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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 16:32, 29 March 2012


Name:astrocytoma cell line:TM-31
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 stage42 year old adult
sexfemale
age42
cell typeastrocyte
cell lineTM-31
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-0.0777
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-lymphoma0.422
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
C110-leukemia-chronic-Eosinophils-acute-Whole-CD34-Lymphatic0
C111-medulla-lung-trachea-testis-caudate-epididymis-throat0
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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: CNhs10742

Jaspar motifP-value
MA0002.20.135
MA0003.10.179
MA0004.10.26
MA0006.10.538
MA0007.10.193
MA0009.10.0689
MA0014.10.539
MA0017.10.00673
MA0018.20.319
MA0019.10.793
MA0024.12.22918e-4
MA0025.10.845
MA0027.10.733
MA0028.10.795
MA0029.10.982
MA0030.10.901
MA0031.10.2
MA0035.20.152
MA0038.10.0519
MA0039.20.0298
MA0040.10.555
MA0041.10.729
MA0042.10.704
MA0043.10.74
MA0046.10.583
MA0047.20.153
MA0048.10.512
MA0050.10.15
MA0051.10.385
MA0052.10.739
MA0055.10.407
MA0057.10.366
MA0058.10.201
MA0059.10.0485
MA0060.10.00153
MA0061.10.00248
MA0062.20.233
MA0065.20.00125
MA0066.10.262
MA0067.10.286
MA0068.10.739
MA0069.10.457
MA0070.10.16
MA0071.10.0537
MA0072.10.424
MA0073.10.252
MA0074.10.0458
MA0076.10.551
MA0077.10.0112
MA0078.10.0529
MA0079.20.339
MA0080.21.6453e-12
MA0081.10.0238
MA0083.10.895
MA0084.10.355
MA0087.10.0911
MA0088.10.219
MA0090.10.0067
MA0091.10.0134
MA0092.10.93
MA0093.10.309
MA0099.24.73133e-25
MA0100.10.787
MA0101.10.0053
MA0102.20.0137
MA0103.10.0125
MA0104.20.169
MA0105.10.00901
MA0106.10.15
MA0107.10.0235
MA0108.20.169
MA0111.10.852
MA0112.22.25956e-4
MA0113.10.0339
MA0114.10.0504
MA0115.10.571
MA0116.10.00218
MA0117.10.534
MA0119.10.828
MA0122.10.0751
MA0124.10.582
MA0125.10.67
MA0131.10.75
MA0135.10.694
MA0136.11.15367e-11
MA0137.20.179
MA0138.20.0894
MA0139.10.691
MA0140.10.534
MA0141.10.00236
MA0142.12.24202e-5
MA0143.10.00154
MA0144.10.0208
MA0145.10.483
MA0146.10.00684
MA0147.10.0854
MA0148.10.0804
MA0149.10.898
MA0150.10.222
MA0152.10.541
MA0153.10.383
MA0154.10.00632
MA0155.10.748
MA0156.11.2375e-6
MA0157.10.215
MA0159.10.028
MA0160.10.00286
MA0162.10.211
MA0163.15.7332e-5
MA0164.10.674
MA0258.10.0122
MA0259.10.229



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: CNhs10742

Novel motifP-value
10.169
100.133
1000.687
1010.412
1020.823
1030.7
1040.786
1050.624
1060.19
1070.211
1080.669
1090.0207
110.0754
1100.0437
1110.0448
1120.21
1130.0543
1140.00534
1150.0436
1160.372
1170.0449
1180.163
1190.175
120.0397
1200.332
1210.927
1220.811
1230.485
1240.216
1250.928
1260.613
1270.275
1280.225
1290.863
130.147
1300.229
1310.838
1320.462
1330.952
1340.414
1350.201
1360.845
1370.336
1380.852
1390.0548
140.836
1400.774
1410.0431
1420.695
1430.042
1440.934
1450.847
1460.831
1470.835
1480.168
1490.044
150.483
1500.912
1510.23
1520.421
1530.985
1540.969
1550.181
1560.211
1570.532
1580.992
1590.465
160.0588
1600.109
1610.453
1620.259
1630.666
1640.191
1650.792
1660.41
1670.291
1680.909
1690.018
170.0389
180.391
190.196
20.283
200.862
210.259
220.183
230.24
240.789
250.186
260.204
270.0945
280.248
290.15
30.0532
300.396
310.722
320.00133
330.833
340.672
350.663
360.894
370.151
380.0576
390.302
40.428
400.234
410.756
420.741
430.0918
440.00374
450.871
460.07
470.349
480.131
490.133
50.424
500.964
510.226
520.573
530.909
540.758
550.31
560.941
570.589
580.0873
590.0357
60.65
600.12
610.239
620.068
630.751
640.369
650.0454
660.274
670.425
680.403
690.475
70.352
700.172
710.0528
720.0395
730.107
740.201
750.149
760.356
770.148
780.674
790.0794
80.0455
800.456
810.439
820.249
830.784
840.496
850.159
860.707
870.911
880.963
890.0899
90.108
900.715
910.98
920.112
930.774
940.902
950.0182
960.684
970.936
980.13
990.421



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: CNhs10742


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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