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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:0000126,CL:0000127,CL:0000128,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,CL:0002453
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000004,CL:0000012,CL:0000030,CL:0000055,CL:0000095,CL:0000123,CL:0000125,CL:0000126,CL:0000127,CL:0000128,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,CL:0002453
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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 16:42, 29 March 2012


Name:glioblastoma cell line:T98G
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
sexmale
age61
cell typeglioblast
cell lineT98G
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-penis-3.014979e-4
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-lymphoma0.61
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: CNhs11272

Jaspar motifP-value
MA0002.20.0191
MA0003.10.0185
MA0004.10.227
MA0006.10.973
MA0007.10.241
MA0009.10.543
MA0014.10.831
MA0017.10.0134
MA0018.20.267
MA0019.10.781
MA0024.12.05695e-7
MA0025.10.518
MA0027.10.669
MA0028.10.0036
MA0029.10.439
MA0030.10.661
MA0031.10.701
MA0035.20.205
MA0038.17.19311e-6
MA0039.20.849
MA0040.10.765
MA0041.10.192
MA0042.10.53
MA0043.10.434
MA0046.10.886
MA0047.20.35
MA0048.10.0437
MA0050.12.34039e-4
MA0051.10.00144
MA0052.10.048
MA0055.10.066
MA0057.10.612
MA0058.10.0488
MA0059.10.279
MA0060.12.70681e-16
MA0061.10.00609
MA0062.20.0238
MA0065.20.00485
MA0066.10.0728
MA0067.10.69
MA0068.10.208
MA0069.10.555
MA0070.10.168
MA0071.10.129
MA0072.10.26
MA0073.10.991
MA0074.10.319
MA0076.18.01862e-4
MA0077.10.165
MA0078.10.916
MA0079.20.973
MA0080.22.01526e-9
MA0081.10.396
MA0083.10.223
MA0084.10.32
MA0087.10.882
MA0088.10.371
MA0090.10.414
MA0091.10.178
MA0092.10.284
MA0093.10.199
MA0099.20.0469
MA0100.10.327
MA0101.10.172
MA0102.20.198
MA0103.11.20709e-4
MA0104.20.585
MA0105.10.00145
MA0106.10.589
MA0107.10.0405
MA0108.20.0109
MA0111.10.9
MA0112.20.00192
MA0113.10.0935
MA0114.10.266
MA0115.10.6
MA0116.10.00843
MA0117.10.247
MA0119.10.947
MA0122.10.136
MA0124.10.379
MA0125.10.439
MA0131.10.172
MA0135.10.173
MA0136.14.22339e-5
MA0137.20.515
MA0138.20.0183
MA0139.10.221
MA0140.10.931
MA0141.10.0432
MA0142.10.934
MA0143.10.955
MA0144.10.0151
MA0145.10.278
MA0146.10.484
MA0147.10.558
MA0148.10.341
MA0149.10.771
MA0150.10.35
MA0152.10.0336
MA0153.10.837
MA0154.10.0139
MA0155.10.03
MA0156.10.502
MA0157.10.789
MA0159.10.106
MA0160.10.0546
MA0162.10.347
MA0163.11.95228e-4
MA0164.10.503
MA0258.10.00973
MA0259.10.897



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: CNhs11272

Novel motifP-value
10.778
100.454
1000.397
1010.415
1020.551
1030.501
1040.761
1050.843
1060.00103
1070.178
1080.53
1090.205
110.594
1100.95
1110.707
1120.00902
1130.663
1140.361
1150.225
1160.392
1170.75
1180.939
1190.197
120.463
1200.829
1210.427
1220.598
1230.349
1240.472
1250.442
1260.289
1270.336
1284.95285e-4
1290.00215
130.782
1300.00326
1310.0995
1320.542
1330.294
1340.673
1350.201
1360.631
1370.255
1380.456
1390.00824
140.489
1400.796
1410.396
1420.802
1430.0677
1440.769
1450.106
1460.59
1470.874
1480.281
1490.169
150.49
1500.909
1510.153
1520.134
1530.237
1540.256
1550.00757
1560.811
1570.904
1580.149
1590.627
160.313
1600.0729
1610.701
1620.559
1630.495
1640.41
1650.605
1660.818
1670.83
1680.616
1690.16
170.236
180.266
190.608
20.178
200.78
210.967
220.365
230.123
240.549
250.464
260.572
270.205
280.898
290.66
30.605
300.876
310.145
320.056
330.377
340.305
350.344
360.333
370.257
380.264
390.752
40.611
400.273
410.143
420.723
430.0775
440.202
450.487
460.27
470.836
480.672
490.0843
50.508
500.841
510.216
520.178
530.956
540.376
550.51
560.701
570.595
580.354
590.0953
60.831
600.0676
610.464
620.0655
630.468
640.422
650.142
660.00416
670.533
680.455
690.423
70.449
700.0145
710.697
720.365
730.174
740.0277
750.48
760.848
770.285
780.194
790.415
80.429
800.381
810.315
820.0739
830.895
840.911
850.00116
860.379
870.374
880.319
890.0498
90.337
900.827
910.119
920.0204
930.334
940.983
950.278
960.233
970.82
980.0788
990.829



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: CNhs11272


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)
0000126 (macroglial cell)
0000127 (astrocyte)
0000128 (oligodendrocyte)
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)
0002453 (oligodendrocyte precursor 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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