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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 16:54, 29 March 2012


Name:neuroblastoma cell line:NBsusSR
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuepelvis
dev stageNA
sexmale
age18
cell typeneuroblast
cell lineNBsusSR
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-penis0.118
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-lymphoma0.336
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: CNhs11818

Jaspar motifP-value
MA0002.22.16692e-5
MA0003.10.142
MA0004.10.0986
MA0006.10.253
MA0007.10.14
MA0009.10.45
MA0014.10.971
MA0017.10.0141
MA0018.20.386
MA0019.10.313
MA0024.10.00114
MA0025.10.505
MA0027.10.157
MA0028.10.00166
MA0029.10.57
MA0030.10.0716
MA0031.10.0573
MA0035.20.885
MA0038.10.00417
MA0039.20.126
MA0040.10.00362
MA0041.10.107
MA0042.10.13
MA0043.10.0439
MA0046.10.335
MA0047.20.194
MA0048.10.237
MA0050.17.46629e-11
MA0051.19.55155e-6
MA0052.10.0494
MA0055.10.234
MA0057.10.094
MA0058.10.0675
MA0059.10.323
MA0060.11.52131e-12
MA0061.10.00973
MA0062.28.6093e-4
MA0065.20.0242
MA0066.10.101
MA0067.10.79
MA0068.10.21
MA0069.10.834
MA0070.10.0204
MA0071.10.601
MA0072.10.421
MA0073.10.0658
MA0074.10.583
MA0076.11.79987e-5
MA0077.10.332
MA0078.10.72
MA0079.20.325
MA0080.24.49545e-14
MA0081.10.278
MA0083.11.66595e-4
MA0084.10.124
MA0087.10.0109
MA0088.10.0353
MA0090.10.0958
MA0091.10.698
MA0092.10.208
MA0093.10.0786
MA0099.27.68078e-30
MA0100.10.193
MA0101.10.0792
MA0102.20.0223
MA0103.10.615
MA0104.20.0145
MA0105.10.0882
MA0106.10.457
MA0107.10.0166
MA0108.20.0675
MA0111.10.78
MA0112.21.59773e-5
MA0113.10.0662
MA0114.10.0917
MA0115.10.822
MA0116.10.0487
MA0117.10.905
MA0119.10.319
MA0122.10.621
MA0124.10.813
MA0125.10.472
MA0131.10.247
MA0135.10.65
MA0136.11.10123e-6
MA0137.20.0715
MA0138.20.246
MA0139.10.538
MA0140.10.346
MA0141.10.128
MA0142.13.4205e-4
MA0143.10.27
MA0144.10.0108
MA0145.10.00592
MA0146.10.209
MA0147.10.0281
MA0148.10.397
MA0149.10.0012
MA0150.11.13407e-4
MA0152.10.721
MA0153.10.414
MA0154.10.0249
MA0155.10.577
MA0156.10.0229
MA0157.10.0345
MA0159.10.213
MA0160.10.0745
MA0162.10.16
MA0163.10.454
MA0164.10.7
MA0258.10.00581
MA0259.10.0944



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: CNhs11818

Novel motifP-value
10.463
100.413
1000.489
1010.938
1020.807
1030.225
1040.717
1050.0769
1062.87645e-4
1070.00963
1080.543
1090.117
110.308
1100.527
1110.331
1120.416
1130.226
1140.00276
1150.639
1160.95
1170.691
1180.897
1190.216
120.318
1200.236
1210.331
1220.205
1230.802
1240.986
1250.671
1260.412
1270.379
1280.051
1290.945
130.846
1300.365
1310.16
1320.794
1330.911
1340.694
1350.787
1360.772
1370.132
1380.799
1390.221
140.718
1400.276
1410.58
1420.553
1430.00361
1440.796
1450.29
1460.787
1470.935
1480.0761
1490.0566
150.331
1500.441
1510.166
1520.00783
1530.334
1540.896
1550.659
1560.449
1570.81
1580.231
1590.412
160.242
1600.223
1610.426
1620.828
1630.341
1640.763
1650.625
1660.76
1670.587
1680.18
1690.00677
170.11
180.702
190.0848
20.101
200.437
210.375
220.0747
230.00791
240.327
250.641
260.223
270.144
280.94
290.832
30.422
300.284
310.513
320.0175
330.776
340.257
350.744
360.241
370.275
380.292
390.359
40.769
400.67
410.126
420.84
430.176
440.345
450.407
460.321
470.579
480.592
490.348
50.346
500.648
510.377
520.154
530.511
540.103
550.517
560.386
570.99
580.21
590.0218
60.528
600.0601
610.204
620.0586
630.33
640.941
650.096
660.373
670.241
680.167
690.357
70.854
700.00627
710.138
720.449
730.0418
740.275
750.61
760.715
770.0622
780.158
790.173
80.45
800.0851
810.569
820.0933
830.272
840.596
850.00466
860.843
870.704
880.566
890.0914
90.0987
900.899
910.418
920.0701
930.375
940.381
950.393
960.212
970.582
980.254
990.771



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: CNhs11818


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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