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{{f5samples
{{f5samples
|F5samples=
|ancestors_in_anatomy_facet=UBERON:0000033,UBERON:0000061,UBERON:0000073,UBERON:0000153,UBERON:0000465,UBERON:0000467,UBERON:0000468,UBERON:0000475,UBERON:0000480,UBERON:0000481,UBERON:0000922,UBERON:0000923,UBERON:0000924,UBERON:0000955,UBERON:0001016,UBERON:0001017,UBERON:0001062,UBERON:0002050,UBERON:0002532,UBERON:0004121,UBERON:0005423,UBERON:0005743
|ancestors_in_anatomy_facet=UBERON:0000033,UBERON:0000061,UBERON:0000073,UBERON:0000153,UBERON:0000465,UBERON:0000467,UBERON:0000468,UBERON:0000475,UBERON:0000480,UBERON:0000481,UBERON:0000922,UBERON:0000923,UBERON:0000924,UBERON:0000955,UBERON:0001016,UBERON:0001017,UBERON:0001062,UBERON:0002050,UBERON:0002532,UBERON:0004121,UBERON:0005423,UBERON:0005743
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000004,CL:0000012,CL:0000030,CL:0000055,CL:0000095,CL:0000123,CL:0000125,CL:0000133,CL:0000144,CL:0000219,CL:0000220,CL:0000221,CL:0000243,CL:0000255,CL:0000333,CL:0000339,CL:0000548,CL:0002319,CL:0002321,CL:0002371
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000004,CL:0000012,CL:0000030,CL:0000055,CL:0000095,CL:0000123,CL:0000125,CL:0000133,CL:0000144,CL:0000219,CL:0000220,CL:0000221,CL:0000243,CL:0000255,CL:0000333,CL:0000339,CL:0000548,CL:0002319,CL:0002321,CL:0002371
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|creation_date=
|creation_date=
|def=
|def=
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|fonse_cell_line=FF:0100255
|fonse_cell_line=FF:0100255
|fonse_cell_line_closure=FF:0100255
|fonse_cell_line_closure=FF:0100255

Revision as of 16:57, 29 March 2012


Name:medulloblastoma cell line:ONS-76
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuebrain
dev stageNA
sexfemale
age2
cell typeneurectodermal cell
cell lineONS-76
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-penis0.207
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-lymphoma0.528
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
C110-leukemia-chronic-Eosinophils-acute-Whole-CD34-Lymphatic0
C111-medulla-lung-trachea-testis-caudate-epididymis-throat0
C112-gastric-pancreas-temporal-duodenum-small-extraskeletal-adrenal0
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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: CNhs11861

Jaspar motifP-value
MA0002.26.89174e-4
MA0003.10.0429
MA0004.10.962
MA0006.10.918
MA0007.10.594
MA0009.10.406
MA0014.10.678
MA0017.10.119
MA0018.20.0367
MA0019.10.748
MA0024.12.00983e-7
MA0025.10.727
MA0027.10.851
MA0028.10.00113
MA0029.10.956
MA0030.10.512
MA0031.10.744
MA0035.20.679
MA0038.12.63438e-4
MA0039.20.292
MA0040.10.259
MA0041.10.408
MA0042.10.821
MA0043.10.382
MA0046.10.578
MA0047.20.0704
MA0048.10.25
MA0050.15.81507e-6
MA0051.10.00184
MA0052.10.418
MA0055.10.0243
MA0057.10.465
MA0058.10.713
MA0059.10.838
MA0060.12.36552e-19
MA0061.10.013
MA0062.21.46325e-5
MA0065.20.103
MA0066.10.201
MA0067.10.343
MA0068.10.458
MA0069.10.561
MA0070.10.172
MA0071.10.167
MA0072.10.469
MA0073.10.968
MA0074.10.273
MA0076.15.15105e-5
MA0077.10.01
MA0078.10.452
MA0079.20.673
MA0080.27.82578e-9
MA0081.10.552
MA0083.10.00966
MA0084.10.527
MA0087.10.965
MA0088.10.88
MA0090.10.507
MA0091.10.00681
MA0092.10.264
MA0093.10.903
MA0099.20.75
MA0100.10.0869
MA0101.10.507
MA0102.20.00291
MA0103.10.219
MA0104.20.51
MA0105.11.23122e-4
MA0106.10.00279
MA0107.10.206
MA0108.20.459
MA0111.10.793
MA0112.27.42303e-5
MA0113.10.0736
MA0114.10.294
MA0115.10.536
MA0116.10.00277
MA0117.10.258
MA0119.10.759
MA0122.10.594
MA0124.10.518
MA0125.10.0195
MA0131.10.147
MA0135.10.484
MA0136.10.00347
MA0137.20.193
MA0138.20.08
MA0139.10.207
MA0140.10.738
MA0141.10.443
MA0142.10.0866
MA0143.10.619
MA0144.10.109
MA0145.10.197
MA0146.10.66
MA0147.10.484
MA0148.10.0112
MA0149.10.454
MA0150.10.285
MA0152.10.928
MA0153.10.962
MA0154.10.00931
MA0155.10.0916
MA0156.10.71
MA0157.10.562
MA0159.10.0148
MA0160.10.501
MA0162.10.235
MA0163.12.00905e-6
MA0164.10.949
MA0258.16.72908e-4
MA0259.10.255



