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{{f5samples
{{f5samples
|id=FF:10441-106E9
|F5samples=
|name=synovial sarcoma cell line:HS-SY-II
|ancestors_in_anatomy_facet=UBERON:0000042,UBERON:0000061,UBERON:0000062,UBERON:0000064,UBERON:0000119,UBERON:0000465,UBERON:0000467,UBERON:0000468,UBERON:0000477,UBERON:0000479,UBERON:0000480,UBERON:0000483,UBERON:0000486,UBERON:0000922,UBERON:0000923,UBERON:0000926,UBERON:0000982,UBERON:0001062,UBERON:0001434,UBERON:0002018,UBERON:0002050,UBERON:0002204,UBERON:0002217,UBERON:0002384,UBERON:0002532,UBERON:0004120,UBERON:0004457,UBERON:0004458,UBERON:0004765,UBERON:0004770,UBERON:0004905,UBERON:0004923,UBERON:0005423,UBERON:0006914,UBERON:0006915,UBERON:0007616
|sample_id=10441
|rna_tube_id=106E9
|rna_box=106
|rna_position=E9
|sample_cell_lot=
|sample_cell_catalog=RCB2231
|sample_company=RIKEN Bioresource centre
|rna_lot_number=
|rna_catalog_number=
|sample_species=Human (Homo sapiens)
|sample_strain=
|sample_dev_stage=
|sample_tissue=synovium
|sample_donor(cell lot)=
|sample_sex=unknown
|sample_age=
|sample_ethnicity=
|rna_rin=9.5
|rna_od260/230=0.76
|rna_od260/280=2.09
|sample_cell_type=unclassifiable
|sample_cell_line=HS-SY-II
|sample_collaboration=Yukio Nakamura (RIKEN BRC)
|sample_experimental_condition=
|sample_disease=synovial sarcoma
|rna_sample_type=total RNA
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0
|rna_weight_ug=20.71675
|rna_concentration=0.82867
|sample_note=
|profile_hcage=CNhs11244,LSID757,release008,COMPLETED
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|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:0000151,CL:0000153,CL:0000213,CL:0000214,CL:0000215,CL:0000219,CL:0000220,CL:0000222,CL:0000255,CL:0000327,CL:0000447,CL:0000499,CL:0000548,CL:0000723,CL:0002078,CL:0002320,CL:0002321,CL:0002371
|ancestors_in_anatomy_facet=UBERON:0000042,UBERON:0000061,UBERON:0000062,UBERON:0000064,UBERON:0000119,UBERON:0000465,UBERON:0000467,UBERON:0000468,UBERON:0000477,UBERON:0000479,UBERON:0000480,UBERON:0000483,UBERON:0000486,UBERON:0000922,UBERON:0000923,UBERON:0000926,UBERON:0000982,UBERON:0001062,UBERON:0001434,UBERON:0002018,UBERON:0002050,UBERON:0002204,UBERON:0002217,UBERON:0002384,UBERON:0002532,UBERON:0004120,UBERON:0004457,UBERON:0004458,UBERON:0004765,UBERON:0004770,UBERON:0004905,UBERON:0004923,UBERON:0005423,UBERON:0006914,UBERON:0006915,UBERON:0007616
|ancestors_in_disease_facet=DOID:0050687,DOID:1115,DOID:14566,DOID:162,DOID:4
|ancestors_in_disease_facet=DOID:0050687,DOID:1115,DOID:14566,DOID:162,DOID:4
|sample_description=
|comment=
|created_by=
|creation_date=
|def=
|fonse_cell_line=FF:0100400
|fonse_cell_line=FF:0100400
|fonse_cell_line_closure=FF:0100400
|fonse_cell_line_closure=FF:0100400
Line 66: Line 34:
|fonse_treatment=
|fonse_treatment=
|fonse_treatment_closure=
|fonse_treatment_closure=
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|comment=
|created_by=
|creation_date=
|def=
|has_quality=
|has_quality=
|id=FF:10441-106E9
|is_a=CL:0000214;;EFO:0002091;;FF:0000003;;FF:0000210;;FF:0100400
|is_a=CL:0000214;;EFO:0002091;;FF:0000003;;FF:0000210;;FF:0100400
|name=synovial sarcoma cell line:HS-SY-II
|namespace=FANTOM5
|namespace=FANTOM5
|part_of=
|part_of=
|profile_cagescan=NCig10066,,,
|profile_hcage=CNhs11244,LSID757,release008,COMPLETED
|profile_rnaseq=,,,
|profile_srnaseq=,,,
|rna_box=106
|rna_catalog_number=
|rna_concentration=0.82867
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0
|rna_lot_number=
|rna_od260/230=0.76
|rna_od260/280=2.09
|rna_position=E9
|rna_rin=9.5
|rna_sample_type=total RNA
|rna_tube_id=106E9
|rna_weight_ug=20.71675
|sample_age=
|sample_cell_catalog=RCB2231
|sample_cell_line=HS-SY-II
|sample_cell_lot=
|sample_cell_type=unclassifiable
|sample_collaboration=Yukio Nakamura (RIKEN BRC)
|sample_company=RIKEN Bioresource centre
|sample_description=
|sample_dev_stage=
|sample_disease=synovial sarcoma
|sample_donor(cell lot)=
|sample_ethnicity=
|sample_experimental_condition=
|sample_id=10441
|sample_note=
|sample_sex=unknown
|sample_species=Human (Homo sapiens)
|sample_strain=
|sample_tissue=synovium
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}}
}}

