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{{f5samples
{{f5samples
|F5samples=
|ancestors_in_anatomy_facet=
|ancestors_in_anatomy_facet=
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000004,CL:0000012,CL:0000063,CL:0000066,CL:0000255,CL:0000548
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000004,CL:0000012,CL:0000063,CL:0000066,CL:0000255,CL:0000548
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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 17:01, 29 March 2012


Name:clear cell carcinoma cell line:TEN
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueendometrium
dev stageNA
sexfemale
age74
cell typeunclassifiable
cell lineTEN
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-penis0.0179
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-lymphoma0.517
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
C110-leukemia-chronic-Eosinophils-acute-Whole-CD34-Lymphatic0
C111-medulla-lung-trachea-testis-caudate-epididymis-throat0.123
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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: CNhs11930

Jaspar motifP-value
MA0002.20.165
MA0003.10.621
MA0004.10.7
MA0006.10.71
MA0007.10.396
MA0009.10.825
MA0014.10.0955
MA0017.10.0988
MA0018.20.997
MA0019.10.975
MA0024.10.00104
MA0025.10.295
MA0027.10.872
MA0028.10.0226
MA0029.10.429
MA0030.10.129
MA0031.10.153
MA0035.20.985
MA0038.13.21793e-5
MA0039.20.0136
MA0040.10.77
MA0041.10.697
MA0042.10.224
MA0043.10.0186
MA0046.11.8487e-28
MA0047.20.333
MA0048.10.19
MA0050.10.824
MA0051.10.182
MA0052.10.115
MA0055.16.1916e-4
MA0057.10.657
MA0058.10.705
MA0059.10.303
MA0060.19.87019e-14
MA0061.10.107
MA0062.20.0994
MA0065.20.0331
MA0066.10.341
MA0067.10.426
MA0068.10.729
MA0069.10.0763
MA0070.10.874
MA0071.10.825
MA0072.10.477
MA0073.10.425
MA0074.10.67
MA0076.10.095
MA0077.12.12479e-4
MA0078.10.692
MA0079.20.247
MA0080.23.09976e-4
MA0081.10.0533
MA0083.13.32343e-4
MA0084.10.635
MA0087.10.0726
MA0088.10.248
MA0090.10.00102
MA0091.10.00323
MA0092.10.303
MA0093.10.6
MA0099.20.0254
MA0100.10.038
MA0101.10.0268
MA0102.20.00677
MA0103.17.89547e-8
MA0104.20.23
MA0105.10.209
MA0106.10.51
MA0107.10.0614
MA0108.20.872
MA0111.10.813
MA0112.20.21
MA0113.10.478
MA0114.10.0128
MA0115.10.197
MA0116.10.225
MA0117.10.734
MA0119.10.318
MA0122.10.0468
MA0124.10.628
MA0125.10.37
MA0131.10.855
MA0135.10.00246
MA0136.10.176
MA0137.20.195
MA0138.20.158
MA0139.10.00616
MA0140.10.901
MA0141.10.901
MA0142.10.267
MA0143.10.873
MA0144.10.676
MA0145.10.441
MA0146.10.963
MA0147.10.111
MA0148.10.0426
MA0149.10.0672
MA0150.10.635
MA0152.10.465
MA0153.12.29618e-17
MA0154.10.596
MA0155.10.431
MA0156.10.14
MA0157.10.439
MA0159.10.00286
MA0160.10.265
MA0162.10.455
MA0163.10.526
MA0164.10.368
MA0258.10.57
MA0259.10.439



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: CNhs11930

Novel motifP-value
10.19
100.141
1000.032
1010.857
1020.932
1030.578
1040.553
1050.98
1060.992
1070.98
1080.577
1090.0935
110.764
1100.169
1110.789
1120.557
1130.195
1140.602
1150.114
1160.649
1170.106
1180.148
1190.646
120.0498
1200.598
1210.95
1220.968
1230.514
1240.251
1250.829
1260.0537
1270.205
1280.0209
1290.168
131.01952e-4
1300.557
1310.17
1320.331
1330.133
1340.064
1350.0918
1360.0477
1370.467
1380.0253
1391.38749e-4
140.833
1400.556
1410.485
1420.911
1430.00201
1440.435
1450.451
1460.499
1470.913
1480.88
1490.302
150.434
1500.517
1510.8
1520.461
1530.998
1540.734
1550.884
1560.518
1570.267
1580.236
1590.338
160.401
1600.56
1610.947
1620.55
1630.917
1640.372
1650.676
1660.825
1670.158
1680.492
1690.583
170.606
180.0464
190.997
20.391
200.0784
210.34
220.892
230.547
240.204
250.551
260.0666
270.436
280.223
290.154
30.65
300.816
310.17
320.0185
330.00893
340.108
350.375
360.0886
370.713
380.838
390.53
40.476
400.0185
410.141
420.968
430.798
440.751
450.947
460.768
470.243
480.781
490.834
50.665
500.809
510.92
520.977
530.973
540.502
550.823
560.991
570.385
580.531
590.937
60.19
600.973
610.22
620.86
630.321
640.867
650.241
660.0105
670.938
681.0466e-5
690.586
70.121
700.312
710.0863
720.61
730.589
740.242
750.178
760.6
770.129
780.691
790.0302
80.688
800.103
810.537
820.034
830.92
840.869
850.0576
860.959
870.0565
880.86
890.798
90.194
900.398
910.0214
920.361
930.598
940.0353
950.163
960.715
970.897
980.665
990.537



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: CNhs11930


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)
0000066 (epithelial cell)
0000255 (eukaryotic cell)
0000548 (animal cell)

DOID: Disease
0050686 (organ system cancer)
0050687 (cell type cancer)
120 (female reproductive organ cancer)
14566 (disease of cellular proliferation)
162 (cancer)
193 (reproductive organ cancer)
299 (adenocarcinoma)
305 (carcinoma)
4 (disease)
4468 (clear cell adenocarcinoma)

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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