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{{f5samples
{{f5samples
|F5samples=
|ancestors_in_anatomy_facet=UBERON:0000061,UBERON:0000062,UBERON:0000079,UBERON:0000464,UBERON:0000465,UBERON:0000466,UBERON:0000467,UBERON:0000468,UBERON:0000473,UBERON:0000479,UBERON:0000480,UBERON:0000922,UBERON:0000923,UBERON:0000926,UBERON:0000990,UBERON:0000991,UBERON:0001048,UBERON:0001062,UBERON:0002050,UBERON:0002323,UBERON:0002532,UBERON:0002553,UBERON:0003101,UBERON:0003133,UBERON:0003135,UBERON:0004120,UBERON:0004176,UBERON:0004458,UBERON:0005156,UBERON:0005423,UBERON:0005564,UBERON:0009117,UBERON:0009196
|ancestors_in_anatomy_facet=UBERON:0000061,UBERON:0000062,UBERON:0000079,UBERON:0000464,UBERON:0000465,UBERON:0000466,UBERON:0000467,UBERON:0000468,UBERON:0000473,UBERON:0000479,UBERON:0000480,UBERON:0000922,UBERON:0000923,UBERON:0000926,UBERON:0000990,UBERON:0000991,UBERON:0001048,UBERON:0001062,UBERON:0002050,UBERON:0002323,UBERON:0002532,UBERON:0002553,UBERON:0003101,UBERON:0003133,UBERON:0003135,UBERON:0004120,UBERON:0004176,UBERON:0004458,UBERON:0005156,UBERON:0005423,UBERON:0005564,UBERON:0009117,UBERON:0009196
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000004,CL:0000012,CL:0000039,CL:0000063,CL:0000066,CL:0000144,CL:0000255,CL:0000548,CL:0000586
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000004,CL:0000012,CL:0000039,CL:0000063,CL:0000066,CL:0000144,CL:0000255,CL:0000548,CL:0000586
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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 16:49, 29 March 2012


Name:testicular germ cell embryonal carcinoma cell line:NEC8
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuetestis
dev stageNA
sexmale
age24
cell typeunclassifiable
cell lineNEC8
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-penis0.322
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-lymphoma0.561
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
C110-leukemia-chronic-Eosinophils-acute-Whole-CD34-Lymphatic0
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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: CNhs11726

Jaspar motifP-value
MA0002.20.00363
MA0003.10.187
MA0004.10.187
MA0006.10.986
MA0007.10.327
MA0009.10.553
MA0014.10.0872
MA0017.10.909
MA0018.20.566
MA0019.10.355
MA0024.19.77619e-5
MA0025.10.372
MA0027.10.992
MA0028.10.014
MA0029.10.21
MA0030.10.325
MA0031.10.567
MA0035.20.309
MA0038.10.00742
MA0039.22.39251e-4
MA0040.10.277
MA0041.10.0476
MA0042.10.223
MA0043.10.536
MA0046.10.203
MA0047.20.0979
MA0048.10.137
MA0050.19.10808e-11
MA0051.11.78301e-6
MA0052.19.93916e-4
MA0055.10.0016
MA0057.10.773
MA0058.10.206
MA0059.10.00583
MA0060.12.03859e-13
MA0061.10.00665
MA0062.20.403
MA0065.20.00831
MA0066.10.974
MA0067.10.121
MA0068.10.577
MA0069.10.882
MA0070.10.608
MA0071.10.289
MA0072.10.52
MA0073.10.368
MA0074.10.479
MA0076.10.0701
MA0077.10.233
MA0078.10.966
MA0079.20.542
MA0080.27.33439e-9
MA0081.10.0365
MA0083.12.2102e-4
MA0084.10.707
MA0087.10.721
MA0088.10.0801
MA0090.10.149
MA0091.10.056
MA0092.10.0368
MA0093.10.186
MA0099.24.50689e-14
MA0100.10.268
MA0101.10.0131
MA0102.20.00512
MA0103.10.00282
MA0104.20.00478
MA0105.10.738
MA0106.10.928
MA0107.14.96225e-4
MA0108.20.134
MA0111.10.691
MA0112.20.834
MA0113.10.0737
MA0114.10.0743
MA0115.10.00873
MA0116.10.452
MA0117.10.831
MA0119.10.0583
MA0122.10.486
MA0124.10.557
MA0125.10.772
MA0131.10.47
MA0135.10.488
MA0136.17.80505e-8
MA0137.20.0354
MA0138.20.567
MA0139.10.218
MA0140.10.405
MA0141.10.105
MA0142.12.12511e-12
MA0143.10.00284
MA0144.10.00692
MA0145.10.919
MA0146.10.345
MA0147.14.95369e-4
MA0148.10.213
MA0149.10.542
MA0150.17.45375e-4
MA0152.10.882
MA0153.10.271
MA0154.10.462
MA0155.10.914
MA0156.11.21435e-4
MA0157.10.286
MA0159.10.387
MA0160.10.925
MA0162.10.906
MA0163.10.424
MA0164.10.977
MA0258.10.511
MA0259.10.00239