Revision as of 14:07, 21 March 2012


Name:synovial sarcoma cell line:HS-SY-II
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuesynovium
dev stageNA
sexunknown
ageNA
cell typeunclassifiable
cell lineHS-SY-II
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]





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
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C87-retinoblastoma-left-nonsmall-heart-small-diaphragm-bronchogenic0
C88-Melanocyte-melanoma-Macrophage-Mesenchymal-migratory-Dendritic-Monocytederived0
C89-small-retinoblastoma-medulloblastoma-iPS-acantholytic-eye-bronchogenic0
C9-skeletal-diaphragm-tongue-throat-penis-heart-left0
C90-neuroectodermal-peripheral-neuroepithelioma-neuroblastoma-carcinoid-parietal-putamen0
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: CNhs11244

Jaspar motifP-value
MA0002.21.11433e-5
MA0003.10.0719
MA0004.10.308
MA0006.10.296
MA0007.10.236
MA0009.10.815
MA0014.10.745
MA0017.10.00425
MA0018.20.229
MA0019.10.627
MA0024.14.8641e-4
MA0025.10.355
MA0027.10.681
MA0028.10.204
MA0029.10.632
MA0030.10.335
MA0031.10.662
MA0035.20.641
MA0038.10.00298
MA0039.20.297
MA0040.10.414
MA0041.10.197
MA0042.10.4
MA0043.10.95
MA0046.10.376
MA0047.20.199
MA0048.10.183
MA0050.11.11938e-6
MA0051.10.0019
MA0052.15.47995e-4
MA0055.10.0615
MA0057.10.0421
MA0058.10.273
MA0059.10.749
MA0060.18.21668e-12
MA0061.10.0112
MA0062.20.491
MA0065.20.00167
MA0066.10.0915
MA0067.10.909
MA0068.10.00102
MA0069.10.888
MA0070.10.506
MA0071.10.578
MA0072.10.559
MA0073.10.537
MA0074.10.456
MA0076.10.112
MA0077.10.544
MA0078.10.671
MA0079.20.142
MA0080.27.65858e-13
MA0081.10.124
MA0083.10.36
MA0084.10.795
MA0087.10.895
MA0088.10.919
MA0090.10.664
MA0091.10.201
MA0092.10.222
MA0093.10.242
MA0099.28.46623e-20
MA0100.10.31
MA0101.10.0813
MA0102.20.00777
MA0103.10.08
MA0104.20.159
MA0105.10.0173
MA0106.10.553
MA0107.10.0246
MA0108.20.102
MA0111.10.867
MA0112.27.39488e-5
MA0113.10.142
MA0114.10.039
MA0115.10.617
MA0116.10.0192
MA0117.10.591
MA0119.10.165
MA0122.10.35
MA0124.10.259
MA0125.10.0517
MA0131.10.179
MA0135.10.298
MA0136.13.66449e-9
MA0137.20.00846
MA0138.20.0427
MA0139.10.114
MA0140.10.398
MA0141.10.108
MA0142.10.59
MA0143.10.664
MA0144.10.00842
MA0145.10.0366
MA0146.10.0827
MA0147.10.255
MA0148.10.236
MA0149.10.0276
MA0150.17.66672e-5
MA0152.10.365
MA0153.10.214
MA0154.10.0243
MA0155.10.373
MA0156.13.85732e-4
MA0157.10.565
MA0159.10.00395
MA0160.10.0605
MA0162.10.22
MA0163.10.00429
MA0164.10.823
MA0258.10.00895
MA0259.10.199



