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{{f5samples
{{f5samples
|F5samples=
|ancestors_in_anatomy_facet=UBERON:0000010,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:0002532,UBERON:0004121,UBERON:0005423
|ancestors_in_anatomy_facet=UBERON:0000010,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:0002532,UBERON:0004121,UBERON:0005423
|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,CL:0002573
|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,CL:0002573
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|creation_date=
|creation_date=
|def=
|def=
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|fonse_cell_line=FF:0103225
|fonse_cell_line=FF:0103225
|fonse_cell_line_closure=FF:0103225
|fonse_cell_line_closure=FF:0103225

Revision as of 16:57, 29 March 2012


Name:neurofibroma cell line:Hs 53.T
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueperipheral nervous system
dev stageNA
sexfemale
age13
cell typeschwann cell
cell lineHs 53.T
companyATCC
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-penis-0.0395
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-lymphoma-0.0198
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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: CNhs11854

Jaspar motifP-value
MA0002.20.122
MA0003.10.737
MA0004.10.0588
MA0006.10.312
MA0007.10.486
MA0009.10.102
MA0014.10.316
MA0017.10.115
MA0018.26.62905e-5
MA0019.10.188
MA0024.13.97016e-4
MA0025.10.00371
MA0027.10.954
MA0028.13.61516e-7
MA0029.10.223
MA0030.10.0232
MA0031.10.0565
MA0035.20.164
MA0038.19.7212e-4
MA0039.20.0541
MA0040.10.97
MA0041.10.443
MA0042.10.647
MA0043.19.5516e-5
MA0046.10.313
MA0047.20.383
MA0048.10.00899
MA0050.10.00402
MA0051.10.0342
MA0052.10.522
MA0055.10.905
MA0057.10.666
MA0058.12.45783e-4
MA0059.10.244
MA0060.13.86277e-9
MA0061.10.00243
MA0062.22.36215e-15
MA0065.20.0296
MA0066.10.964
MA0067.13.16146e-4
MA0068.10.0763
MA0069.10.485
MA0070.10.767
MA0071.10.974
MA0072.10.212
MA0073.10.708
MA0074.10.707
MA0076.14.2384e-9
MA0077.10.6
MA0078.10.847
MA0079.20.902
MA0080.22.88026e-9
MA0081.11.08785e-4
MA0083.18.79074e-6
MA0084.10.503
MA0087.10.922
MA0088.10.616
MA0090.12.18479e-7
MA0091.10.192
MA0092.10.0278
MA0093.10.0365
MA0099.20.0196
MA0100.10.576
MA0101.10.00106
MA0102.20.00667
MA0103.14.80022e-4
MA0104.20.00155
MA0105.19.51161e-4
MA0106.10.402
MA0107.10.00112
MA0108.20.108
MA0111.10.212
MA0112.20.882
MA0113.10.171
MA0114.10.0188
MA0115.10.0512
MA0116.10.058
MA0117.10.384
MA0119.10.0153
MA0122.10.0469
MA0124.10.583
MA0125.10.078
MA0131.10.905
MA0135.10.0692
MA0136.11.67555e-14
MA0137.20.0205
MA0138.20.597
MA0139.10.182
MA0140.10.933
MA0141.10.421
MA0142.10.32
MA0143.10.658
MA0144.10.606
MA0145.10.775
MA0146.10.58
MA0147.10.0375
MA0148.10.405
MA0149.10.989
MA0150.10.33
MA0152.10.00175
MA0153.10.528
MA0154.10.262
MA0155.10.775
MA0156.15.34919e-11
MA0157.10.325
MA0159.10.948
MA0160.10.0253
MA0162.10.197
MA0163.10.352
MA0164.10.997
MA0258.10.872
MA0259.10.661



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: CNhs11854

Novel motifP-value
10.723
100.245
1000.512
1010.35
1020.0571
1030.592
1040.697
1050.58
1060.0688
1070.0123
1080.125
1090.306
110.777
1100.675
1110.847
1120.395
1130.177
1140.329
1150.0937
1160.0207
1170.0894
1180.241
1190.279
120.338
1200.926
1210.929
1220.356
1230.64
1240.599
1250.806
1260.351
1270.413
1280.235
1290.14
130.214
1300.711
1310.821
1320.17
1330.358
1340.483
1350.658
1360.39
1370.136
1380.553
1390.355
140.265
1400.985
1410.588
1420.545
1430.956
1440.696
1450.756
1460.337
1470.0552
1480.0343
1490.0529
150.564
1500.133
1510.678
1520.0395
1530.433
1540.237
1550.0118
1560.379
1570.217
1580.00158
1590.158
160.0674
1600.774
1610.6
1620.243
1630.525
1640.471
1650.316
1660.0184
1670.737
1680.477
1690.346
170.539
180.0772
190.0772
20.507
200.47
210.104
220.703
230.0701
240.194
250.216
260.688
270.87
280.377
290.134
30.823
300.43
310.512
321.53443e-12
330.498
340.617
350.145
360.0277
370.962
380.453
390.207
40.748
400.0408
410.535
420.62
430.943
440.806
450.977
460.379
470.686
480.856
490.837
50.415
500.489
510.807
520.27
530.83
540.659
550.206
560.897
570.383
580.351
590.412
60.447
600.451
610.446
620.874
630.443
640.69
650.572
660.569
670.974
680.384
690.523
70.272
700.44
710.462
720.289
730.12
740.268
750.284
760.274
770.153
780.151
790.0143
80.127
800.285
810.73
820.67
830.292
840.926
850.0508
860.81
870.824
880.456
890.661
90.994
900.977
910.741
920.15
930.839
940.393
950.326
960.946
970.624
980.539
990.00513



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: CNhs11854


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)
0002573 (Schwann cell)

DOID: Disease
0050686 (organ system cancer)
1192 (peripheral nervous system neoplasm)
14566 (disease of cellular proliferation)
162 (cancer)
3093 (nervous system cancer)
3193 (peripheral nerve sheath neoplasm)
4 (disease)
962 (neurofibroma)

UBERON: Anatomy
0000010 (peripheral 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)
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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