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{{f5samples
{{f5samples
|F5samples=
|ancestors_in_anatomy_facet=UBERON:0000014,UBERON:0000061,UBERON:0000062,UBERON:0000064,UBERON:0000465,UBERON:0000467,UBERON:0000468,UBERON:0000475,UBERON:0000480,UBERON:0001062,UBERON:0002097,UBERON:0002199,UBERON:0002416,UBERON:0003102
|ancestors_in_anatomy_facet=UBERON:0000014,UBERON:0000061,UBERON:0000062,UBERON:0000064,UBERON:0000465,UBERON:0000467,UBERON:0000468,UBERON:0000475,UBERON:0000480,UBERON:0001062,UBERON:0002097,UBERON:0002199,UBERON:0002416,UBERON:0003102
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000004,CL:0000012,CL:0000063,CL:0000066,CL:0000255,CL:0000548
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000004,CL:0000012,CL:0000063,CL:0000066,CL:0000255,CL:0000548
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|creation_date=
|creation_date=
|def=
|def=
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|fonse_cell_line=FF:0101120
|fonse_cell_line=FF:0101120
|fonse_cell_line_closure=FF:0101120
|fonse_cell_line_closure=FF:0101120

Revision as of 17:01, 29 March 2012


Name:basal cell carcinoma cell line:TE 354.T
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueskin
dev stageNA
sexfemale
ageNA
cell typeunclassifiable
cell lineTE 354.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-0.0648
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-0.281
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
C110-leukemia-chronic-Eosinophils-acute-Whole-CD34-Lymphatic0
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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: CNhs11932

Jaspar motifP-value
MA0002.20.899
MA0003.10.998
MA0004.10.0449
MA0006.10.357
MA0007.10.776
MA0009.10.532
MA0014.10.967
MA0017.10.348
MA0018.21.33778e-5
MA0019.10.381
MA0024.11.21e-5
MA0025.10.0137
MA0027.10.907
MA0028.16.05417e-4
MA0029.10.31
MA0030.10.0885
MA0031.10.239
MA0035.20.0059
MA0038.10.00103
MA0039.20.306
MA0040.10.358
MA0041.10.491
MA0042.10.444
MA0043.12.38145e-5
MA0046.10.102
MA0047.20.789
MA0048.10.0368
MA0050.16.42107e-4
MA0051.10.0573
MA0052.10.608
MA0055.10.505
MA0057.10.21
MA0058.10.00209
MA0059.10.737
MA0060.14.71058e-13
MA0061.10.4
MA0062.23.88123e-10
MA0065.20.618
MA0066.10.226
MA0067.10.0377
MA0068.10.245
MA0069.10.027
MA0070.10.813
MA0071.10.976
MA0072.10.97
MA0073.10.855
MA0074.10.987
MA0076.17.01667e-5
MA0077.10.4
MA0078.10.614
MA0079.20.589
MA0080.21.92747e-7
MA0081.10.00144
MA0083.13.68462e-4
MA0084.10.809
MA0087.10.593
MA0088.10.321
MA0090.11.8871e-4
MA0091.10.207
MA0092.10.03
MA0093.10.0212
MA0099.20.413
MA0100.10.428
MA0101.10.0291
MA0102.20.0442
MA0103.10.126
MA0104.20.00193
MA0105.10.754
MA0106.10.0105
MA0107.10.111
MA0108.20.897
MA0111.10.389
MA0112.20.00136
MA0113.10.413
MA0114.10.153
MA0115.10.108
MA0116.10.328
MA0117.10.74
MA0119.10.0927
MA0122.10.443
MA0124.10.648
MA0125.10.392
MA0131.10.151
MA0135.10.204
MA0136.11.26767e-10
MA0137.20.23
MA0138.20.809
MA0139.10.413
MA0140.10.217
MA0141.10.979
MA0142.10.608
MA0143.10.702
MA0144.10.736
MA0145.10.535
MA0146.10.294
MA0147.10.0655
MA0148.10.961
MA0149.10.882
MA0150.10.735
MA0152.10.0109
MA0153.10.416
MA0154.10.286
MA0155.10.592
MA0156.11.73012e-6
MA0157.10.969
MA0159.10.0291
MA0160.10.586
MA0162.10.0201
MA0163.10.0812
MA0164.10.942
MA0258.10.108
MA0259.10.929



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: CNhs11932

Novel motifP-value
10.521
100.847
1000.592
1010.776
1020.404
1030.248
1040.621
1050.104
1060.00751
1070.00916
1080.145
1090.999
110.476
1100.917
1110.506
1120.0488
1130.0557
1140.0903
1150.185
1160.138
1170.797
1180.944
1190.129
120.179
1200.29
1210.774
1220.352
1230.0508
1240.392
1250.371
1260.516
1270.401
1280.0868
1290.866
130.683
1300.414
1310.396
1320.211
1330.306
1340.681
1350.986
1360.49
1370.548
1380.84
1390.222
140.218
1400.776
1410.247
1420.533
1430.389
1440.72
1450.24
1460.343
1470.0922
1480.961
1490.00614
150.353
1500.178
1510.64
1520.0172
1530.321
1540.592
1550.128
1560.733
1570.429
1580.053
1590.271
160.0265
1600.944
1610.768
1620.597
1630.554
1640.224
1650.297
1660.0503
1670.411
1680.701
1690.105
170.367
180.0627
190.00655
20.677
200.773
210.182
220.306
230.0145
240.686
250.534
260.13
270.576
280.223
290.34
30.529
300.706
310.269
322.38343e-12
330.973
340.995
350.766
360.0229
370.0554
380.701
390.143
40.769
400.289
410.735
420.564
430.129
440.283
450.94
460.0685
470.774
480.889
490.492
50.303
500.869
510.931
520.505
530.238
540.551
550.255
560.942
570.348
580.763
590.0204
60.431
600.302
610.534
620.395
630.286
640.479
650.404
660.383
670.242
680.73
690.272
70.41
700.0399
710.357
720.624
730.00842
740.049
750.441
760.678
770.0236
780.895
790.0108
80.131
800.8
810.56
820.28
830.883
840.218
859.08655e-4
860.408
870.37
880.491
890.0294
90.929
900.343
910.531
920.0255
930.629
940.399
950.728
960.343
970.713
980.575
990.0654



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: CNhs11932


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)
0000066 (epithelial cell)
0000255 (eukaryotic cell)
0000548 (animal cell)

DOID: Disease
0050686 (organ system cancer)
0050687 (cell type cancer)
0060122 (integumentary system cancer)
14566 (disease of cellular proliferation)
162 (cancer)
2513 (basal cell carcinoma)
305 (carcinoma)
3451 (skin carcinoma)
4 (disease)
4159 (skin cancer)

UBERON: Anatomy
0000014 (zone of skin)
0000061 (anatomical structure)
0000062 (organ)
0000064 (organ part)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000475 (organism subdivision)
0000480 (anatomical group)
0001062 (anatomical entity)
0002097 (skin of body)
0002199 (integument)
0002416 (integumental system)
0003102 (surface 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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