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{{f5samples
{{f5samples
|F5samples=
|ancestors_in_anatomy_facet=UBERON:0000061,UBERON:0000062,UBERON:0000465,UBERON:0000467,UBERON:0000468,UBERON:0000474,UBERON:0000479,UBERON:0000480,UBERON:0000922,UBERON:0000923,UBERON:0000926,UBERON:0000990,UBERON:0000995,UBERON:0001062,UBERON:0002050,UBERON:0002384,UBERON:0002532,UBERON:0003100,UBERON:0003133,UBERON:0003134,UBERON:0003975,UBERON:0004120,UBERON:0004175,UBERON:0005156,UBERON:0005423,UBERON:0005795
|ancestors_in_anatomy_facet=UBERON:0000061,UBERON:0000062,UBERON:0000465,UBERON:0000467,UBERON:0000468,UBERON:0000474,UBERON:0000479,UBERON:0000480,UBERON:0000922,UBERON:0000923,UBERON:0000926,UBERON:0000990,UBERON:0000995,UBERON:0001062,UBERON:0002050,UBERON:0002384,UBERON:0002532,UBERON:0003100,UBERON:0003133,UBERON:0003134,UBERON:0003975,UBERON:0004120,UBERON:0004175,UBERON:0005156,UBERON:0005423,UBERON:0005795
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000004,CL:0000012,CL:0000034,CL:0000048,CL:0000063,CL:0000066,CL:0000134,CL:0000144,CL:0000219,CL:0000220,CL:0000223,CL:0000255,CL:0000499,CL:0000548,CL:0000723,CL:0002076,CL:0002149,CL:0002255,CL:0002320,CL:0002321,CL:0002371
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000004,CL:0000012,CL:0000034,CL:0000048,CL:0000063,CL:0000066,CL:0000134,CL:0000144,CL:0000219,CL:0000220,CL:0000223,CL:0000255,CL:0000499,CL:0000548,CL:0000723,CL:0002076,CL:0002149,CL:0002255,CL:0002320,CL:0002321,CL:0002371
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|creation_date=
|creation_date=
|def=
|def=
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|fonse_cell_line=FF:0101120,FF:0101555
|fonse_cell_line=FF:0101120,FF:0101555
|fonse_cell_line_closure=FF:0101120,FF:0101555
|fonse_cell_line_closure=FF:0101120,FF:0101555

Revision as of 16:51, 29 March 2012


Name:endometrioid adenocarcinoma cell line:JHUEM-1
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueuterus
dev stageNA
sexfemale
age56
cell typeunclassifiable
cell lineJHUEM-1
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-penis0.201
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-lymphoma0.185
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
C110-leukemia-chronic-Eosinophils-acute-Whole-CD34-Lymphatic0
C111-medulla-lung-trachea-testis-caudate-epididymis-throat0
C112-gastric-pancreas-temporal-duodenum-small-extraskeletal-adrenal0
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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: CNhs11748

Jaspar motifP-value
MA0002.20.285
MA0003.10.921
MA0004.10.158
MA0006.10.116
MA0007.10.206
MA0009.10.0984
MA0014.10.0565
MA0017.10.236
MA0018.20.00864
MA0019.10.8
MA0024.10.544
MA0025.10.718
MA0027.10.991
MA0028.10.158
MA0029.10.741
MA0030.10.286
MA0031.10.145
MA0035.20.621
MA0038.10.457
MA0039.26.86199e-4
MA0040.10.535
MA0041.10.858
MA0042.10.414
MA0043.10.00883
MA0046.10.817
MA0047.20.684
MA0048.10.913
MA0050.11.17834e-6
MA0051.13.50915e-4
MA0052.14.93576e-4
MA0055.10.00107
MA0057.10.3
MA0058.10.0304
MA0059.10.374
MA0060.11.14902e-5
MA0061.10.0197
MA0062.20.715
MA0065.20.014
MA0066.10.41
MA0067.10.00864
MA0068.12.62603e-6
MA0069.10.15
MA0070.10.837
MA0071.10.548
MA0072.10.807
MA0073.10.418
MA0074.10.957
MA0076.10.489
MA0077.10.158
MA0078.10.543
MA0079.20.349
MA0080.22.38813e-7
MA0081.10.0225
MA0083.10.179
MA0084.10.205
MA0087.10.44
MA0088.10.542
MA0090.10.00122
MA0091.10.105
MA0092.10.466
MA0093.10.114
MA0099.27.57555e-6
MA0100.10.503
MA0101.10.0095
MA0102.20.00872
MA0103.18.14226e-11
MA0104.20.259
MA0105.10.229
MA0106.10.0443
MA0107.10.00179
MA0108.20.133
MA0111.10.78
MA0112.20.0315
MA0113.10.756
MA0114.10.013
MA0115.10.135
MA0116.10.844
MA0117.10.218
MA0119.10.752
MA0122.10.122
MA0124.10.0507
MA0125.10.685
MA0131.10.783
MA0135.10.216
MA0136.11.38143e-5
MA0137.21.86253e-4
MA0138.20.811
MA0139.10.29
MA0140.10.756
MA0141.10.00281
MA0142.10.0693
MA0143.10.0546
MA0144.10.031
MA0145.10.0832
MA0146.10.0135
MA0147.10.499
MA0148.10.436
MA0149.10.0781
MA0150.10.00166
MA0152.10.169
MA0153.10.639
MA0154.10.934
MA0155.10.7
MA0156.11.65923e-4
MA0157.10.364
MA0159.10.0232
MA0160.10.162
MA0162.10.401
MA0163.10.688
MA0164.10.305
MA0258.10.176
MA0259.10.45



