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{{f5samples
{{f5samples
|id=FF:10706-109H4
|F5samples=
|name=pleomorphic hepatocellular carcinoma cell line:SNU-387
|ancestors_in_anatomy_facet=UBERON:0000015,UBERON:0000061,UBERON:0000062,UBERON:0000077,UBERON:0000465,UBERON:0000466,UBERON:0000467,UBERON:0000468,UBERON:0000475,UBERON:0000479,UBERON:0000480,UBERON:0000481,UBERON:0000916,UBERON:0000922,UBERON:0000923,UBERON:0000925,UBERON:0000926,UBERON:0000949,UBERON:0001007,UBERON:0001041,UBERON:0001048,UBERON:0001062,UBERON:0001555,UBERON:0002050,UBERON:0002100,UBERON:0002107,UBERON:0002330,UBERON:0002365,UBERON:0002368,UBERON:0002405,UBERON:0002417,UBERON:0002423,UBERON:0002530,UBERON:0002532,UBERON:0003104,UBERON:0003894,UBERON:0004119,UBERON:0004120,UBERON:0004161,UBERON:0004185,UBERON:0004921,UBERON:0005057,UBERON:0005172,UBERON:0005173,UBERON:0005177,UBERON:0005256,UBERON:0005423,UBERON:0006235,UBERON:0006925,UBERON:0007026,UBERON:0008835,UBERON:0008836,UBERON:0009142
|sample_id=10706
|rna_tube_id=109H4
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|rna_position=H4
|sample_cell_lot=
|sample_cell_catalog=CRL-2237
|sample_company=ATCC
|rna_lot_number=
|rna_catalog_number=
|sample_species=Human (Homo sapiens)
|sample_strain=
|sample_dev_stage=
|sample_tissue=liver
|sample_donor(cell lot)=
|sample_sex=female
|sample_age=41
|sample_ethnicity=K
|rna_rin=
|rna_od260/230=1.51
|rna_od260/280=2.02
|sample_cell_type=hepatocyte
|sample_cell_line=SNU-387
|sample_collaboration=FANTOM5 OSC CORE (contact: Al Forrest)
|sample_experimental_condition=
|sample_disease=pleomorphic hepatocellular carcinoma
|rna_sample_type=total RNA
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0
|rna_weight_ug=8.85546
|rna_concentration=0.32798
|sample_note=
|profile_hcage=CNhs11933,LSID835,release010,COMPLETED
|profile_cagescan=,,,
|profile_srnaseq=,,,
|profile_rnaseq=,,,
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000004,CL:0000012,CL:0000063,CL:0000066,CL:0000255,CL:0000548
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000004,CL:0000012,CL:0000063,CL:0000066,CL:0000255,CL:0000548
|ancestors_in_anatomy_facet=UBERON:0000015,UBERON:0000061,UBERON:0000062,UBERON:0000077,UBERON:0000465,UBERON:0000466,UBERON:0000467,UBERON:0000468,UBERON:0000475,UBERON:0000479,UBERON:0000480,UBERON:0000481,UBERON:0000916,UBERON:0000922,UBERON:0000923,UBERON:0000925,UBERON:0000926,UBERON:0000949,UBERON:0001007,UBERON:0001041,UBERON:0001048,UBERON:0001062,UBERON:0001555,UBERON:0002050,UBERON:0002100,UBERON:0002107,UBERON:0002330,UBERON:0002365,UBERON:0002368,UBERON:0002405,UBERON:0002417,UBERON:0002423,UBERON:0002530,UBERON:0002532,UBERON:0003104,UBERON:0003894,UBERON:0004119,UBERON:0004120,UBERON:0004161,UBERON:0004185,UBERON:0004921,UBERON:0005057,UBERON:0005172,UBERON:0005173,UBERON:0005177,UBERON:0005256,UBERON:0005423,UBERON:0006235,UBERON:0006925,UBERON:0007026,UBERON:0008835,UBERON:0008836,UBERON:0009142
|ancestors_in_disease_facet=DOID:0050687,DOID:14566,DOID:162,DOID:305,DOID:4,DOID:5662,DOID:7
|ancestors_in_disease_facet=DOID:0050687,DOID:14566,DOID:162,DOID:305,DOID:4,DOID:5662,DOID:7
|sample_description=
|comment=
|created_by=
|creation_date=
|def=
|fonse_cell_line=FF:0100224,FF:0101120
|fonse_cell_line=FF:0100224,FF:0101120
|fonse_cell_line_closure=FF:0100224,FF:0101120
|fonse_cell_line_closure=FF:0100224,FF:0101120
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:10706-109H4
|is_a=DOID:5662;;EFO:0002091;;FF:0000003;;FF:0000210;;FF:0103191
|is_a=DOID:5662;;EFO:0002091;;FF:0000003;;FF:0000210;;FF:0103191
|name=pleomorphic hepatocellular carcinoma cell line:SNU-387
|namespace=FANTOM5
|namespace=FANTOM5
|part_of=
|part_of=
|profile_cagescan=,,,
|profile_hcage=CNhs11933,LSID835,release010,COMPLETED
|profile_rnaseq=,,,
|profile_srnaseq=,,,
|rna_box=109
|rna_catalog_number=
|rna_concentration=0.32798
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0
|rna_lot_number=
|rna_od260/230=1.51
|rna_od260/280=2.02
|rna_position=H4
|rna_rin=
|rna_sample_type=total RNA
|rna_tube_id=109H4
|rna_weight_ug=8.85546
|sample_age=41
|sample_cell_catalog=CRL-2237
|sample_cell_line=SNU-387
|sample_cell_lot=
|sample_cell_type=hepatocyte
|sample_collaboration=FANTOM5 OSC CORE (contact: Al Forrest)
|sample_company=ATCC
|sample_description=
|sample_dev_stage=
|sample_disease=pleomorphic hepatocellular carcinoma
|sample_donor(cell lot)=
|sample_ethnicity=K
|sample_experimental_condition=
|sample_id=10706
|sample_note=
|sample_sex=female
|sample_species=Human (Homo sapiens)
|sample_strain=
|sample_tissue=liver
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}}
}}

