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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 16:59, 29 March 2012


Name:teratocarcinoma cell line:NCR-G1
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
ageembryo
cell typegerm cell
cell lineNCR-G1
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-penis0.286
C106-Hep2-epitheloid-placenta-cervical-rectal-anaplastic-glassy0
C107-Neutrophils-CD14-Eosinophils-Monocytederived-Whole-Peripheral-blood0
C108-breast-hepatoblastoma-MCF7-parotid-salivary-submaxillary-prostate0
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C90-neuroectodermal-peripheral-neuroepithelioma-neuroblastoma-carcinoid-parietal-putamen0
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: CNhs11884

Jaspar motifP-value
MA0002.28.0371e-5
MA0003.10.0603
MA0004.10.518
MA0006.10.366
MA0007.10.341
MA0009.10.286
MA0014.10.713
MA0017.10.106
MA0018.20.334
MA0019.10.435
MA0024.11.96866e-5
MA0025.10.777
MA0027.10.333
MA0028.15.01327e-5
MA0029.10.699
MA0030.10.278
MA0031.10.285
MA0035.20.0373
MA0038.12.49384e-4
MA0039.20.209
MA0040.10.669
MA0041.10.265
MA0042.10.637
MA0043.10.977
MA0046.10.219
MA0047.20.0807
MA0048.10.0293
MA0050.17.16955e-11
MA0051.12.23249e-8
MA0052.10.313
MA0055.10.0232
MA0057.10.256
MA0058.10.363
MA0059.10.172
MA0060.16.91175e-13
MA0061.10.00224
MA0062.23.77901e-4
MA0065.20.756
MA0066.10.472
MA0067.10.109
MA0068.13.93039e-7
MA0069.10.8
MA0070.10.0378
MA0071.10.633
MA0072.10.464
MA0073.10.731
MA0074.10.453
MA0076.14.57797e-6
MA0077.10.79
MA0078.10.148
MA0079.20.816
MA0080.21.50455e-11
MA0081.10.132
MA0083.10.487
MA0084.10.38
MA0087.10.638
MA0088.10.092
MA0090.10.999
MA0091.10.0172
MA0092.10.546
MA0093.10.565
MA0099.21.6098e-16
MA0100.10.476
MA0101.10.0569
MA0102.20.00289
MA0103.10.399
MA0104.20.364
MA0105.10.00465
MA0106.10.141
MA0107.10.0111
MA0108.20.666
MA0111.10.838
MA0112.21.56202e-5
MA0113.10.101
MA0114.10.688
MA0115.10.325
MA0116.10.0335
MA0117.10.263
MA0119.10.0671
MA0122.10.848
MA0124.10.811
MA0125.10.49
MA0131.10.281
MA0135.10.445
MA0136.11.44728e-7
MA0137.20.0443
MA0138.20.277
MA0139.10.399
MA0140.10.624
MA0141.10.146
MA0142.10.985
MA0143.10.721
MA0144.10.00421
MA0145.10.73
MA0146.10.786
MA0147.10.365
MA0148.10.0686
MA0149.10.259
MA0150.12.99277e-5
MA0152.10.395
MA0153.10.711
MA0154.10.0169
MA0155.10.888
MA0156.10.00363
MA0157.10.155
MA0159.19.85836e-4
MA0160.10.115
MA0162.10.949
MA0163.10.00202
MA0164.10.568
MA0258.10.0209
MA0259.10.365



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: CNhs11884

Novel motifP-value
10.149
100.239
1000.359
1010.797
1020.424
1030.0245
1040.422
1050.273
1060.16
1070.952
1080.969
1090.0473
110.0893
1100.963
1110.00149
1120.0516
1130.0717
1140.0281
1150.41
1160.888
1170.752
1180.475
1190.215
120.929
1200.765
1210.681
1220.887
1230.966
1240.547
1250.995
1260.59
1270.0503
1280.744
1290.296
130.472
1300.0217
1310.486
1320.656
1330.172
1340.764
1355.69805e-5
1360.209
1370.059
1380.178
1390.00534
140.947
1400.108
1410.177
1420.435
1430.00606
1440.892
1450.748
1460.495
1470.802
1480.0113
1490.0327
150.164
1500.824
1510.0354
1520.663
1530.485
1540.807
1550.596
1560.685
1570.915
1580.168
1590.417
160.375
1600.481
1610.397
1620.754
1630.289
1640.375
1650.219
1660.613
1670.202
1680.027
1690.0279
170.219
180.141
190.545
20.342
200.491
210.932
220.362
230.00959
240.659
250.119
260.959
270.0928
280.575
290.393
30.243
300.854
310.672
320.13
330.94
340.643
350.341
360.962
370.916
380.535
390.551
40.971
400.259
410.162
420.547
430.163
440.855
450.698
460.206
470.763
480.72
490.232
50.13
500.766
510.529
520.4
530.987
540.489
550.0145
560.829
570.978
580.0907
590.134
60.96
600.065
610.533
620.0471
630.163
640.228
650.119
660.367
670.484
680.558
690.621
70.48
700.00264
710.158
720.165
730.43
740.183
750.76
760.958
770.585
780.746
790.341
80.242
800.0663
810.164
820.0614
830.0881
840.985
850.00348
860.166
870.178
880.762
890.00537
90.275
900.272
910.145
920.0444
930.664
940.122
950.977
960.102
970.864
980.29
990.698



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: CNhs11884


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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