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Revision as of 18:12, 27 November 2014


Name:teratocarcinoma cell line:PA-1
Species:Human (Homo sapiens)
Library ID:CNhs11890
Sample type:cell lines
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueovary
dev stageNA
sexfemale
age12
cell typeunclassifiable
cell linePA-1
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

CAGE Accession numbers
MethodSample accession id
CAGE  SAMD00005647
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11890 CAGE DRX008021 DRR008893
Accession ID Hg19

Library idBAMCTSS
CNhs11890 DRZ000318 DRZ001703
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-penis0.16
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-lymphoma0.567
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
C110-leukemia-chronic-Eosinophils-acute-Whole-CD34-Lymphatic0
C111-medulla-lung-trachea-testis-caudate-epididymis-throat0
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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



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: CNhs11890

Jaspar motifP-value
MA0002.20.00226
MA0003.10.12
MA0004.10.99
MA0006.10.592
MA0007.10.319
MA0009.10.948
MA0014.10.659
MA0017.10.291
MA0018.20.426
MA0019.10.478
MA0024.12.24369e-7
MA0025.10.975
MA0027.10.637
MA0028.10.104
MA0029.10.506
MA0030.10.076
MA0031.10.177
MA0035.20.348
MA0038.13.1162e-5
MA0039.20.162
MA0040.10.165
MA0041.10.0794
MA0042.10.215
MA0043.10.628
MA0046.10.0953
MA0047.20.11
MA0048.10.0842
MA0050.12.13725e-11
MA0051.11.23834e-8
MA0052.10.00307
MA0055.10.116
MA0057.10.254
MA0058.10.616
MA0059.10.837
MA0060.17.61703e-20
MA0061.19.91376e-4
MA0062.20.954
MA0065.20.769
MA0066.10.427
MA0067.10.151
MA0068.10.00442
MA0069.10.29
MA0070.10.0463
MA0071.10.629
MA0072.10.182
MA0073.10.433
MA0074.10.181
MA0076.10.128
MA0077.10.0245
MA0078.10.427
MA0079.20.175
MA0080.21.15891e-13
MA0081.10.0514
MA0083.10.034
MA0084.10.335
MA0087.10.459
MA0088.10.422
MA0090.10.775
MA0091.10.0528
MA0092.10.266
MA0093.10.927
MA0099.21.16523e-13
MA0100.10.291
MA0101.10.0527
MA0102.22.99949e-5
MA0103.10.426
MA0104.20.918
MA0105.13.97198e-4
MA0106.10.869
MA0107.10.00231
MA0108.20.621
MA0111.10.873
MA0112.22.1683e-5
MA0113.10.11
MA0114.10.954
MA0115.10.14
MA0116.10.00812
MA0117.10.833
MA0119.10.0619
MA0122.10.727
MA0124.10.331
MA0125.10.299
MA0131.10.317
MA0135.10.143
MA0136.12.16169e-12
MA0137.20.0395
MA0138.20.345
MA0139.10.952
MA0140.10.369
MA0141.10.371
MA0142.16.30811e-14
MA0143.16.05812e-6
MA0144.10.0074
MA0145.10.354
MA0146.10.55
MA0147.10.847
MA0148.10.114
MA0149.10.779
MA0150.10.00125
MA0152.10.415
MA0153.10.0191
MA0154.10.00384
MA0155.10.575
MA0156.19.05102e-8
MA0157.10.252
MA0159.10.0319
MA0160.10.295
MA0162.10.348
MA0163.10.00113
MA0164.10.67
MA0258.10.0226
MA0259.10.436



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: CNhs11890

Novel motifP-value
10.397
100.288
1000.644
1010.752
1020.671
1030.162
1040.56
1050.256
1060.0209
1070.752
1080.893
1090.166
110.269
1100.496
1110.827
1120.00405
1130.0748
1140.0693
1150.874
1160.863
1170.306
1180.851
1190.402
120.625
1200.632
1210.502
1220.427
1230.542
1240.735
1250.337
1260.675
1270.156
1280.324
1290.325
130.69
1300.151
1310.604
1320.945
1330.0776
1340.475
1350.0255
1360.0294
1370.126
1380.404
1390.04
140.738
1400.846
1410.696
1420.731
1430.184
1440.814
1450.748
1460.489
1470.288
1480.0128
1490.0226
150.303
1500.824
1510.11
1520.255
1530.254
1540.927
1550.913
1560.851
1570.826
1580.149
1590.396
160.292
1600.118
1610.42
1620.382
1630.464
1640.108
1650.297
1660.569
1670.884
1680.466
1690.0464
170.234
180.21
190.259
20.203
200.631
210.915
220.118
230.0206
240.573
250.355
260.975
270.0461
280.704
290.536
30.288
300.579
310.506
320.00963
330.86
340.33
350.431
360.128
370.154
380.296
390.515
40.33
400.302
410.245
420.86
430.157
440.999
450.359
460.185
470.896
480.67
490.293
50.403
500.878
510.634
520.455
530.787
540.552
550.0604
560.491
570.693
580.123
590.106
60.534
600.112
610.903
620.0658
630.212
640.586
650.0647
660.00561
670.306
680.389
690.709
70.837
700.0344
710.0535
720.325
730.098
740.633
750.519
760.576
770.0886
780.771
790.173
80.452
800.158
810.56
820.0143
830.916
840.785
850.0337
860.66
870.227
880.452
890.0242
90.0524
900.534
910.153
920.0158
930.879
940.156
950.445
960.178
970.826
980.647
990.909



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: CNhs11890


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

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

UBERON: Anatomy
0000468 (multi-cellular organism)
0000992 (female gonad)
0000991 (gonad)
0003134 (female reproductive organ)
0005156 (reproductive structure)
0000466 (immaterial anatomical entity)
0000062 (organ)
0004120 (mesoderm-derived structure)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000990 (reproductive system)
0002553 (anatomical cavity)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0003133 (reproductive organ)
0002323 (body cavity)
0000464 (anatomical space)
0004458 (body cavity or lining)
0010317 (germ layer / neural crest derived structure)
0003100 (female organism)
0000474 (female reproductive system)

FF: FANTOM5
0000102 (sample by type)
0000003 (cell line sample)
0000210 (human sample)
0000101 (sample by species)
0000001 (sample)
0100297 (carcinoma cell line sample)
0101120 (epithelial cell line sample)
0100977 (ovary cell line sample)
0100306 (teratocarcinoma cell line sample)
0100811 (ovary cancer cell line sample)
0101591 (PA-1 cell sample)

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
UBERON:0009117 (indifferent gonad)
UBERON:0002532 (epiblast (generic))
UBERON:0006603 (presumptive mesoderm)
UBERON:0005564 (gonad primordium)
UBERON:0010316 (germ layer / neural crest)

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