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Revision as of 17:34, 27 November 2014


Name:testicular germ cell embryonal carcinoma cell line:NEC14
Species:Human (Homo sapiens)
Library ID:CNhs12351
Sample type:cell lines
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuetestis
dev stageNA
sexmale
age26
cell typeunclassifiable
cell lineNEC14
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

CAGE Accession numbers
MethodSample accession id
CAGE  SAMD00004817
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs12351 CAGE DRX008023 DRR008895
Accession ID Hg19

Library idBAMCTSS
CNhs12351 DRZ000320 DRZ001705
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-penis0.186
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-lymphoma0.454
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
C110-leukemia-chronic-Eosinophils-acute-Whole-CD34-Lymphatic0
C111-medulla-lung-trachea-testis-caudate-epididymis-throat0
C112-gastric-pancreas-temporal-duodenum-small-extraskeletal-adrenal0
C113-thyroid-throat-lung-lymph-small-colon-trachea0
C114-teratocarcinoma-medulloblastoma-carcinosarcoma-iPS-anaplastic-acute-neuroblastoma0
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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: CNhs12351

Jaspar motifP-value
MA0002.26.78226e-4
MA0003.10.415
MA0004.10.0743
MA0006.10.54
MA0007.10.901
MA0009.10.824
MA0014.10.412
MA0017.10.735
MA0018.20.024
MA0019.10.167
MA0024.19.12145e-5
MA0025.10.167
MA0027.10.483
MA0028.16.74185e-5
MA0029.10.987
MA0030.10.447
MA0031.10.472
MA0035.21
MA0038.16.62832e-4
MA0039.27.09783e-4
MA0040.10.792
MA0041.10.185
MA0042.10.658
MA0043.10.0421
MA0046.10.439
MA0047.20.451
MA0048.10.114
MA0050.15.00476e-15
MA0051.17.91281e-9
MA0052.10.0467
MA0055.10.0049
MA0057.10.466
MA0058.10.00949
MA0059.10.0389
MA0060.17.64175e-13
MA0061.10.0142
MA0062.20.00638
MA0065.20.115
MA0066.10.657
MA0067.10.699
MA0068.10.015
MA0069.10.75
MA0070.10.29
MA0071.10.304
MA0072.10.895
MA0073.10.696
MA0074.10.0549
MA0076.12.74889e-4
MA0077.10.0531
MA0078.10.6
MA0079.20.632
MA0080.21.653e-10
MA0081.10.0797
MA0083.10.00457
MA0084.10.38
MA0087.10.852
MA0088.10.149
MA0090.10.609
MA0091.10.00894
MA0092.10.0376
MA0093.10.0274
MA0099.23.50326e-8
MA0100.10.301
MA0101.10.128
MA0102.20.025
MA0103.17.80937e-4
MA0104.20.0289
MA0105.10.312
MA0106.10.575
MA0107.10.00987
MA0108.20.0995
MA0111.10.922
MA0112.20.0739
MA0113.10.0512
MA0114.10.285
MA0115.10.0777
MA0116.10.909
MA0117.10.651
MA0119.10.0571
MA0122.10.807
MA0124.10.958
MA0125.10.132
MA0131.10.288
MA0135.10.748
MA0136.13.65808e-7
MA0137.20.533
MA0138.20.403
MA0139.10.282
MA0140.10.411
MA0141.11
MA0142.16.29259e-24
MA0143.11.62707e-6
MA0144.10.0219
MA0145.10.718
MA0146.10.784
MA0147.10.0337
MA0148.10.447
MA0149.10.872
MA0150.10.0163
MA0152.10.981
MA0153.10.514
MA0154.10.743
MA0155.10.65
MA0156.10.00373
MA0157.10.0858
MA0159.10.898
MA0160.10.651
MA0162.10.933
MA0163.10.268
MA0164.10.646
MA0258.10.516
MA0259.10.073



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: CNhs12351

Novel motifP-value
10.558
100.526
1000.405
1010.658
1020.458
1030.0237
1040.258
1050.437
1060.00965
1070.203
1080.797
1090.467
110.467
1100.942
1110.212
1120.643
1130.0639
1140.0768
1150.442
1160.889
1170.969
1180.66
1190.533
120.756
1200.189
1210.576
1220.406
1230.382
1240.0924
1250.929
1260.833
1270.218
1280.448
1290.908
130.546
1300.7
1310.82
1320.751
1331.72092e-4
1340.0174
1350.015
1360.094
1370.529
1380.136
1390.358
140.853
1400.746
1410.83
1420.448
1430.00328
1440.277
1450.314
1460.278
1470.897
1480.0448
1490.00668
150.138
1500.379
1510.037
1520.1
1530.679
1540.441
1550.607
1560.0876
1570.548
1580.723
1590.987
160.384
1600.767
1610.879
1620.601
1630.884
1640.738
1650.997
1660.308
1670.344
1680.355
1690.281
170.682
180.878
190.182
20.369
200.939
210.736
220.209
230.00876
240.675
250.787
260.861
270.594
280.563
290.486
30.221
300.537
310.463
320.00413
330.534
340.591
350.831
360.742
370.407
380.829
390.365
40.866
400.293
410.294
420.84
430.231
440.769
450.602
460.614
470.0556
480.437
490.28
50.0557
500.67
510.897
520.527
530.832
540.479
550.535
560.88
570.694
580.0631
590.258
60.688
600.274
610.418
620.018
630.354
640.747
650.141
660.451
670.725
680.261
690.488
70.824
700.0346
710.177
720.619
730.0363
740.95
750.719
760.824
770.149
780.92
790.0779
80.0711
800.135
810.266
820.336
830.0196
840.907
850.178
860.806
870.206
880.586
890.0502
90.108
900.123
910.291
920.0612
930.277
940.515
950.677
960.0398
970.731
980.906
990.733



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: CNhs12351


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)
0000039 (germ line cell)
0000586 (germ 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)
0000922 (embryo)
0000473 (testis)
0000991 (gonad)
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)
0003135 (male reproductive organ)
0003133 (reproductive organ)
0002323 (body cavity)
0000464 (anatomical space)
0004458 (body cavity or lining)
0010317 (germ layer / neural crest derived structure)
0003101 (male organism)
0000079 (male 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)

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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