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{{f5samples
{{f5samples
|F5samples=
|ancestors_in_anatomy_facet=
|ancestors_in_anatomy_facet=
|ancestors_in_cell_lineage_facet=
|ancestors_in_cell_lineage_facet=
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|creation_date=
|creation_date=
|def=
|def=
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|fonse_cell_line=FF:10695-109G2
|fonse_cell_line=FF:10695-109G2
|fonse_cell_line_closure=FF:10695-109G2
|fonse_cell_line_closure=FF:10695-109G2

Revision as of 16:55, 29 March 2012


Name:sacrococcigeal teratoma cell line:HTST
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueANATOMICAL SYSTEM
dev stageNA
sexmale
age2 months
cell typeunclassifiable
cell lineHTST
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-penis-0.0271
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-lymphoma-0.261
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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: CNhs11829

Jaspar motifP-value
MA0002.20.0435
MA0003.10.66
MA0004.10.111
MA0006.10.419
MA0007.10.577
MA0009.10.726
MA0014.10.141
MA0017.10.155
MA0018.21.75336e-4
MA0019.10.295
MA0024.10.0016
MA0025.10.0187
MA0027.10.679
MA0028.15.73368e-7
MA0029.10.942
MA0030.10.0255
MA0031.10.269
MA0035.20.789
MA0038.10.182
MA0039.23.64689e-4
MA0040.10.0193
MA0041.10.216
MA0042.10.0362
MA0043.10.0373
MA0046.10.336
MA0047.20.957
MA0048.10.8
MA0050.10.0812
MA0051.10.245
MA0052.10.826
MA0055.10.043
MA0057.10.611
MA0058.10.00958
MA0059.10.00838
MA0060.11.94852e-10
MA0061.10.335
MA0062.25.39183e-13
MA0065.20.0451
MA0066.10.271
MA0067.10.168
MA0068.11.39869e-5
MA0069.10.366
MA0070.10.379
MA0071.10.755
MA0072.10.74
MA0073.10.534
MA0074.10.206
MA0076.13.20503e-9
MA0077.10.944
MA0078.10.556
MA0079.20.881
MA0080.22.97623e-7
MA0081.16.55426e-4
MA0083.17.75371e-10
MA0084.10.893
MA0087.10.783
MA0088.10.05
MA0090.10.00375
MA0091.10.00513
MA0092.10.202
MA0093.10.0705
MA0099.20.0242
MA0100.10.173
MA0101.10.332
MA0102.20.492
MA0103.10.00174
MA0104.20.0023
MA0105.10.0374
MA0106.10.826
MA0107.10.457
MA0108.24.27438e-7
MA0111.10.46
MA0112.20.17
MA0113.10.661
MA0114.10.0602
MA0115.10.0106
MA0116.10.0125
MA0117.10.51
MA0119.10.166
MA0122.10.367
MA0124.10.966
MA0125.10.73
MA0131.10.367
MA0135.10.27
MA0136.12.87914e-12
MA0137.20.171
MA0138.20.923
MA0139.10.101
MA0140.10.94
MA0141.10.18
MA0142.10.706
MA0143.10.522
MA0144.10.684
MA0145.10.641
MA0146.10.197
MA0147.10.00239
MA0148.10.91
MA0149.10.237
MA0150.10.0569
MA0152.10.0737
MA0153.10.339
MA0154.10.192
MA0155.10.664
MA0156.14.23592e-12
MA0157.10.654
MA0159.10.0517
MA0160.10.561
MA0162.10.846
MA0163.10.0317
MA0164.10.975
MA0258.10.272
MA0259.10.0494



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: CNhs11829

Novel motifP-value
10.0554
100.0644
1000.377
1010.323
1020.00602
1030.843
1040.685
1050.894
1060.139
1070.0274
1080.286
1090.0217
110.393
1100.288
1110.0367
1120.325
1130.698
1140.366
1150.672
1160.241
1170.00862
1180.018
1190.695
120.417
1200.21
1210.0138
1220.161
1230.097
1240.75
1250.0107
1260.806
1270.387
1280.011
1290.104
130.0168
1300.548
1310.353
1320.603
1330.107
1340.176
1350.39
1360.255
1370.18
1380.92
1390.811
140.499
1400.402
1410.188
1420.683
1430.758
1440.363
1450.821
1460.614
1470.346
1480.54
1490.751
150.0897
1500.918
1510.979
1520.199
1530.413
1540.515
1550.0682
1560.644
1570.78
1580.127
1590.877
160.611
1600.629
1610.325
1620.218
1630.928
1640.867
1650.816
1660.00547
1670.2
1680.473
1690.792
170.964
180.328
190.563
20.558
200.409
210.361
220.852
230.0493
240.0729
250.0187
260.787
270.527
280.464
290.00398
30.553
300.169
310.592
327.27765e-6
330.0939
340.364
350.968
360.0195
370.212
380.301
390.325
40.735
400.0159
410.587
420.657
430.728
440.512
450.415
460.835
470.0674
480.0461
490.714
50.493
500.747
510.84
520.0962
530.444
540.466
550.168
560.978
570.417
580.513
590.502
60.227
600.61
610.279
620.713
630.895
640.459
650.503
660.372
670.51
680.241
690.935
70.0796
700.845
710.0792
720.558
730.415
740.279
750.0331
760.649
770.904
780.133
790.141
80.814
800.998
810.87
820.408
830.144
840.632
850.562
860.682
870.16
880.463
890.986
90.37
900.344
910.756
920.59
930.25
940.717
950.014
960.993
970.454
980.373
990.0909



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: CNhs11829


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

DOID: Disease
0050687 (cell type cancer)
14566 (disease of cellular proliferation)
162 (cancer)
2994 (germ cell cancer)
3095 (germ cell and embryonal cancer)
3307 (teratoma)
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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