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{{f5samples
{{f5samples
|id=FF:10439-106E7
|F5samples=
|name=prostate cancer cell line:PC-3
|ancestors_in_anatomy_facet=UBERON:0000061,UBERON:0000062,UBERON:0000077,UBERON:0000079,UBERON:0000119,UBERON:0000161,UBERON:0000162,UBERON:0000163,UBERON:0000164,UBERON:0000465,UBERON:0000467,UBERON:0000468,UBERON:0000477,UBERON:0000479,UBERON:0000480,UBERON:0000481,UBERON:0000483,UBERON:0000922,UBERON:0000923,UBERON:0000925,UBERON:0000926,UBERON:0000990,UBERON:0001007,UBERON:0001046,UBERON:0001062,UBERON:0001353,UBERON:0001555,UBERON:0002050,UBERON:0002367,UBERON:0002530,UBERON:0002532,UBERON:0003064,UBERON:0003101,UBERON:0003104,UBERON:0003353,UBERON:0003820,UBERON:0003929,UBERON:0003937,UBERON:0004111,UBERON:0004119,UBERON:0004120,UBERON:0004122,UBERON:0004185,UBERON:0004902,UBERON:0004921,UBERON:0005153,UBERON:0005156,UBERON:0005291,UBERON:0005399,UBERON:0005423,UBERON:0005911,UBERON:0006866,UBERON:0007026,UBERON:0009142
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|sample_cell_lot=
|sample_cell_catalog=RCB2145
|sample_company=RIKEN Bioresource centre
|rna_lot_number=
|rna_catalog_number=
|sample_species=Human (Homo sapiens)
|sample_strain=
|sample_dev_stage=62 year old adult
|sample_tissue=prostate
|sample_donor(cell lot)=
|sample_sex=male
|sample_age=62
|sample_ethnicity=C
|rna_rin=
|rna_od260/230=1.94
|rna_od260/280=2.07
|sample_cell_type=unclassifiable
|sample_cell_line=PC-3
|sample_collaboration=Yukio Nakamura (RIKEN BRC)
|sample_experimental_condition=
|sample_disease=prostate cancer
|rna_sample_type=total RNA
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0
|rna_weight_ug=59.243
|rna_concentration=2.36972
|sample_note=
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|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:0000061,UBERON:0000062,UBERON:0000077,UBERON:0000079,UBERON:0000119,UBERON:0000161,UBERON:0000162,UBERON:0000163,UBERON:0000164,UBERON:0000465,UBERON:0000467,UBERON:0000468,UBERON:0000477,UBERON:0000479,UBERON:0000480,UBERON:0000481,UBERON:0000483,UBERON:0000922,UBERON:0000923,UBERON:0000925,UBERON:0000926,UBERON:0000990,UBERON:0001007,UBERON:0001046,UBERON:0001062,UBERON:0001353,UBERON:0001555,UBERON:0002050,UBERON:0002367,UBERON:0002530,UBERON:0002532,UBERON:0003064,UBERON:0003101,UBERON:0003104,UBERON:0003353,UBERON:0003820,UBERON:0003929,UBERON:0003937,UBERON:0004111,UBERON:0004119,UBERON:0004120,UBERON:0004122,UBERON:0004185,UBERON:0004902,UBERON:0004921,UBERON:0005153,UBERON:0005156,UBERON:0005291,UBERON:0005399,UBERON:0005423,UBERON:0005911,UBERON:0006866,UBERON:0007026,UBERON:0009142
|ancestors_in_disease_facet=DOID:0050687,DOID:14566,DOID:162,DOID:305,DOID:4,DOID:7
|ancestors_in_disease_facet=DOID:0050687,DOID:14566,DOID:162,DOID:305,DOID:4,DOID:7
|sample_description=
|comment=
|created_by=
|creation_date=
|def=
|fonse_cell_line=FF:0101019,FF:0101120
|fonse_cell_line=FF:0101019,FF:0101120
|fonse_cell_line_closure=FF:0101019,FF:0101120
|fonse_cell_line_closure=FF:0101019,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:10439-106E7
|is_a=EFO:0002091;;FF:0000003;;FF:0000210;;FF:0101061
|is_a=EFO:0002091;;FF:0000003;;FF:0000210;;FF:0101061
|name=prostate cancer cell line:PC-3
|namespace=FANTOM5
|namespace=FANTOM5
|part_of=
|part_of=
|profile_cagescan=,,,
|profile_hcage=CNhs11243,LSID757,release008,COMPLETED
|profile_rnaseq=,,,
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|rna_catalog_number=
|rna_concentration=2.36972
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0
|rna_lot_number=
|rna_od260/230=1.94
|rna_od260/280=2.07
|rna_position=E7
|rna_rin=
|rna_sample_type=total RNA
|rna_tube_id=106E7
|rna_weight_ug=59.243
|sample_age=62
|sample_cell_catalog=RCB2145
|sample_cell_line=PC-3
|sample_cell_lot=
|sample_cell_type=unclassifiable
|sample_collaboration=Yukio Nakamura (RIKEN BRC)
|sample_company=RIKEN Bioresource centre
|sample_description=
|sample_dev_stage=62 year old adult
|sample_disease=prostate cancer
|sample_donor(cell lot)=
|sample_ethnicity=C
|sample_experimental_condition=
|sample_id=10439
|sample_note=
|sample_sex=male
|sample_species=Human (Homo sapiens)
|sample_strain=
|sample_tissue=prostate
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}}
}}