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: CNhs11861

Novel motifP-value
10.361
100.133
1000.864
1010.308
1020.545
1030.277
1040.872
1050.817
1060.00693
1070.202
1080.717
1090.352
110.116
1100.219
1110.836
1120.00976
1130.858
1140.193
1150.722
1160.379
1170.218
1180.487
1190.0846
120.584
1200.498
1210.828
1220.762
1230.798
1240.0712
1250.478
1260.252
1270.841
1280.0397
1290.185
130.394
1300.0786
1310.807
1320.925
1330.033
1340.125
1350.0514
1360.279
1370.0482
1380.216
1390.00984
140.67
1400.101
1410.383
1420.659
1430.0362
1440.146
1450.164
1460.942
1470.521
1480.113
1490.0508
150.171
1500.768
1510.462
1520.392
1530.298
1540.582
1550.727
1560.975
1570.187
1580.665
1590.651
160.243
1600.612
1610.637
1620.699
1630.317
1640.0699
1650.659
1660.0495
1670.629
1680.218
1690.0824
170.116
180.0787
190.0979
20.177
200.761
210.153
220.229
230.0451
240.6
250.63
260.508
270.148
280.802
290.331
30.152
300.943
310.503
320.00238
330.479
340.277
350.0559
360.371
370.0938
380.556
390.389
40.859
400.474
410.367
420.967
430.0477
440.335
450.529
460.164
470.679
480.505
490.0984
50.0581
500.698
510.436
520.105
530.623
540.515
550.505
560.503
570.77
580.0733
590.0435
60.289
600.0277
610.477
620.00791
630.319
640.383
650.119
660.085
670.424
680.683
690.788
70.505
700.0124
710.147
720.255
730.273
740.591
750.189
760.754
770.182
780.262
790.00823
80.226
800.0639
810.176
820.00834
830.844
840.303
857.20424e-4
860.179
870.585
880.4
890.133
90.183
900.0424
910.184
920.00524
930.387
940.126
950.501
960.0482
970.787
980.434
990.919



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: CNhs11861


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)
0000030 (glioblast)
0000055 (non-terminally differentiated cell)
0000095 (neuron associated cell)
0000123 (neuron associated cell (sensu Vertebrata))
0000125 (glial cell)
0000133 (neurectodermal cell)
0000219 (motile cell)
0000221 (ectodermal cell)
0000243 (glial cell (sensu Vertebrata))
0000255 (eukaryotic cell)
0000333 (migratory neural crest cell)
0000339 (glioblast (sensu Vertebrata))
0000548 (animal cell)
0002319 (neural cell)
0002321 (embryonic cell)
0002371 (somatic cell)

DOID: Disease
0050686 (organ system cancer)
14566 (disease of cellular proliferation)
162 (cancer)
3093 (nervous system cancer)
4 (disease)

UBERON: Anatomy
0000033 (head)
0000061 (anatomical structure)
0000073 (regional part of nervous system)
0000153 (anterior region of body)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000475 (organism subdivision)
0000480 (anatomical group)
0000481 (multi-tissue structure)
0000922 (embryo)
0000923 (germ layer)
0000924 (ectoderm)
0000955 (brain)
0001016 (nervous system)
0001017 (central nervous system)
0001062 (anatomical entity)
0002050 (embryonic structure)
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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