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: CNhs11748

Novel motifP-value
10.17
100.569
1000.0496
1010.307
1020.243
1030.128
1040.218
1050.987
1060.477
1070.755
1080.279
1090.00735
110.62
1100.0984
1110.72
1120.39
1130.0383
1140.652
1150.225
1160.863
1170.209
1180.391
1190.743
120.0431
1200.302
1210.254
1220.521
1230.0944
1240.614
1250.96
1260.571
1270.491
1280.194
1290.111
130.00997
1300.99
1310.329
1320.265
1330.186
1340.153
1350.168
1360.00373
1370.588
1380.396
1390.747
140.775
1400.444
1410.381
1420.926
1430.312
1440.559
1450.771
1460.927
1470.392
1480.405
1490.422
150.607
1500.782
1510.412
1520.33
1530.102
1540.396
1550.106
1560.94
1570.855
1580.284
1590.603
160.0843
1600.551
1610.532
1620.14
1630.512
1640.399
1650.835
1660.85
1670.472
1680.324
1690.0854
170.242
180.354
190.899
20.479
200.572
210.747
220.534
230.822
240.137
250.921
260.529
270.479
280.811
290.727
30.839
300.527
310.727
320.659
330.372
340.309
350.29
360.829
370.374
380.419
390.85
40.248
400.124
410.0833
420.734
430.883
440.00916
450.79
460.694
470.344
480.622
490.636
50.617
500.578
510.627
520.798
530.318
540.756
550.418
560.744
570.777
580.785
590.964
60.569
600.997
610.249
620.824
630.365
640.667
650.797
660.0224
670.87
680.0308
690.519
70.405
700.452
710.725
720.359
730.0755
740.375
750.125
760.772
770.179
780.125
790.383
80.381
800.00489
810.844
820.841
830.788
840.341
850.382
860.619
870.0434
880.353
890.0821
90.211
900.125
910.0889
920.534
930.442
940.345
950.0112
960.352
970.895
980.301
990.272



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: CNhs11748


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)
0000034 (stem cell)
0000048 (multi fate stem cell)
0000066 (epithelial cell)
0000134 (mesenchymal cell)
0000219 (motile cell)
0000223 (endodermal cell)
0000255 (eukaryotic cell)
0000499 (stromal cell)
0000548 (animal cell)
0000723 (somatic stem cell)
0002076 (endo-epithelial cell)
0002149 (epithelial cell of uterus)
0002255 (stromal cell of endometrium)
0002320 (connective tissue cell)
0002321 (embryonic cell)
0002371 (somatic 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)
3001 (female reproductive endometrioid cancer)
305 (carcinoma)
4 (disease)

UBERON: Anatomy
0000061 (anatomical structure)
0000062 (organ)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000474 (female reproductive system)
0000479 (tissue)
0000480 (anatomical group)
0000922 (embryo)
0000923 (germ layer)
0000926 (mesoderm)
0000990 (reproductive system)
0000995 (uterus)
0001062 (anatomical entity)
0002050 (embryonic structure)
0002384 (connective tissue)
0002532 (epiblast (generic))
0003100 (female organism)
0003133 (reproductive organ)
0003134 (female reproductive organ)
0003975 (internal female genitalia)
0004120 (mesoderm-derived structure)
0004175 (internal genitalia)
0005156 (reproductive structure)
0005423 (developing anatomical structure)
0005795 (embryonic uterus)

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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