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{{f5samples
{{f5samples
|F5samples=
|ancestors_in_anatomy_facet=UBERON:0000010,UBERON:0000013,UBERON:0000061,UBERON:0000073,UBERON:0000465,UBERON:0000467,UBERON:0000468,UBERON:0000480,UBERON:0000922,UBERON:0000923,UBERON:0000924,UBERON:0001016,UBERON:0001062,UBERON:0002050,UBERON:0002410,UBERON:0002532,UBERON:0004121,UBERON:0005423
|ancestors_in_anatomy_facet=UBERON:0000010,UBERON:0000013,UBERON:0000061,UBERON:0000073,UBERON:0000465,UBERON:0000467,UBERON:0000468,UBERON:0000480,UBERON:0000922,UBERON:0000923,UBERON:0000924,UBERON:0001016,UBERON:0001062,UBERON:0002050,UBERON:0002410,UBERON:0002532,UBERON:0004121,UBERON:0005423
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000004,CL:0000012,CL:0000133,CL:0000144,CL:0000219,CL:0000220,CL:0000221,CL:0000255,CL:0000333,CL:0000548,CL:0002321
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000004,CL:0000012,CL:0000133,CL:0000144,CL:0000219,CL:0000220,CL:0000221,CL:0000255,CL:0000333,CL:0000548,CL:0002321
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|creation_date=
|creation_date=
|def=
|def=
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|fonse_cell_line=FF:0100932
|fonse_cell_line=FF:0100932
|fonse_cell_line_closure=FF:0100932
|fonse_cell_line_closure=FF:0100932

Revision as of 16:43, 29 March 2012


Name:neuroblastoma cell line:NB-1
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueadrenal gland
dev stageNA
sexmale
age2
cell typeneuroblast
cell lineNB-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-iPS0.895
C103-CD4-CD8-Natural-Peripheral-Whole-Neutrophils-Basophils0
C104-Mast-Basophils-immature-CD14-CD34-eye-Natural0
C105-heart-skeletal-occipital-hippocampus-acute-Sebocyte-penis-0.017
C106-Hep2-epitheloid-placenta-cervical-rectal-anaplastic-glassy0
C107-Neutrophils-CD14-Eosinophils-Monocytederived-Whole-Peripheral-blood0
C108-breast-hepatoblastoma-MCF7-parotid-salivary-submaxillary-prostate0
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C90-neuroectodermal-peripheral-neuroepithelioma-neuroblastoma-carcinoid-parietal-putamen0
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: CNhs11284

Jaspar motifP-value
MA0002.27.3319e-6
MA0003.10.218
MA0004.10.595
MA0006.10.127
MA0007.10.123
MA0009.10.0828
MA0014.10.618
MA0017.10.00449
MA0018.20.00722
MA0019.10.673
MA0024.18.66201e-6
MA0025.10.529
MA0027.10.471
MA0028.10.152
MA0029.10.872
MA0030.10.792
MA0031.10.224
MA0035.20.826
MA0038.13.87367e-5
MA0039.20.0465
MA0040.10.39
MA0041.10.196
MA0042.10.425
MA0043.10.0302
MA0046.10.781
MA0047.20.0564
MA0048.10.687
MA0050.12.38343e-6
MA0051.10.00248
MA0052.10.536
MA0055.10.759
MA0057.10.149
MA0058.10.58
MA0059.10.842
MA0060.11.22781e-13
MA0061.10.00589
MA0062.20.259
MA0065.20.0164
MA0066.10.249
MA0067.10.841
MA0068.10.00168
MA0069.10.745
MA0070.10.241
MA0071.10.283
MA0072.10.96
MA0073.10.427
MA0074.10.0808
MA0076.10.0207
MA0077.10.0259
MA0078.10.3
MA0079.20.288
MA0080.26.51808e-12
MA0081.10.15
MA0083.10.00158
MA0084.10.339
MA0087.10.924
MA0088.10.627
MA0090.17.75637e-4
MA0091.10.508
MA0092.10.39
MA0093.10.418
MA0099.24.29058e-13
MA0100.10.0364
MA0101.10.0223
MA0102.20.00464
MA0103.10.0123
MA0104.20.171
MA0105.10.0152
MA0106.10.158
MA0107.10.00643
MA0108.20.0187
MA0111.10.625
MA0112.22.44434e-4
MA0113.10.175
MA0114.10.0734
MA0115.10.575
MA0116.10.0103
MA0117.10.998
MA0119.10.118
MA0122.10.428
MA0124.10.392
MA0125.10.0173
MA0131.10.309
MA0135.10.767
MA0136.12.85455e-9
MA0137.20.0848
MA0138.20.864
MA0139.10.357
MA0140.10.472
MA0141.10.0345
MA0142.10.34
MA0143.10.757
MA0144.10.00862
MA0145.10.19
MA0146.10.0468
MA0147.10.224
MA0148.10.0788
MA0149.10.209
MA0150.12.56168e-4
MA0152.10.353
MA0153.10.278
MA0154.10.0383
MA0155.10.373
MA0156.14.48911e-4
MA0157.10.0313
MA0159.10.00506
MA0160.10.0594
MA0162.10.121
MA0163.10.00737
MA0164.10.473
MA0258.10.00738
MA0259.10.262