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: CNhs11726

Novel motifP-value
10.859
100.669
1000.0865
1010.942
1020.331
1030.299
1040.408
1050.149
1060.0614
1070.397
1080.498
1090.776
110.918
1100.858
1110.949
1120.715
1130.0412
1140.878
1150.687
1160.657
1170.242
1180.544
1190.667
120.298
1200.581
1210.771
1220.418
1230.141
1240.31
1250.484
1260.385
1270.128
1280.479
1290.922
130.0108
1300.406
1310.554
1320.847
1330.0414
1340.0222
1350.0085
1360.0336
1370.919
1380.186
1390.513
140.407
1400.611
1410.856
1420.835
1430.375
1440.536
1450.541
1460.224
1470.661
1480.355
1490.0545
150.379
1500.931
1510.0522
1520.122
1530.907
1540.934
1550.361
1560.277
1570.839
1580.737
1590.773
160.737
1600.477
1610.476
1620.258
1630.458
1640.77
1650.961
1660.36
1670.248
1680.658
1690.227
170.848
180.595
190.401
20.218
200.439
210.458
220.18
230.0184
240.864
250.551
260.406
270.272
280.869
290.188
30.549
300.12
310.323
320.0187
330.251
340.347
350.768
360.249
370.821
380.762
390.541
40.222
400.0527
410.436
420.854
430.646
440.434
450.618
460.985
470.1
480.352
490.965
50.284
500.62
510.665
520.536
530.963
540.922
550.399
560.685
570.585
580.651
590.504
60.368
600.356
610.574
620.647
630.707
640.885
650.179
660.00228
670.639
680.275
690.216
70.402
700.201
710.969
720.858
730.283
740.804
750.534
760.259
770.197
780.118
790.471
80.591
800.027
810.421
820.444
830.123
840.965
850.301
860.877
870.093
880.588
890.025
90.0406
900.753
910.0933
920.0563
930.618
940.715
950.521
960.0628
970.638
980.794
990.89



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: CNhs11726


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)
0000039 (germ line cell)
0000066 (epithelial cell)
0000255 (eukaryotic cell)
0000548 (animal cell)
0000586 (germ cell)

DOID: Disease
0050687 (cell type cancer)
14566 (disease of cellular proliferation)
162 (cancer)
2994 (germ cell cancer)
305 (carcinoma)
3095 (germ cell and embryonal cancer)
4 (disease)

UBERON: Anatomy
0000061 (anatomical structure)
0000062 (organ)
0000079 (male reproductive system)
0000464 (anatomical space)
0000465 (material anatomical entity)
0000466 (immaterial anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000473 (testis)
0000479 (tissue)
0000480 (anatomical group)
0000922 (embryo)
0000923 (germ layer)
0000926 (mesoderm)
0000990 (reproductive system)
0000991 (gonad)
0001048 (primordium)
0001062 (anatomical entity)
0002050 (embryonic structure)
0002323 (body cavity)
0002532 (epiblast (generic))
0002553 (anatomical cavity)
0003101 (male organism)
0003133 (reproductive organ)
0003135 (male reproductive organ)
0004120 (mesoderm-derived structure)
0004176 (external genitalia)
0004458 (body cavity or lining)
0005156 (reproductive structure)
0005423 (developing anatomical structure)
0005564 (gonad primordium)
0009117 (indifferent gonad)
0009196 (indifferent external genitalia)

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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