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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:15242A
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-v1.3
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-penis0.0691
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-0.361
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
C113-thyroid-throat-lung-lymph-small-colon-trachea0
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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: CNhs11723

Jaspar motifP-value
MA0002.20.528
MA0003.10.286
MA0004.10.764
MA0006.10.255
MA0007.10.139
MA0009.10.454
MA0014.10.882
MA0017.10.834
MA0018.23.99606e-6
MA0019.10.329
MA0024.11.10191e-7
MA0025.13.41601e-4
MA0027.10.67
MA0028.10.323
MA0029.10.918
MA0030.10.0451
MA0031.10.0866
MA0035.20.412
MA0038.10.00117
MA0039.20.512
MA0040.10.572
MA0041.10.563
MA0042.10.964
MA0043.19.78173e-8
MA0046.10.395
MA0047.20.605
MA0048.10.906
MA0050.12.91287e-4
MA0051.10.243
MA0052.10.194
MA0055.10.519
MA0057.10.0195
MA0058.10.592
MA0059.10.254
MA0060.14.47865e-11
MA0061.10.85
MA0062.20.00943
MA0065.20.0217
MA0066.10.0879
MA0067.10.0331
MA0068.10.337
MA0069.10.0828
MA0070.10.0147
MA0071.10.424
MA0072.10.695
MA0073.10.807
MA0074.10.219
MA0076.10.178
MA0077.10.245
MA0078.10.754
MA0079.20.554
MA0080.23.63632e-6
MA0081.10.077
MA0083.10.05
MA0084.10.531
MA0087.10.852
MA0088.10.804
MA0090.10.0961
MA0091.10.263
MA0092.10.289
MA0093.10.693
MA0099.20.0287
MA0100.10.0947
MA0101.10.0451
MA0102.20.00245
MA0103.10.899
MA0104.20.401
MA0105.10.0253
MA0106.10.0401
MA0107.10.0742
MA0108.20.854
MA0111.10.646
MA0112.22.27298e-4
MA0113.10.746
MA0114.10.47
MA0115.10.989
MA0116.10.0409
MA0117.10.958
MA0119.10.0428
MA0122.10.681
MA0124.17.58592e-4
MA0125.10.364
MA0131.10.492
MA0135.10.332
MA0136.11.01939e-6
MA0137.20.0561
MA0138.20.741
MA0139.10.195
MA0140.10.409
MA0141.10.277
MA0142.10.363
MA0143.10.346
MA0144.10.761
MA0145.10.0824
MA0146.10.178
MA0147.10.771
MA0148.10.594
MA0149.10.333
MA0150.10.352
MA0152.10.975
MA0153.10.928
MA0154.10.272
MA0155.10.223
MA0156.15.4302e-4
MA0157.10.501
MA0159.10.0627
MA0160.10.911
MA0162.10.0753
MA0163.15.63833e-4
MA0164.10.409
MA0258.10.0765
MA0259.10.934



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: CNhs11723

Novel motifP-value
10.0734
100.576
1000.799
1010.887
1020.966
1030.0222
1040.816
1050.114
1060.0767
1070.299
1080.251
1090.195
110.0448
1100.185
1110.655
1120.0283
1130.359
1140.0122
1150.0808
1160.0579
1170.268
1180.281
1190.197
120.776
1200.23
1210.731
1220.398
1230.0427
1240.564
1250.301
1260.924
1270.569
1280.229
1290.829
130.717
1300.617
1310.415
1320.926
1330.524
1340.303
1350.783
1360.771
1370.649
1380.809
1390.00804
140.609
1400.935
1410.71
1420.888
1430.03
1440.644
1450.363
1460.962
1470.0518
1480.0612
1490.0217
150.287
1500.511
1510.524
1520.0593
1530.877
1540.655
1550.162
1560.503
1570.974
1580.0846
1590.257
160.0188
1600.245
1610.609
1620.487
1630.277
1640.166
1650.683
1660.231
1670.849
1680.93
1690.00964
170.236
180.0599
190.0546
20.396
200.499
210.499
220.0903
230.174
240.465
250.632
260.503
270.153
280.721
290.189
30.146
300.619
310.189
328.11325e-5
330.949
340.792
350.236
360.352
370.0173
380.745
390.243
40.843
400.542
410.654
420.674
430.133
440.00535
450.555
460.0399
470.106
480.264
490.427
50.526
500.896
510.47
520.812
530.424
540.385
550.162
560.524
570.703
580.742
590.023
60.809
600.482
610.295
620.33
630.278
640.408
650.233
660.49
670.25
680.849
690.0585
70.734
700.00802
710.114
720.66
730.0149
740.454
750.163
760.881
770.0106
780.786
790.0157
80.0293
800.643
810.234
820.00962
830.748
840.505
850.0147
860.665
870.0635
880.897
890.00256
90.591
900.879
910.311
920.19
930.994
940.48
950.317
960.339
970.688
980.601
990.056



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: CNhs11723


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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