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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 16:42, 29 March 2012


Name:endometrial carcinoma cell line:OMC-2
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
age59
cell typeunclassifiable
cell lineOMC-2
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-penis0.109
C106-Hep2-epitheloid-placenta-cervical-rectal-anaplastic-glassy0
C107-Neutrophils-CD14-Eosinophils-Monocytederived-Whole-Peripheral-blood0
C108-breast-hepatoblastoma-MCF7-parotid-salivary-submaxillary-prostate0
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C91-Fibroblast-Smooth-mesenchymal-Mesothelial-Small-Preadipocyte-Hair0
C92-CD14CD16-CD14-Eosinophils-Basophils-Neutrophils-Macrophage-Whole0
C93-chronic-acute-leukemia-acantholytic-medulloblastoma-testis-papillotubular0
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: CNhs11266

Jaspar motifP-value
MA0002.20.0354
MA0003.10.894
MA0004.10.247
MA0006.10.59
MA0007.10.42
MA0009.10.455
MA0014.10.271
MA0017.10.0156
MA0018.20.0145
MA0019.10.998
MA0024.10.18
MA0025.10.159
MA0027.10.895
MA0028.17.06449e-8
MA0029.10.401
MA0030.10.932
MA0031.10.857
MA0035.20.445
MA0038.10.00183
MA0039.20.00629
MA0040.10.608
MA0041.10.268
MA0042.10.089
MA0043.10.418
MA0046.11.79216e-22
MA0047.20.889
MA0048.10.496
MA0050.10.405
MA0051.10.0214
MA0052.12.57389e-4
MA0055.10.00988
MA0057.10.87
MA0058.10.04
MA0059.10.00255
MA0060.16.59794e-5
MA0061.10.544
MA0062.21.31194e-7
MA0065.21.50982e-5
MA0066.10.619
MA0067.10.03
MA0068.10.288
MA0069.10.84
MA0070.10.521
MA0071.10.417
MA0072.10.854
MA0073.10.74
MA0074.10.637
MA0076.16.97788e-9
MA0077.10.146
MA0078.10.392
MA0079.20.525
MA0080.21.41494e-6
MA0081.10.0583
MA0083.10.533
MA0084.10.0379
MA0087.10.737
MA0088.10.145
MA0090.10.875
MA0091.10.00732
MA0092.10.581
MA0093.10.119
MA0099.20.98
MA0100.10.266
MA0101.10.273
MA0102.20.665
MA0103.11.23189e-7
MA0104.20.138
MA0105.10.0445
MA0106.10.54
MA0107.10.36
MA0108.22.62217e-6
MA0111.10.922
MA0112.20.159
MA0113.10.239
MA0114.16.96878e-5
MA0115.10.0017
MA0116.10.918
MA0117.10.0705
MA0119.10.296
MA0122.10.259
MA0124.10.48
MA0125.10.141
MA0131.10.243
MA0135.10.0469
MA0136.10.0136
MA0137.20.339
MA0138.20.259
MA0139.10.185
MA0140.10.212
MA0141.10.862
MA0142.10.183
MA0143.10.54
MA0144.10.867
MA0145.10.0442
MA0146.10.0771
MA0147.10.0784
MA0148.10.651
MA0149.10.73
MA0150.10.399
MA0152.10.495
MA0153.13.14106e-20
MA0154.10.381
MA0155.10.554
MA0156.10.933
MA0157.10.872
MA0159.10.0128
MA0160.10.548
MA0162.10.771
MA0163.10.747
MA0164.10.15
MA0258.10.215
MA0259.10.583



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: CNhs11266

Novel motifP-value
10.289
100.948
1000.103
1010.393
1020.397
1030.622
1040.77
1050.363
1060.982
1070.439
1080.934
1090.298
110.996
1100.233
1110.186
1120.844
1130.256
1140.93
1150.0652
1160.512
1170.011
1180.772
1190.875
120.244
1200.249
1210.617
1220.312
1230.751
1240.485
1250.169
1260.635
1270.221
1280.258
1290.228
130.0056
1300.852
1310.509
1320.539
1330.0125
1340.198
1350.00522
1360.07
1370.125
1380.457
1390.514
140.985
1400.0998
1410.274
1420.915
1430.00132
1440.382
1450.748
1460.777
1470.216
1480.735
1490.339
150.904
1500.572
1510.992
1520.169
1530.277
1540.0975
1550.915
1560.796
1570.487
1580.651
1590.318
160.631
1600.402
1610.338
1620.871
1630.996
1640.154
1650.475
1660.693
1670.87
1680.462
1690.0705
170.448
180.29
190.92
20.367
200.158
210.877
220.967
230.532
240.271
250.491
260.931
270.351
280.297
290.887
30.567
300.172
310.896
320.0807
330.227
340.883
350.971
360.489
370.137
380.582
390.84
40.995
400.383
410.00161
420.56
430.996
440.727
450.243
460.995
470.258
480.512
490.779
50.824
500.203
510.803
520.645
530.828
540.886
550.928
560.526
570.324
580.589
590.542
60.764
600.458
610.0411
620.236
630.453
640.966
650.69
660.263
670.403
680.043
690.395
70.781
700.851
710.183
720.912
730.46
740.148
750.0347
760.88
770.196
780.776
790.00252
80.505
800.229
810.0346
820.201
830.334
840.274
850.259
860.471
870.0192
880.0352
890.62
90.403
900.178
910.268
920.783
930.58
940.136
950.172
960.23
970.765
980.849
990.85



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: CNhs11266


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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