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: CNhs11284

Novel motifP-value
10.216
100.24
1000.77
1010.864
1020.571
1030.0221
1040.317
1050.594
1068.45173e-4
1070.0234
1080.724
1090.0491
110.112
1100.258
1110.226
1120.0783
1130.24
1140.0218
1150.52
1160.298
1170.1
1180.362
1190.383
120.806
1200.206
1210.983
1220.638
1230.663
1240.146
1250.967
1260.142
1270.127
1280.0162
1290.0554
130.0228
1300.0135
1310.55
1320.929
1330.86
1340.993
1350.965
1360.643
1370.285
1380.432
1390.0952
140.651
1400.0307
1410.399
1420.717
1430.0986
1440.65
1450.231
1460.959
1470.609
1480.0328
1490.104
150.122
1500.284
1510.403
1520.0171
1530.705
1540.791
1550.574
1560.628
1570.643
1580.927
1590.179
160.0936
1600.0739
1610.271
1620.619
1630.896
1640.0144
1650.0774
1660.964
1670.311
1680.0306
1690.0149
170.218
180.291
190.0814
20.354
200.535
210.392
220.15
230.0207
240.249
250.789
260.0225
270.324
280.617
290.234
30.0493
300.618
310.6
320.00102
330.367
340.593
350.614
360.959
370.159
380.189
390.253
40.525
400.385
410.208
420.271
430.0948
440.249
450.365
460.141
470.326
480.177
490.18
50.306
500.455
510.56
520.11
530.852
540.467
550.0188
560.276
570.853
580.275
590.0333
60.714
600.0151
610.415
620.163
630.109
640.691
650.0928
660.64
670.292
680.316
690.144
70.197
700.00687
710.0494
720.278
730.0229
740.303
750.211
760.466
770.0806
780.123
790.372
80.0771
800.145
810.49
820.151
830.0192
840.429
850.0573
860.67
870.227
880.431
890.151
90.279
900.432
910.0215
920.063
930.29
940.107
950.0282
960.507
970.894
980.509
990.426



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: CNhs11284


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)
0000133 (neurectodermal cell)
0000219 (motile cell)
0000221 (ectodermal cell)
0000255 (eukaryotic cell)
0000333 (migratory neural crest cell)
0000548 (animal cell)
0002321 (embryonic cell)

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

UBERON: Anatomy
0000010 (peripheral nervous system)
0000013 (sympathetic nervous system)
0000061 (anatomical structure)
0000073 (regional part of nervous system)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000480 (anatomical group)
0000922 (embryo)
0000923 (germ layer)
0000924 (ectoderm)
0001016 (nervous system)
0001062 (anatomical entity)
0002050 (embryonic structure)
0002410 (autonomic nervous system)
0002532 (epiblast (generic))
0004121 (ectoderm-derived structure)
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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