000924 (ectoderm)
0001062 (anatomical entity)
0002050 (embryonic structure)
0002346 (neurectoderm)
0002532 (epiblast (generic))
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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