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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:10694-109G1
|fonse_cell_line=FF:10694-109G1
|fonse_cell_line_closure=FF:10694-109G1
|fonse_cell_line_closure=FF:10694-109G1

Revision as of 16:55, 29 March 2012


Name:tridermal teratoma cell line:HGRT
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
sexfemale
age3 months
cell typeunclassifiable
cell lineHGRT
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-0.118
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-lymphoma0.161
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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: CNhs11828

Jaspar motifP-value
MA0002.20.586
MA0003.10.332
MA0004.10.333
MA0006.10.416
MA0007.10.185
MA0009.10.502
MA0014.10.0249
MA0017.10.239
MA0018.20.00778
MA0019.10.308
MA0024.10.727
MA0025.10.192
MA0027.10.561
MA0028.18.16265e-11
MA0029.10.334
MA0030.10.277
MA0031.10.545
MA0035.20.511
MA0038.10.58
MA0039.20.00223
MA0040.10.714
MA0041.10.152
MA0042.10.0597
MA0043.10.00425
MA0046.10.0109
MA0047.20.33
MA0048.10.55
MA0050.15.30264e-5
MA0051.10.00352
MA0052.10.817
MA0055.10.313
MA0057.10.327
MA0058.10.0515
MA0059.10.0697
MA0060.10.052
MA0061.10.466
MA0062.22.33291e-18
MA0065.20.0627
MA0066.10.857
MA0067.10.091
MA0068.16.41662e-4
MA0069.10.378
MA0070.10.633
MA0071.10.838
MA0072.10.359
MA0073.10.419
MA0074.10.596
MA0076.12.02932e-11
MA0077.10.725
MA0078.10.0309
MA0079.20.418
MA0080.23.41199e-7
MA0081.10.00191
MA0083.10.00107
MA0084.10.018
MA0087.10.426
MA0088.10.0506
MA0090.16.34769e-5
MA0091.10.169
MA0092.10.236
MA0093.10.277
MA0099.20.202
MA0100.10.788
MA0101.10.385
MA0102.20.713
MA0103.10.00847
MA0104.20.0055
MA0105.10.261
MA0106.10.937
MA0107.10.634
MA0108.20.00603
MA0111.10.508
MA0112.20.139
MA0113.10.706
MA0114.10.052
MA0115.10.147
MA0116.10.0642
MA0117.10.437
MA0119.10.0314
MA0122.10.944
MA0124.10.651
MA0125.10.881
MA0131.10.0608
MA0135.10.328
MA0136.12.44345e-9
MA0137.20.298
MA0138.20.969
MA0139.10.00463
MA0140.10.798
MA0141.10.503
MA0142.10.0747
MA0143.10.231
MA0144.10.854
MA0145.10.731
MA0146.10.61
MA0147.10.0142
MA0148.10.315
MA0149.10.733
MA0150.10.69
MA0152.10.0107
MA0153.10.575
MA0154.10.132
MA0155.10.806
MA0156.15.48846e-9
MA0157.10.595
MA0159.10.222
MA0160.10.634
MA0162.10.807
MA0163.10.0346
MA0164.10.281
MA0258.10.282
MA0259.10.103



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: CNhs11828

Novel motifP-value
10.756
100.0685
1000.294
1010.685
1020.0298
1030.939
1040.499
1050.104
1060.277
1070.009
1080.5
1090.14
110.864
1100.696
1110.665
1120.0411
1130.485
1140.45
1150.618
1160.761
1170.0182
1180.19
1190.238
120.0473
1200.0576
1210.00773
1220.188
1230.705
1240.0367
1250.456
1260.93
1270.191
1280.0121
1290.307
130.0133
1300.381
1310.299
1320.523
1330.474
1340.401
1350.543
1360.0346
1370.173
1380.745
1390.815
140.717
1400.726
1410.121
1420.872
1430.633
1440.87
1450.819
1460.513
1470.0993
1480.14
1490.906
150.8
1500.596
1510.951
1520.912
1530.629
1540.744
1550.726
1560.453
1570.173
1580.809
1590.884
160.7
1600.696
1610.317
1620.0421
1630.423
1640.0904
1650.582
1660.129
1670.685
1680.841
1690.757
170.0492
180.193
190.515
20.434
200.272
210.559
220.382
230.00504
240.927
250.0593
260.537
270.993
280.471
290.00124
30.738
300.169
310.619
327.08089e-4
330.103
340.31
350.452
360.193
370.198
380.612
390.764
40.563
400.0508
410.653
420.845
430.885
440.0845
450.337
460.668
470.141
480.175
490.398
50.51
500.39
510.278
520.0697
530.979
540.232
550.14
560.422
570.462
580.575
590.394
60.345
600.597
610.511
620.889
630.517
640.826
650.223
660.848
670.915
680.584
690.665
70.078
700.719
710.0582
720.596
730.0981
740.166
750.0101
760.222
770.662
780.137
790.848
80.768
800.846
810.615
820.517
830.961
840.97
850.79
860.59
870.0212
880.143
890.406
90.142
900.398
910.837
920.134
930.822
940.0381
950.00464
960.307
970.166
980.465
990.0188



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: CNhs11828


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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