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: CNhs11244

Novel motifP-value
10.2
100.283
1000.384
1010.701
1020.933
1030.0385
1040.582
1050.429
1060.00474
1070.0878
1080.356
1090.0641
110.0713
1100.381
1110.576
1120.0498
1130.727
1140.0267
1150.731
1160.912
1170.348
1180.308
1190.122
120.474
1200.7
1210.666
1220.364
1230.85
1240.835
1250.625
1260.795
1270.0826
1280.0419
1290.31
130.748
1300.0255
1310.0739
1320.591
1330.649
1340.924
1350.137
1360.976
1370.0778
1380.117
1390.025
140.242
1400.313
1410.31
1420.986
1430.00548
1440.902
1450.824
1460.278
1470.502
1480.00531
1490.0991
150.181
1500.702
1510.218
1520.0814
1530.515
1540.994
1550.985
1560.178
1570.936
1580.901
1590.161
160.206
1600.478
1610.467
1620.665
1630.129
1640.27
1650.504
1660.498
1670.713
1680.0217
1690.0106
170.212
180.142
190.155
20.106
200.393
210.512
220.103
230.0379
240.8
250.425
260.437
270.0935
280.66
290.638
30.285
300.491
310.422
320.0326
330.385
340.443
350.554
360.181
370.0628
380.373
390.624
40.655
400.181
410.078
420.827
430.154
440.272
450.308
460.187
470.473
480.323
490.284
50.264
500.723
510.471
520.186
530.51
540.462
550.0493
560.407
570.756
580.285
590.0282
60.572
600.0353
610.415
620.105
630.284
640.295
650.0934
660.203
670.971
680.133
690.417
70.511
709.67851e-4
710.21
720.238
730.091
740.124
750.151
760.818
770.223
780.802
790.245
80.31
800.0344
810.538
820.0108
830.288
840.874
850.00579
860.261
870.156
880.696
890.0227
90.182
900.415
910.444
920.0276
930.324
940.182
950.36
960.132
970.792
980.179
990.704



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: CNhs11244


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)
0000151 (secretory cell)
0000153 (GAG secreting cell)
0000213 (lining cell)
0000214 (synovial cell)
0000215 (barrier cell)
0000219 (motile cell)
0000222 (mesodermal cell)
0000255 (eukaryotic cell)
0000327 (extracellular matrix secreting cell)
0000447 (carbohydrate secreting cell)
0000499 (stromal cell)
0000548 (animal cell)
0000723 (somatic stem cell)
0002078 (meso-epithelial cell)
0002320 (connective tissue cell)
0002321 (embryonic cell)
0002371 (somatic cell)

DOID: Disease
0050687 (cell type cancer)
1115 (sarcoma)
14566 (disease of cellular proliferation)
162 (cancer)
4 (disease)

UBERON: Anatomy
0000042 (serous membrane)
0000061 (anatomical structure)
0000062 (organ)
0000064 (organ part)
0000119 (cell layer)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000477 (anatomical cluster)
0000479 (tissue)
0000480 (anatomical group)
0000483 (epithelium)
0000486 (multilaminar epithelium)
0000922 (embryo)
0000923 (germ layer)
0000926 (mesoderm)
0000982 (skeletal joint)
0001062 (anatomical entity)
0001434 (skeletal system)
0002018 (synovial membrane of synovial joint)
0002050 (embryonic structure)
0002204 (musculoskeletal system)
0002217 (synovial joint)
0002384 (connective tissue)
0002532 (epiblast (generic))
0004120 (mesoderm-derived structure)
0004457 (cavity lining)
0004458 (body cavity or lining)
0004765 (skeletal element)
0004770 (articular system)
0004905 (articulation)
0004923 (organ component layer)
0005423 (developing anatomical structure)
0006914 (squamous epithelium)
0006915 (stratified squamous epithelium)
0007616 (layer of synovial tissue)

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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