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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:10774-110F9
|fonse_cell_line=FF:10774-110F9
|fonse_cell_line_closure=FF:10774-110F9
|fonse_cell_line_closure=FF:10774-110F9

Revision as of 16:57, 29 March 2012


Name:neuroectodermal tumor cell line:TASK1
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuethorax
dev stageNA
sexfemale
age21
cell typeunclassifiable
cell lineTASK1
companyJAPAN HEALTH SCIENCES FOUNDATION - Health Science Research Resources Bank
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-penis0.114
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-lymphoma0.444
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: CNhs11866

Jaspar motifP-value
MA0002.20.003
MA0003.10.316
MA0004.10.0563
MA0006.10.0545
MA0007.10.413
MA0009.10.334
MA0014.10.72
MA0017.10.106
MA0018.20.37
MA0019.10.012
MA0024.11.90084e-8
MA0025.10.255
MA0027.10.22
MA0028.18.27716e-4
MA0029.10.878
MA0030.10.125
MA0031.10.412
MA0035.20.561
MA0038.10.0527
MA0039.20.653
MA0040.10.214
MA0041.10.224
MA0042.10.466
MA0043.10.723
MA0046.10.293
MA0047.20.507
MA0048.10.0492
MA0050.17.7863e-10
MA0051.17.55975e-5
MA0052.10.0147
MA0055.13.83195e-4
MA0057.10.606
MA0058.10.029
MA0059.10.0039
MA0060.12.59273e-9
MA0061.10.0189
MA0062.20.00123
MA0065.20.523
MA0066.10.382
MA0067.10.92
MA0068.10.0397
MA0069.10.926
MA0070.10.709
MA0071.10.614
MA0072.10.99
MA0073.10.126
MA0074.10.478
MA0076.17.0469e-5
MA0077.10.528
MA0078.10.513
MA0079.20.102
MA0080.24.96672e-10
MA0081.10.124
MA0083.13.56728e-5
MA0084.10.302
MA0087.10.327
MA0088.12.46323e-4
MA0090.10.173
MA0091.10.376
MA0092.10.478
MA0093.10.0444
MA0099.21.1205e-16
MA0100.10.582
MA0101.10.011
MA0102.20.00419
MA0103.10.9
MA0104.23.25098e-4
MA0105.10.579
MA0106.10.877
MA0107.10.00185
MA0108.22.38491e-4
MA0111.10.722
MA0112.20.00839
MA0113.10.42
MA0114.10.698
MA0115.10.843
MA0116.10.606
MA0117.10.983
MA0119.10.251
MA0122.10.619
MA0124.10.236
MA0125.10.705
MA0131.10.188
MA0135.10.037
MA0136.14.73959e-6
MA0137.20.0324
MA0138.20.557
MA0139.10.945
MA0140.10.762
MA0141.10.99
MA0142.10.982
MA0143.10.327
MA0144.10.00301
MA0145.10.00205
MA0146.10.989
MA0147.17.31634e-5
MA0148.10.474
MA0149.14.80459e-5
MA0150.12.10988e-4
MA0152.10.881
MA0153.10.0383
MA0154.10.321
MA0155.10.369
MA0156.10.0626
MA0157.10.513
MA0159.10.139
MA0160.10.414
MA0162.10.381
MA0163.10.0389
MA0164.10.68
MA0258.10.262
MA0259.10.00844



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: CNhs11866

Novel motifP-value
10.185
100.367
1000.0667
1010.501
1020.836
1030.0685
1040.641
1050.567
1061.84871e-4
1070.0266
1080.699
1090.703
110.741
1100.419
1110.549
1120.167
1130.172
1140.0576
1150.319
1160.372
1170.318
1180.447
1190.489
120.814
1200.962
1210.715
1220.786
1239.44134e-4
1240.687
1250.766
1260.59
1270.379
1280.0332
1290.722
130.0672
1300.401
1310.147
1320.524
1330.321
1340.372
1350.0589
1360.868
1370.0661
1380.964
1390.82
140.397
1400.572
1410.387
1420.678
1430.0437
1440.807
1450.877
1460.89
1470.756
1480.165
1490.369
150.913
1500.578
1510.33
1520.00507
1530.955
1540.477
1550.678
1560.825
1570.852
1580.264
1590.123
160.345
1600.426
1610.761
1620.545
1630.0543
1640.135
1650.559
1660.971
1670.111
1680.0872
1690.13
170.518
180.283
190.134
20.0126
200.331
210.75
220.16
233.84795e-4
240.66
250.897
260.677
270.234
280.986
290.508
30.554
300.183
310.555
320.0514
330.958
340.285
350.598
360.072
370.272
380.771
390.398
40.739
400.265
410.147
420.254
430.261
440.719
450.302
460.622
470.317
480.266
490.875
50.45
500.957
510.799
520.0526
530.397
540.48
550.24
560.558
570.124
580.557
590.0369
60.148
600.027
610.825
620.213
630.885
640.298
650.304
660.291
670.644
680.737
690.654
70.51
700.149
710.983
720.225
730.0376
740.543
750.338
760.231
770.228
780.359
790.131
80.484
800.061
810.993
820.484
830.924
840.538
850.00357
860.372
870.998
880.601
890.138
90.0705
900.142
910.3
920.188
930.973
940.606
950.839
960.629
970.538
980.815
990.604



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: CNhs11866


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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