Revision as of 14:07, 21 March 2012


Name:prostate cancer cell line:PC-3
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueprostate
dev stage62 year old adult
sexmale
age62
cell typeunclassifiable
cell linePC-3
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
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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: CNhs11243

Jaspar motifP-value
MA0002.20.00293
MA0003.10.3
MA0004.10.376
MA0006.10.67
MA0007.10.773
MA0009.10.307
MA0014.10.0189
MA0017.10.227
MA0018.20.00256
MA0019.10.432
MA0024.12.27227e-4
MA0025.10.27
MA0027.10.87
MA0028.10.0112
MA0029.10.458
MA0030.10.229
MA0031.10.00518
MA0035.20.525
MA0038.10.0504
MA0039.20.00113
MA0040.10.877
MA0041.10.54
MA0042.10.742
MA0043.10.0033
MA0046.10.143
MA0047.20.0203
MA0048.10.2
MA0050.10.00212
MA0051.10.117
MA0052.10.0286
MA0055.19.64394e-4
MA0057.10.386
MA0058.10.0734
MA0059.10.244
MA0060.14.51387e-12
MA0061.10.00407
MA0062.20.101
MA0065.20.357
MA0066.10.092
MA0067.10.0137
MA0068.10.891
MA0069.10.964
MA0070.10.5
MA0071.10.375
MA0072.10.316
MA0073.10.821
MA0074.10.702
MA0076.10.0542
MA0077.10.983
MA0078.10.739
MA0079.20.973
MA0080.27.52368e-9
MA0081.10.149
MA0083.10.167
MA0084.10.554
MA0087.10.252
MA0088.10.45
MA0090.10.223
MA0091.12.2821e-5
MA0092.10.0994
MA0093.10.336
MA0099.20.484
MA0100.10.4
MA0101.10.14
MA0102.20.00273
MA0103.15.58221e-5
MA0104.20.963
MA0105.10.00161
MA0106.10.597
MA0107.10.03
MA0108.20.838
MA0111.10.384
MA0112.20.0244
MA0113.10.191
MA0114.10.977
MA0115.10.878
MA0116.10.0766
MA0117.10.0284
MA0119.10.933
MA0122.10.644
MA0124.10.432
MA0125.10.424
MA0131.10.297
MA0135.10.114
MA0136.13.24242e-5
MA0137.20.0826
MA0138.20.142
MA0139.10.901
MA0140.10.323
MA0141.10.119
MA0142.10.122
MA0143.10.16
MA0144.10.47
MA0145.10.596
MA0146.10.353
MA0147.10.745
MA0148.10.00378
MA0149.10.141
MA0150.10.212
MA0152.10.639
MA0153.10.15
MA0154.10.0136
MA0155.10.116
MA0156.10.0114
MA0157.10.06
MA0159.10.601
MA0160.10.166
MA0162.10.891
MA0163.10.00265
MA0164.10.752
MA0258.10.0067
MA0259.10.0681



