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{{f5samples
{{f5samples
|F5samples=
|ancestors_in_anatomy_facet=UBERON:0000061,UBERON:0000062,UBERON:0000465,UBERON:0000467,UBERON:0000468,UBERON:0000474,UBERON:0000480,UBERON:0000922,UBERON:0000923,UBERON:0000926,UBERON:0000990,UBERON:0000995,UBERON:0001062,UBERON:0002050,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:0000480,UBERON:0000922,UBERON:0000923,UBERON:0000926,UBERON:0000990,UBERON:0000995,UBERON:0001062,UBERON:0002050,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
|ancestors_in_cell_lineage_facet=CL:0000000
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|creation_date=
|creation_date=
|def=
|def=
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|fonse_cell_line=FF:0102694
|fonse_cell_line=FF:0102694
|fonse_cell_line_closure=FF:0102694
|fonse_cell_line_closure=FF:0102694

Revision as of 16:49, 29 March 2012


Name:leiomyoma cell line:15425
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
ageNA
cell typesmooth muscle cell
cell lineNA
companyCoriell
collaborationNA
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-v1.2
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-penis0.122
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-0.0608
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: CNhs11724

Jaspar motifP-value
MA0002.20.797
MA0003.10.36
MA0004.10.415
MA0006.10.0829
MA0007.10.379
MA0009.10.762
MA0014.10.468
MA0017.10.763
MA0018.22.31418e-7
MA0019.10.39
MA0024.17.72143e-5
MA0025.14.066e-4
MA0027.10.795
MA0028.10.162
MA0029.10.444
MA0030.10.0134
MA0031.10.0441
MA0035.20.129
MA0038.10.0204
MA0039.20.0764
MA0040.10.939
MA0041.10.691
MA0042.10.832
MA0043.16.1377e-8
MA0046.10.302
MA0047.20.18
MA0048.10.651
MA0050.12.52663e-4
MA0051.10.0167
MA0052.10.0029
MA0055.10.142
MA0057.10.0559
MA0058.10.252
MA0059.10.999
MA0060.11.42354e-7
MA0061.10.684
MA0062.23.49812e-4
MA0065.20.369
MA0066.10.0976
MA0067.10.00173
MA0068.10.599
MA0069.10.126
MA0070.10.39
MA0071.10.87
MA0072.10.83
MA0073.10.947
MA0074.10.281
MA0076.10.185
MA0077.10.067
MA0078.10.592
MA0079.20.537
MA0080.21.36817e-6
MA0081.10.0574
MA0083.10.219
MA0084.10.544
MA0087.10.931
MA0088.10.846
MA0090.10.262
MA0091.10.664
MA0092.10.58
MA0093.10.378
MA0099.20.42
MA0100.10.405
MA0101.10.00237
MA0102.27.73373e-4
MA0103.10.221
MA0104.20.093
MA0105.10.0124
MA0106.10.0764
MA0107.10.00228
MA0108.20.0898
MA0111.10.519
MA0112.20.00171
MA0113.10.84
MA0114.10.691
MA0115.10.936
MA0116.10.0417
MA0117.10.806
MA0119.10.113
MA0122.10.849
MA0124.10.00124
MA0125.10.428
MA0131.10.357
MA0135.10.432
MA0136.14.2878e-9
MA0137.20.00307
MA0138.20.309
MA0139.10.197
MA0140.10.109
MA0141.10.409
MA0142.10.101
MA0143.10.358
MA0144.10.156
MA0145.10.115
MA0146.10.512
MA0147.10.24
MA0148.10.961
MA0149.10.959
MA0150.10.467
MA0152.10.886
MA0153.10.268
MA0154.10.569
MA0155.10.277
MA0156.14.11115e-6
MA0157.10.364
MA0159.10.225
MA0160.10.524
MA0162.10.125
MA0163.14.16385e-4
MA0164.10.557
MA0258.10.271
MA0259.10.425



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: CNhs11724

Novel motifP-value
10.212
100.384
1000.586
1010.628
1020.662
1030.0993
1040.927
1050.0723
1060.135
1070.0448
1080.289
1090.143
110.124
1100.199
1110.83
1120.193
1130.0314
1140.0723
1150.00422
1160.0652
1170.575
1180.415
1190.485
120.34
1200.052
1210.296
1220.149
1230.0179
1240.971
1250.0784
1260.942
1270.97
1280.191
1290.579
130.881
1300.468
1310.648
1320.661
1330.569
1340.295
1350.702
1360.276
1370.496
1380.668
1390.634
140.477
1400.585
1410.561
1420.794
1430.147
1440.298
1450.503
1460.382
1470.113
1480.15
1490.00105
150.858
1500.622
1510.826
1520.0909
1530.516
1540.584
1550.179
1560.712
1570.762
1580.00594
1590.158
160.00697
1600.553
1610.904
1620.465
1630.27
1640.355
1650.743
1660.118
1670.59
1680.68
1690.0114
170.388
180.121
190.0167
20.331
200.429
210.164
220.115
230.235
240.753
250.63
260.34
270.138
280.416
290.314
30.23
300.475
310.382
323.09885e-6
330.665
341
350.373
360.0197
370.0546
380.953
390.29
40.451
400.574
410.478
420.905
430.276
440.00573
450.746
460.0651
470.569
480.525
490.926
50.9
500.912
510.59
520.793
530.145
540.741
550.182
560.433
570.846
580.656
590.0242
60.852
600.56
610.762
620.758
630.491
640.485
650.411
660.607
670.341
680.325
690.187
70.363
700.115
710.101
720.934
730.0541
740.698
750.295
760.603
770.00559
780.637
798.63998e-4
80.0399
800.182
810.274
820.0675
830.564
840.567
850.14
860.482
870.0548
880.76
890.00762
90.331
900.522
910.463
920.0834
930.779
940.638
950.397
960.873
970.973
980.847
990.0126



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: CNhs11724


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)

DOID: Disease
0060072 (benign neoplasm)
0060084 (cell type benign neoplasm)
127 (leiomyoma)
14566 (disease of cellular proliferation)
4 (disease)

UBERON: Anatomy
0000061 (anatomical structure)
0000062 (organ)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000474 (female reproductive system)
0000480 (anatomical group)
0000922 (embryo)
0000923 (germ layer)
0000926 (mesoderm)
0000990 (reproductive system)
0000995 (uterus)
0001062 (anatomical entity)
0002050 (embryonic structure)
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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