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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 16:50, 29 March 2012


Name:serous adenocarcinoma cell line:JHOS-2
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueovary
dev stageNA
sexfemale
age45
cell typeunclassifiable
cell lineJHOS-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-penis0.0751
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-lymphoma0.24
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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: CNhs11746

Jaspar motifP-value
MA0002.25.49065e-4
MA0003.10.837
MA0004.10.101
MA0006.10.351
MA0007.10.398
MA0009.10.651
MA0014.10.125
MA0017.10.0614
MA0018.20.125
MA0019.10.741
MA0024.10.00247
MA0025.10.0911
MA0027.10.868
MA0028.10.04
MA0029.10.615
MA0030.10.0244
MA0031.10.608
MA0035.20.135
MA0038.10.18
MA0039.20.0141
MA0040.10.261
MA0041.10.717
MA0042.10.317
MA0043.10.351
MA0046.10.424
MA0047.20.591
MA0048.10.747
MA0050.10.437
MA0051.10.00473
MA0052.10.936
MA0055.10.256
MA0057.10.223
MA0058.10.0387
MA0059.10.0323
MA0060.12.15637e-4
MA0061.10.244
MA0062.20.237
MA0065.20.0272
MA0066.10.0677
MA0067.10.346
MA0068.10.931
MA0069.10.197
MA0070.10.664
MA0071.10.352
MA0072.10.764
MA0073.10.765
MA0074.10.751
MA0076.10.0551
MA0077.10.193
MA0078.10.317
MA0079.20.127
MA0080.22.04078e-7
MA0081.10.0267
MA0083.10.505
MA0084.10.619
MA0087.10.392
MA0088.10.0317
MA0090.11.91406e-4
MA0091.10.0104
MA0092.10.309
MA0093.10.102
MA0099.20.0749
MA0100.10.616
MA0101.10.776
MA0102.20.953
MA0103.19.78089e-4
MA0104.20.0273
MA0105.16.46911e-5
MA0106.10.243
MA0107.10.896
MA0108.20.0414
MA0111.10.635
MA0112.20.0189
MA0113.10.275
MA0114.10.105
MA0115.10.994
MA0116.18.95808e-6
MA0117.10.438
MA0119.10.225
MA0122.10.391
MA0124.10.27
MA0125.10.128
MA0131.10.344
MA0135.10.438
MA0136.10.00123
MA0137.20.336
MA0138.28.05668e-4
MA0139.10.94
MA0140.10.0565
MA0141.10.0303
MA0142.10.979
MA0143.10.563
MA0144.10.418
MA0145.10.809
MA0146.10.73
MA0147.10.0743
MA0148.10.492
MA0149.10.991
MA0150.10.0297
MA0152.10.899
MA0153.10.261
MA0154.19.97126e-4
MA0155.10.504
MA0156.10.0271
MA0157.10.489
MA0159.10.635
MA0160.10.26
MA0162.10.654
MA0163.16.14117e-6
MA0164.10.45
MA0258.10.00469
MA0259.10.17



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: CNhs11746

Novel motifP-value
10.103
100.351
1000.969
1010.297
1020.51
1030.101
1040.707
1050.622
1060.793
1070.586
1080.812
1090.564
110.0335
1100.13
1110.255
1120.169
1130.608
1140.033
1150.811
1160.469
1170.308
1180.813
1190.219
120.594
1200.496
1210.481
1220.671
1230.0933
1240.0201
1250.426
1260.962
1270.758
1280.187
1290.758
130.657
1300.702
1310.463
1320.51
1330.06
1340.326
1350.00478
1360.0109
1370.249
1380.0769
1390.00268
140.687
1400.109
1410.84
1420.614
1435.74488e-4
1440.253
1450.365
1460.998
1470.684
1480.0428
1490.103
150.196
1500.853
1510.406
1520.121
1530.298
1540.97
1550.548
1560.691
1570.579
1580.388
1590.968
160.648
1600.125
1610.177
1620.457
1630.44
1640.682
1650.993
1660.186
1670.335
1680.987
1690.313
170.424
180.047
190.11
20.626
200.22
210.861
220.381
230.194
240.896
250.589
260.898
270.341
280.705
290.868
30.0642
300.78
310.213
320.00535
330.607
340.23
350.0195
360.0145
370.739
380.569
390.827
40.42
400.377
410.051
420.265
430.136
440.757
450.82
460.13
470.15
480.223
490.0661
50.14
500.999
510.137
520.531
530.255
540.111
550.728
560.554
570.459
580.248
590.086
60.892
600.512
610.731
620.0472
630.485
640.173
650.179
660.974
670.7
685.87428e-4
690.962
70.463
700.147
710.368
720.49
730.87
740.0099
750.31
760.739
770.555
780.965
790.0216
80.0591
800.13
810.0782
820.00437
830.191
840.883
850.0175
860.194
870.14
880.549
890.343
90.143
900.244
910.131
920.214
930.49
940.0137
950.665
960.0728
970.942
980.144
990.446



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: CNhs11746


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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