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: CNhs11243

Novel motifP-value
10.397
100.74
1000.288
1010.491
1020.662
1030.227
1040.689
1050.0762
1060.00245
1070.836
1080.734
1090.896
110.191
1100.672
1110.364
1120.00463
1130.151
1140.171
1150.423
1160.238
1170.947
1180.139
1190.363
120.488
1200.938
1210.832
1220.961
1230.518
1240.811
1250.637
1260.81
1270.817
1280.0893
1290.837
130.484
1300.196
1310.172
1320.176
1330.226
1340.435
1350.00833
1360.374
1370.414
1380.364
1390.181
140.185
1400.00668
1410.902
1420.41
1430.796
1440.131
1450.762
1460.247
1470.6
1480.059
1490.0177
150.825
1500.987
1510.401
1520.379
1530.35
1540.951
1550.944
1560.691
1570.859
1580.123
1590.455
160.528
1600.41
1610.958
1620.995
1630.272
1640.0871
1650.848
1660.932
1670.16
1680.278
1690.468
170.702
180.0363
190.0485
20.16
200.0859
210.798
220.0611
230.277
240.627
250.523
260.885
270.296
280.891
290.834
30.394
300.934
310.786
320.0207
330.486
340.0769
350.118
360.945
370.312
380.976
390.707
40.348
400.449
410.0926
420.884
430.213
440.194
450.977
460.157
470.983
480.566
490.47
50.267
500.768
510.247
520.266
530.573
540.296
550.631
560.814
570.447
580.172
590.0352
60.852
600.0372
610.621
620.0575
630.807
640.282
650.394
662.70895e-4
670.888
680.557
690.624
70.615
700.176
710.493
720.192
730.453
740.456
750.868
760.857
770.406
780.704
796.65109e-4
80.246
800.0323
810.11
820.0371
830.298
840.647
850.00658
860.383
870.869
880.761
890.276
90.0139
900.55
910.166
920.0935
930.623
940.092
950.411
960.0232
970.521
980.585
990.192



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: CNhs11243


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)
7 (disease of anatomical entity)

UBERON: Anatomy
0000061 (anatomical structure)
0000062 (organ)
0000077 (mixed endoderm/mesoderm-derived structure)
0000079 (male reproductive system)
0000119 (cell layer)
0000161 (orifice)
0000162 (cloaca)
0000163 (embryonic cloaca)
0000164 (primitive urogenital sinus)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000477 (anatomical cluster)
0000479 (tissue)
0000480 (anatomical group)
0000481 (multi-tissue structure)
0000483 (epithelium)
0000922 (embryo)
0000923 (germ layer)
0000925 (endoderm)
0000926 (mesoderm)
0000990 (reproductive system)
0001007 (digestive system)
0001046 (hindgut)
0001062 (anatomical entity)
0001353 (anal region)
0001555 (digestive tract)
0002050 (embryonic structure)
0002367 (prostate gland)
0002530 (gland)
0002532 (epiblast (generic))
0003064 (intermediate mesoderm)
0003101 (male organism)
0003104 (mesenchyme)
0003353 (epithelium of hindgut)
0003820 (prostate bud)
0003929 (gut epithelium)
0003937 (sex gland)
0004111 (anatomical conduit)
0004119 (endoderm-derived structure)
0004120 (mesoderm-derived structure)
0004122 (genitourinary system)
0004185 (endodermal part of digestive tract)
0004902 (urogenital sinus epithelium)
0004921 (subdivision of digestive tract)
0005153 (epithelial bud)
0005156 (reproductive structure)
0005291 (embryonic tissue)
0005399 (male reproductive gland)
0005423 (developing anatomical structure)
0005911 (endo-epithelium)
0006866 (terminal part of digestive tract)
0007026 (primitive gut)
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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