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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:0100400,FF:0101555
|fonse_cell_line=FF:0100400,FF:0101555
|fonse_cell_line_closure=FF:0100400,FF:0101555
|fonse_cell_line_closure=FF:0100400,FF:0101555

Revision as of 16:40, 29 March 2012


Name:endometrial stromal sarcoma cell line:OMC-9
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 stage55 year old adult
sexfemale
age55
cell typeunclassifiable
cell lineOMC-9
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-penis0.0448
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-lymphoma0.245
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: CNhs11249

Jaspar motifP-value
MA0002.20.0936
MA0003.10.163
MA0004.10.358
MA0006.10.346
MA0007.10.96
MA0009.10.434
MA0014.10.0311
MA0017.10.793
MA0018.20.137
MA0019.10.146
MA0024.10.265
MA0025.10.841
MA0027.10.578
MA0028.13.04713e-6
MA0029.10.967
MA0030.10.0145
MA0031.10.372
MA0035.20.0721
MA0038.10.384
MA0039.20.008
MA0040.10.0543
MA0041.10.786
MA0042.10.14
MA0043.10.00538
MA0046.10.0472
MA0047.20.362
MA0048.10.00254
MA0050.10.0223
MA0051.10.199
MA0052.16.67663e-5
MA0055.10.00244
MA0057.10.297
MA0058.10.498
MA0059.10.506
MA0060.16.94267e-4
MA0061.10.115
MA0062.20.00108
MA0065.20.544
MA0066.10.377
MA0067.10.181
MA0068.10.0041
MA0069.10.849
MA0070.10.0575
MA0071.10.787
MA0072.10.926
MA0073.10.844
MA0074.10.968
MA0076.11.39387e-5
MA0077.10.521
MA0078.10.218
MA0079.20.628
MA0080.24.64974e-7
MA0081.10.0269
MA0083.10.618
MA0084.10.77
MA0087.10.183
MA0088.10.00833
MA0090.10.368
MA0091.10.0342
MA0092.10.454
MA0093.10.247
MA0099.20.885
MA0100.10.0974
MA0101.10.0836
MA0102.22.07564e-4
MA0103.10.517
MA0104.20.144
MA0105.10.739
MA0106.10.178
MA0107.10.058
MA0108.24.35043e-11
MA0111.10.511
MA0112.20.2
MA0113.10.0557
MA0114.10.319
MA0115.10.45
MA0116.10.787
MA0117.10.467
MA0119.10.168
MA0122.10.593
MA0124.10.579
MA0125.10.791
MA0131.10.543
MA0135.10.118
MA0136.13.79707e-5
MA0137.20.0154
MA0138.20.176
MA0139.10.00518
MA0140.10.197
MA0141.10.544
MA0142.10.237
MA0143.10.754
MA0144.10.0293
MA0145.10.932
MA0146.10.574
MA0147.10.0797
MA0148.10.8
MA0149.10.179
MA0150.10.251
MA0152.10.198
MA0153.10.473
MA0154.10.201
MA0155.10.189
MA0156.10.397
MA0157.10.196
MA0159.10.449
MA0160.10.573
MA0162.10.29
MA0163.10.906
MA0164.10.303
MA0258.10.484
MA0259.10.368



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: CNhs11249

Novel motifP-value
10.121
100.426
1000.583
1010.552
1020.911
1030.636
1040.67
1050.534
1060.0868
1070.538
1080.95
1090.698
110.59
1100.459
1110.026
1120.317
1130.202
1140.671
1150.377
1160.428
1170.0713
1180.835
1190.113
120.406
1200.12
1210.306
1220.225
1230.955
1240.317
1250.926
1260.0721
1270.591
1280.142
1290.366
130.0395
1300.921
1310.96
1320.621
1330.587
1340.103
1350.265
1360.778
1370.312
1380.502
1390.0288
140.84
1400.993
1410.188
1420.949
1430.593
1440.331
1450.315
1460.162
1470.984
1480.27
1490.473
150.684
1500.521
1510.157
1520.32
1530.303
1540.273
1550.696
1560.675
1570.541
1580.516
1590.882
160.898
1600.347
1610.162
1620.196
1630.784
1640.249
1650.985
1661
1670.0857
1680.244
1690.695
170.762
180.0241
190.969
20.00313
200.0524
210.0506
220.852
230.368
240.2
250.24
260.363
270.302
280.374
290.234
30.116
300.392
310.83
320.0143
330.749
340.287
350.77
360.296
370.393
380.764
390.826
40.341
400.899
410.0814
420.0828
430.754
440.426
450.327
460.451
470.35
480.231
490.908
50.619
500.962
510.985
520.0281
530.231
540.338
550.984
560.574
570.438
580.342
590.175
60.751
600.287
610.441
620.928
630.634
640.979
650.53
660.00127
670.301
680.0351
690.568
70.583
700.775
710.403
720.996
730.966
740.385
750.069
760.499
770.91
780.439
790.749
80.264
800.0627
810.29
820.332
830.385
840.588
850.152
860.914
870.387
880.817
890.0125
90.104
900.0334
910.558
920.38
930.596
940.955
950.859
960.17
970.711
980.549
990.427



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: CNhs11249


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)
1115 (sarcoma)
120 (female reproductive organ cancer)
14566 (disease of cellular proliferation)
162 (cancer)
193 (reproductive organ cancer)
3001 (female reproductive endometrioid cancer)
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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