Revision as of 14:13, 21 March 2012


Name:pleomorphic hepatocellular carcinoma cell line:SNU-387
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueliver
dev stageNA
sexfemale
age41
cell typehepatocyte
cell lineSNU-387
companyATCC
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
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
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C83-choriocarcinoma-pancreatic-placenta-chorionic-HES3GFP-testicular-amniotic0
C84-choriocarcinoma-pancreatic-Wilms-Mallassezderived-thymus-salivary-colon0
C85-neuroblastoma-carcinoid-retinoblastoma-small-pineal-rhabdomyosarcoma-medulloblastoma0
C86-colon-carcinoid-small-neuroectodermal-giant-large-neuroepithelioma0
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: CNhs11933

Jaspar motifP-value
MA0002.20.401
MA0003.10.423
MA0004.10.00423
MA0006.10.25
MA0007.10.952
MA0009.10.705
MA0014.10.175
MA0017.10.336
MA0018.20.374
MA0019.10.385
MA0024.10.0854
MA0025.10.679
MA0027.10.489
MA0028.10.427
MA0029.10.297
MA0030.10.0942
MA0031.14.2151e-5
MA0035.20.0186
MA0038.10.211
MA0039.20.221
MA0040.10.812
MA0041.10.648
MA0042.10.769
MA0043.10.801
MA0046.10.768
MA0047.20.00967
MA0048.10.386
MA0050.10.0105
MA0051.10.0092
MA0052.10.0999
MA0055.10.229
MA0057.10.192
MA0058.14.54691e-4
MA0059.13.49286e-4
MA0060.10.0478
MA0061.10.213
MA0062.20.023
MA0065.20.275
MA0066.10.59
MA0067.10.631
MA0068.10.519
MA0069.10.814
MA0070.10.559
MA0071.10.399
MA0072.10.276
MA0073.10.497
MA0074.10.659
MA0076.10.28
MA0077.10.00451
MA0078.10.65
MA0079.20.119
MA0080.21.16455e-6
MA0081.10.0196
MA0083.10.722
MA0084.10.0292
MA0087.10.0184
MA0088.10.229
MA0090.10.00515
MA0091.10.828
MA0092.10.224
MA0093.10.00246
MA0099.21.08544e-7
MA0100.10.0153
MA0101.10.958
MA0102.20.479
MA0103.12.21077e-4
MA0104.20.0018
MA0105.10.0842
MA0106.10.593
MA0107.10.841
MA0108.20.0141
MA0111.10.676
MA0112.20.0464
MA0113.10.509
MA0114.10.761
MA0115.10.237
MA0116.10.0206
MA0117.10.206
MA0119.10.0157
MA0122.10.3
MA0124.10.209
MA0125.10.995
MA0131.10.534
MA0135.10.0232
MA0136.14.41268e-4
MA0137.20.774
MA0138.20.702
MA0139.10.467
MA0140.10.548
MA0141.10.118
MA0142.10.98
MA0143.10.165
MA0144.10.481
MA0145.10.904
MA0146.10.366
MA0147.11.03566e-4
MA0148.10.0218
MA0149.10.579
MA0150.10.0205
MA0152.14.8391e-4
MA0153.10.0839
MA0154.10.00751
MA0155.10.171
MA0156.10.0752
MA0157.16.53683e-4
MA0159.10.248
MA0160.10.266
MA0162.10.248
MA0163.10.00414
MA0164.10.956
MA0258.10.46
MA0259.10.0366



