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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,FF:0101560
|fonse_cell_line=FF:0101120,FF:0101560
|fonse_cell_line_closure=FF:0101120,FF:0101560
|fonse_cell_line_closure=FF:0101120,FF:0101560

Revision as of 16:58, 29 March 2012


Name:testicular germ cell embryonal carcinoma cell line:ITO-II
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
ageunknown
cell typeunclassifiable
cell lineITO-II
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-penis0.0696
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-lymphoma0.46
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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: CNhs11876

Jaspar motifP-value
MA0002.20.00213
MA0003.10.808
MA0004.10.484
MA0006.10.126
MA0007.10.983
MA0009.10.76
MA0014.10.0752
MA0017.10.52
MA0018.20.0569
MA0019.10.218
MA0024.12.75422e-5
MA0025.10.299
MA0027.10.654
MA0028.10.0133
MA0029.10.55
MA0030.10.423
MA0031.10.291
MA0035.20.733
MA0038.10.0121
MA0039.20.00455
MA0040.10.695
MA0041.10.214
MA0042.10.485
MA0043.10.307
MA0046.10.935
MA0047.20.0854
MA0048.10.247
MA0050.11.25435e-8
MA0051.12.59534e-5
MA0052.10.0672
MA0055.10.0199
MA0057.10.907
MA0058.10.421
MA0059.10.841
MA0060.11.40345e-9
MA0061.13.84809e-4
MA0062.20.112
MA0065.20.442
MA0066.10.839
MA0067.10.368
MA0068.10.0148
MA0069.10.433
MA0070.10.835
MA0071.10.426
MA0072.10.824
MA0073.10.912
MA0074.10.175
MA0076.10.0478
MA0077.10.0902
MA0078.10.734
MA0079.20.385
MA0080.25.48466e-9
MA0081.10.0309
MA0083.10.364
MA0084.10.271
MA0087.10.866
MA0088.10.885
MA0090.10.264
MA0091.10.00635
MA0092.10.0497
MA0093.10.339
MA0099.23.48538e-5
MA0100.10.944
MA0101.10.0385
MA0102.20.0261
MA0103.13.31904e-4
MA0104.20.639
MA0105.14.41233e-6
MA0106.10.978
MA0107.10.00578
MA0108.29.24011e-5
MA0111.10.6
MA0112.20.0285
MA0113.10.0603
MA0114.10.552
MA0115.10.0807
MA0116.19.73271e-4
MA0117.10.745
MA0119.10.00149
MA0122.10.822
MA0124.10.881
MA0125.10.123
MA0131.10.566
MA0135.10.732
MA0136.16.1217e-7
MA0137.20.361
MA0138.20.192
MA0139.10.16
MA0140.10.438
MA0141.10.947
MA0142.16.36608e-24
MA0143.11.09778e-8
MA0144.10.13
MA0145.10.711
MA0146.10.386
MA0147.10.845
MA0148.10.114
MA0149.10.756
MA0150.10.0241
MA0152.10.655
MA0153.10.841
MA0154.10.0254
MA0155.10.998
MA0156.10.0022
MA0157.10.153
MA0159.10.526
MA0160.10.954
MA0162.10.791
MA0163.10.00145
MA0164.10.747
MA0258.10.545
MA0259.10.778



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: CNhs11876

Novel motifP-value
10.127
100.164
1000.501
1010.842
1020.225
1030.0113
1040.791
1050.334
1060.0783
1070.736
1080.469
1090.437
110.31
1100.128
1110.0432
1120.345
1130.101
1140.0252
1150.979
1160.83
1170.426
1180.596
1190.257
120.833
1200.318
1210.847
1220.988
1230.281
1240.101
1250.906
1260.616
1270.213
1280.667
1290.345
130.749
1300.765
1310.732
1320.499
1335.95488e-4
1340.168
1355.12793e-4
1360.0427
1370.451
1380.0534
1390.0889
140.909
1400.363
1410.575
1420.534
1430.00353
1440.52
1450.178
1460.311
1470.661
1480.0312
1490.00289
150.0895
1500.946
1510.0708
1520.347
1530.528
1540.805
1550.389
1560.0459
1570.749
1580.656
1590.339
160.335
1600.319
1610.242
1620.437
1630.515
1640.787
1650.693
1660.19
1670.361
1680.522
1690.209
170.72
180.55
190.0939
20.741
200.965
210.759
220.253
230.0312
240.556
250.645
260.662
270.616
280.808
290.504
30.0689
300.751
310.553
320.0121
330.887
340.712
350.246
360.599
370.417
380.59
390.509
40.85
400.755
410.301
420.403
430.0932
440.837
450.833
460.119
470.387
480.962
490.146
50.0814
500.488
510.972
520.87
530.402
540.809
550.109
560.993
570.861
580.0668
590.359
60.721
600.262
610.402
620.0249
630.243
640.538
650.191
660.571
670.733
680.277
690.34
70.899
700.0295
710.0355
720.519
730.695
740.0914
750.302
760.936
770.39
780.994
790.0528
80.116
800.0714
810.177
820.0776
830.0919
840.932
850.21
860.689
870.0212
880.149
890.112
90.107
900.26
910.202
920.129
930.314
940.465
950.509
960.0438
970.953
980.265
990.435



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: CNhs11876


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
0050686 (organ system cancer)
0050687 (cell type cancer)
14566 (disease of cellular proliferation)
162 (cancer)
193 (reproductive organ 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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