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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:10637-108I7
|fonse_cell_line=FF:10637-108I7
|fonse_cell_line_closure=FF:10637-108I7
|fonse_cell_line_closure=FF:10637-108I7

Revision as of 16:50, 29 March 2012


Name:neuroectodermal tumor cell line:FU-RPNT-1
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuekidney
dev stageNA
sexmale
age22
cell typeunclassifiable
cell lineFU-RPNT-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-penis0.396
C106-Hep2-epitheloid-placenta-cervical-rectal-anaplastic-glassy0
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C89-small-retinoblastoma-medulloblastoma-iPS-acantholytic-eye-bronchogenic0
C9-skeletal-diaphragm-tongue-throat-penis-heart-left0
C90-neuroectodermal-peripheral-neuroepithelioma-neuroblastoma-carcinoid-parietal-putamen1.024
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: CNhs11744

Jaspar motifP-value
MA0002.20.00183
MA0003.10.142
MA0004.10.48
MA0006.10.0789
MA0007.10.199
MA0009.10.36
MA0014.10.511
MA0017.10.00266
MA0018.20.192
MA0019.10.206
MA0024.10.00194
MA0025.10.0687
MA0027.10.243
MA0028.10.343
MA0029.10.489
MA0030.10.193
MA0031.10.17
MA0035.20.046
MA0038.10.449
MA0039.20.0162
MA0040.10.0823
MA0041.10.165
MA0042.10.335
MA0043.10.847
MA0046.10.00315
MA0047.20.647
MA0048.10.199
MA0050.15.82888e-5
MA0051.10.008
MA0052.10.105
MA0055.10.282
MA0057.10.109
MA0058.10.323
MA0059.10.574
MA0060.10.181
MA0061.10.0818
MA0062.20.648
MA0065.20.0049
MA0066.10.131
MA0067.10.582
MA0068.10.872
MA0069.10.62
MA0070.10.71
MA0071.10.233
MA0072.10.509
MA0073.10.391
MA0074.10.839
MA0076.10.104
MA0077.10.525
MA0078.10.505
MA0079.20.0894
MA0080.22.68985e-10
MA0081.10.134
MA0083.10.00757
MA0084.10.456
MA0087.10.268
MA0088.10.377
MA0090.10.373
MA0091.10.595
MA0092.10.3
MA0093.10.415
MA0099.22.79172e-26
MA0100.10.661
MA0101.10.0596
MA0102.20.00204
MA0103.10.132
MA0104.20.105
MA0105.10.76
MA0106.10.232
MA0107.10.0276
MA0108.29.38782e-4
MA0111.10.969
MA0112.27.29479e-4
MA0113.10.108
MA0114.10.00836
MA0115.10.407
MA0116.10.264
MA0117.10.699
MA0119.10.78
MA0122.10.22
MA0124.10.143
MA0125.10.369
MA0131.10.355
MA0135.10.0181
MA0136.15.9109e-8
MA0137.20.0725
MA0138.20.368
MA0139.10.788
MA0140.10.0157
MA0141.10.0197
MA0142.10.904
MA0143.10.311
MA0144.10.00695
MA0145.10.00692
MA0146.10.101
MA0147.10.0826
MA0148.10.836
MA0149.10.168
MA0150.13.67119e-5
MA0152.10.445
MA0153.10.115
MA0154.10.0796
MA0155.10.358
MA0156.10.00117
MA0157.10.269
MA0159.10.0118
MA0160.10.00195
MA0162.10.265
MA0163.10.798
MA0164.10.676
MA0258.10.0551
MA0259.10.0789



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: CNhs11744

Novel motifP-value
10.717
100.852
1000.476
1010.861
1020.509
1030.0533
1040.303
1050.207
1062.19928e-4
1070.016
1080.603
1090.00552
110.233
1100.532
1110.408
1120.464
1130.442
1140.234
1150.412
1160.454
1170.665
1180.811
1190.734
120.488
1200.754
1210.069
1220.0392
1230.047
1240.899
1250.992
1260.26
1270.146
1280.0371
1290.52
130.694
1300.83
1310.302
1320.645
1330.874
1340.72
1350.206
1360.0583
1370.465
1380.879
1390.192
140.561
1400.507
1410.255
1420.416
1430.0217
1440.408
1450.739
1460.635
1470.741
1480.0345
1490.0836
150.38
1500.238
1510.308
1520.00116
1530.988
1540.535
1550.916
1560.655
1570.703
1580.142
1590.0102
160.163
1600.752
1610.525
1620.443
1630.533
1640.628
1650.826
1660.897
1670.588
1680.246
1690.0208
170.109
180.264
190.081
20.0942
200.702
210.574
220.0451
230.0295
240.0618
250.679
260.336
270.231
280.864
290.67
30.859
300.14
310.52
320.05
330.674
340.246
350.729
360.239
370.0766
380.375
390.313
40.942
400.281
410.0753
420.783
430.369
440.139
450.171
460.358
470.674
480.508
490.554
50.407
500.503
510.616
520.0988
530.796
540.26
550.834
560.477
570.545
580.601
590.0155
60.565
600.0311
610.508
620.291
630.427
640.83
650.152
660.461
670.82
680.518
690.338
70.465
700.0614
710.373
720.29
730.00186
740.714
750.556
760.303
770.0222
780.451
790.721
80.466
800.0444
810.847
820.828
830.563
840.741
850.0519
860.613
870.00554
880.664
890.0272
90.0972
900.282
910.382
920.076
930.907
940.24
950.0156
960.437
970.786
980.343
990.826



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: CNhs11744


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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