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: CNhs11933

Novel motifP-value
10.858
100.117
1000.238
1010.58
1020.363
1030.259
1040.72
1050.404
1060.253
1070.315
1080.139
1090.887
110.364
1100.854
1110.456
1120.108
1130.172
1140.149
1150.442
1160.642
1170.646
1180.774
1190.839
120.418
1200.684
1210.276
1220.228
1230.566
1240.112
1250.718
1260.162
1270.643
1280.4
1290.92
130.491
1300.345
1310.809
1320.455
1330.339
1340.415
1350.341
1360.243
1370.453
1380.817
1390.139
140.522
1400.0657
1410.721
1420.51
1430.299
1440.848
1450.197
1460.536
1470.887
1480.195
1490.924
150.0347
1500.311
1510.917
1520.656
1530.275
1540.411
1550.236
1560.813
1570.171
1580.0831
1590.523
160.812
1600.37
1610.182
1620.763
1630.175
1640.437
1650.179
1660.309
1670.531
1680.244
1690.572
170.0832
180.0752
190.318
20.344
200.287
210.0899
220.992
230.381
240.46
250.179
260.679
270.431
280.177
290.402
30.62
300.453
310.729
320.11
330.997
340.177
350.0957
360.439
370.143
380.271
390.923
40.467
400.0725
410.295
420.447
430.535
440.166
450.323
460.299
470.182
480.619
490.462
50.0291
500.946
510.234
520.824
530.475
540.915
550.0561
560.999
570.812
580.437
590.233
60.662
600.784
610.467
620.441
630.869
640.872
650.263
660.0637
670.506
680.16
690.197
70.829
700.0573
710.599
720.172
730.834
740.223
750.361
760.511
770.743
780.324
790.963
80.637
800.795
810.101
820.231
830.481
840.486
850.705
860.706
870.225
880.881
890.133
90.697
900.653
910.307
920.599
930.398
940.11
950.00204
960.742
970.203
980.00389
990.528



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: CNhs11933


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)
0000066 (epithelial cell)
0000255 (eukaryotic cell)
0000548 (animal cell)

DOID: Disease
0050687 (cell type cancer)
14566 (disease of cellular proliferation)
162 (cancer)
305 (carcinoma)
4 (disease)
5662 (pleomorphic carcinoma)
7 (disease of anatomical entity)

UBERON: Anatomy
0000015 (anatomical boundary)
0000061 (anatomical structure)
0000062 (organ)
0000077 (mixed endoderm/mesoderm-derived structure)
0000465 (material anatomical entity)
0000466 (immaterial anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000475 (organism subdivision)
0000479 (tissue)
0000480 (anatomical group)
0000481 (multi-tissue structure)
0000916 (abdomen)
0000922 (embryo)
0000923 (germ layer)
0000925 (endoderm)
0000926 (mesoderm)
0000949 (endocrine system)
0001007 (digestive system)
0001041 (foregut)
0001048 (primordium)
0001062 (anatomical entity)
0001555 (digestive tract)
0002050 (embryonic structure)
0002100 (trunk)
0002107 (liver)
0002330 (exocrine system)
0002365 (exocrine gland)
0002368 (endocrine gland)
0002405 (immune system)
0002417 (abdominal segment of trunk)
0002423 (hepatobiliary system)
0002530 (gland)
0002532 (epiblast (generic))
0003104 (mesenchyme)
0003894 (liver primordium)
0004119 (endoderm-derived structure)
0004120 (mesoderm-derived structure)
0004161 (septum transversum)
0004185 (endodermal part of digestive tract)
0004921 (subdivision of digestive tract)
0005057 (immune organ)
0005172 (abdomen element)
0005173 (abdominal segment element)
0005177 (trunk region element)
0005256 (trunk mesenchyme)
0005423 (developing anatomical structure)
0006235 (foregut-midgut junction)
0006925 (digestive gland)
0007026 (primitive gut)
0008835 (hepatic diverticulum)
0008836 (liver bud)
0009142 (entire embryonic mesenchyme)

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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