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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 17:17, 29 March 2012


Name:testicular germ cell embryonal carcinoma cell line:NEC15
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
age20
cell typeunclassifiable
cell lineNEC15
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-penis0.0598
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-lymphoma0.326
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
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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: CNhs12362

Jaspar motifP-value
MA0002.23.19636e-5
MA0003.10.689
MA0004.10.204
MA0006.10.316
MA0007.10.514
MA0009.10.597
MA0014.10.243
MA0017.10.417
MA0018.20.302
MA0019.10.941
MA0024.10.0109
MA0025.10.0846
MA0027.10.59
MA0028.10.0731
MA0029.10.685
MA0030.10.786
MA0031.10.827
MA0035.20.558
MA0038.10.0429
MA0039.20.00588
MA0040.10.932
MA0041.10.81
MA0042.10.982
MA0043.10.201
MA0046.10.952
MA0047.20.521
MA0048.10.895
MA0050.11.61403e-10
MA0051.11.41341e-5
MA0052.10.183
MA0055.10.179
MA0057.10.863
MA0058.10.0785
MA0059.10.832
MA0060.15.92974e-7
MA0061.10.00158
MA0062.20.123
MA0065.20.389
MA0066.10.598
MA0067.10.633
MA0068.10.0683
MA0069.10.685
MA0070.10.513
MA0071.10.591
MA0072.10.937
MA0073.10.794
MA0074.10.199
MA0076.10.0523
MA0077.10.357
MA0078.10.97
MA0079.20.165
MA0080.22.51938e-7
MA0081.10.0446
MA0083.10.0468
MA0084.10.645
MA0087.10.741
MA0088.10.905
MA0090.10.241
MA0091.10.0182
MA0092.10.0139
MA0093.10.101
MA0099.20.0019
MA0100.10.88
MA0101.10.135
MA0102.20.168
MA0103.10.00192
MA0104.20.754
MA0105.19.26985e-7
MA0106.10.0331
MA0107.10.0301
MA0108.20.00357
MA0111.10.735
MA0112.20.00279
MA0113.10.0572
MA0114.10.799
MA0115.10.23
MA0116.15.83719e-5
MA0117.10.998
MA0119.11.02452e-4
MA0122.10.761
MA0124.10.357
MA0125.10.206
MA0131.10.945
MA0135.10.282
MA0136.11.62921e-5
MA0137.20.336
MA0138.20.00954
MA0139.10.519
MA0140.10.338
MA0141.10.618
MA0142.11.92562e-20
MA0143.11.94415e-7
MA0144.10.478
MA0145.10.789
MA0146.10.964
MA0147.10.701
MA0148.10.621
MA0149.10.299
MA0150.10.0223
MA0152.10.939
MA0153.10.855
MA0154.10.055
MA0155.10.619
MA0156.10.0267
MA0157.10.286
MA0159.10.236
MA0160.10.91
MA0162.10.527
MA0163.13.41871e-7
MA0164.10.999
MA0258.10.26
MA0259.10.793



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: CNhs12362

Novel motifP-value
10.0827
100.0576
1000.749
1010.351
1020.408
1030.0222
1040.46
1050.622
1060.00432
1070.112
1080.876
1090.087
110.12
1100.1
1110.0104
1120.483
1130.143
1140.0184
1150.856
1160.319
1170.481
1180.995
1190.0508
120.993
1200.1
1210.923
1220.76
1230.613
1240.0148
1250.306
1260.839
1270.27
1280.189
1290.381
130.553
1300.983
1310.68
1320.897
1330.00303
1340.0734
1350.0604
1360.288
1370.565
1380.0498
1390.0843
140.929
1400.489
1410.42
1420.529
1436.61868e-4
1440.205
1450.0564
1460.214
1470.783
1485.23473e-4
1490.00262
150.0366
1500.383
1510.0701
1520.947
1530.791
1540.469
1550.395
1560.0161
1570.879
1580.594
1590.593
160.318
1600.18
1610.673
1620.767
1630.676
1640.804
1650.674
1660.35
1670.104
1680.564
1690.05
170.395
180.443
190.0663
20.835
200.892
210.55
220.476
230.21
240.799
250.578
260.234
270.973
280.495
290.467
30.048
300.921
310.723
329.69948e-4
330.473
340.747
350.194
360.144
370.395
380.608
390.248
40.998
400.489
410.318
420.293
430.111
440.49
450.759
460.113
470.984
480.601
490.0984
50.0541
500.599
510.8
520.766
530.987
540.836
550.269
560.92
570.54
580.072
590.278
60.91
600.119
610.637
620.0288
630.139
640.365
650.225
660.448
670.534
680.169
690.986
70.588
700.022
710.0166
720.305
730.299
740.728
750.349
760.972
770.294
780.828
790.19
80.0134
800.3
810.0995
820.0281
830.194
840.806
850.268
860.699
870.129
880.19
890.0547
90.156
900.0745
910.16
920.174
930.904
940.507
950.813
960.0241
970.685
980.265
990.695



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: CNhs12362


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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