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{{f5samples
{{f5samples
|F5samples=
|ancestors_in_anatomy_facet=
|ancestors_in_anatomy_facet=
|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 16:58, 29 March 2012


Name:teratocarcinoma cell line:NCC-IT-A3
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuemediastinum
dev stageNA
sexmale
age24
cell typegerm cell
cell lineNCC-IT-A3
companyJAPAN HEALTH SCIENCES FOUNDATION - Health Science Research Resources Bank
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-penis0.325
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-lymphoma0.603
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: CNhs11878

Jaspar motifP-value
MA0002.23.09182e-4
MA0003.10.0849
MA0004.10.967
MA0006.10.884
MA0007.10.977
MA0009.10.615
MA0014.10.787
MA0017.10.16
MA0018.20.883
MA0019.10.435
MA0024.12.57259e-6
MA0025.10.26
MA0027.10.735
MA0028.14.21713e-5
MA0029.10.661
MA0030.10.145
MA0031.10.163
MA0035.20.861
MA0038.11.95481e-4
MA0039.20.0294
MA0040.10.208
MA0041.10.149
MA0042.10.424
MA0043.10.767
MA0046.10.191
MA0047.20.00813
MA0048.10.222
MA0050.13.13132e-8
MA0051.13.99188e-7
MA0052.10.00117
MA0055.10.0805
MA0057.10.441
MA0058.10.807
MA0059.10.997
MA0060.12.15902e-15
MA0061.10.00667
MA0062.28.07042e-4
MA0065.20.924
MA0066.10.493
MA0067.10.341
MA0068.10.00634
MA0069.10.44
MA0070.10.568
MA0071.10.692
MA0072.10.598
MA0073.10.536
MA0074.10.167
MA0076.12.31886e-5
MA0077.10.117
MA0078.10.75
MA0079.20.532
MA0080.24.96116e-11
MA0081.10.085
MA0083.13.01388e-4
MA0084.10.0955
MA0087.10.697
MA0088.10.215
MA0090.10.114
MA0091.10.0918
MA0092.10.12
MA0093.10.958
MA0099.21.97587e-16
MA0100.10.347
MA0101.10.0751
MA0102.20.00105
MA0103.10.715
MA0104.20.471
MA0105.10.0188
MA0106.10.142
MA0107.10.00706
MA0108.20.608
MA0111.10.731
MA0112.22.79118e-4
MA0113.10.0808
MA0114.10.78
MA0115.10.0923
MA0116.10.173
MA0117.10.915
MA0119.10.0415
MA0122.10.973
MA0124.10.417
MA0125.10.396
MA0131.10.166
MA0135.10.0531
MA0136.12.7811e-7
MA0137.20.266
MA0138.20.0624
MA0139.10.628
MA0140.10.789
MA0141.10.756
MA0142.15.2373e-18
MA0143.18.14698e-6
MA0144.10.0395
MA0145.10.295
MA0146.10.494
MA0147.10.344
MA0148.10.0525
MA0149.10.981
MA0150.10.00203
MA0152.10.708
MA0153.10.13
MA0154.10.043
MA0155.10.422
MA0156.10.00706
MA0157.10.208
MA0159.10.384
MA0160.10.337
MA0162.10.449
MA0163.10.0459
MA0164.10.934
MA0258.10.171
MA0259.10.201



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: CNhs11878

Novel motifP-value
10.46
100.631
1000.481
1010.955
1020.875
1030.0322
1040.592
1050.159
1060.00259
1070.19
1080.824
1090.264
110.384
1100.572
1110.648
1120.112
1130.0541
1140.184
1150.874
1160.893
1170.973
1180.73
1190.32
120.603
1200.596
1210.275
1220.687
1230.205
1240.548
1250.163
1260.463
1270.282
1280.216
1290.316
130.291
1300.121
1310.48
1320.732
1330.196
1340.41
1350.0143
1360.207
1370.478
1380.167
1390.0418
140.804
1400.609
1410.773
1420.817
1430.0535
1440.892
1450.302
1460.261
1470.879
1480.081
1490.0365
150.183
1500.586
1510.0839
1520.0349
1530.617
1540.908
1550.992
1560.274
1570.729
1580.376
1590.245
160.25
1600.212
1610.55
1620.862
1630.215
1640.322
1650.454
1660.729
1670.542
1680.21
1690.0124
170.196
180.168
190.163
20.12
200.656
210.819
220.107
230.0091
240.622
250.77
260.63
270.0869
280.715
290.956
30.518
300.331
310.605
320.0243
330.911
340.332
350.84
360.948
370.317
380.417
390.426
40.803
400.898
410.197
420.816
430.23
440.909
450.24
460.114
470.558
480.657
490.329
50.305
500.947
510.397
520.45
530.86
540.499
550.189
560.497
570.846
580.205
590.0676
60.475
600.0738
610.734
620.0999
630.208
640.583
650.0546
660.109
670.733
680.158
690.626
70.919
700.0192
710.146
720.424
730.0685
740.832
750.931
760.701
770.075
780.717
790.0227
80.278
800.0227
810.574
820.104
830.633
840.509
850.0212
860.587
870.519
880.42
890.0154
90.0419
900.72
910.513
920.032
930.384
940.281
950.399
960.197
970.761
980.927
990.986



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: CNhs11878


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
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)

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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