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{{f5samples
{{f5samples
|id=FF:10022-101D4
|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:0007023,UBERON:0007026,UBERON:0009142
|name=prostate, adult, pool1
|sample_id=10022
|rna_tube_id=101D4
|rna_box=101
|rna_position=D4
|sample_cell_lot=NA
|sample_cell_catalog=NA
|sample_company=Ambion
|rna_lot_number=0910061 -13
|rna_catalog_number=Cat:AM6000 Lot:0910061 -13
|sample_species=Human (Homo sapiens)
|sample_strain=
|sample_dev_stage=73,79,93 years old adult
|sample_tissue=prostate
|sample_donor(cell lot)=3 pool
|sample_sex=male
|sample_age=
|sample_ethnicity=C
|rna_rin=
|rna_od260/230=
|rna_od260/280=
|sample_cell_type=CELL MIXTURE - tissue sample
|sample_cell_line=
|sample_collaboration=FANTOM5 OSC CORE (contact: Al Forrest)
|sample_experimental_condition=
|sample_disease=normal
|rna_sample_type=total RNA
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-ToTALLY-RNA-v1.0
|rna_weight_ug=10
|rna_concentration=1
|sample_note=
|profile_hcage=CNhs10628,LSID657,release008,COMPLETED
|profile_cagescan=NCig10021,,,
|profile_srnaseq=,,,
|profile_rnaseq=,,,
|ancestors_in_cell_lineage_facet=
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|ancestors_in_disease_facet=
|ancestors_in_disease_facet=
|sample_description=
|comment=
|created_by=
|creation_date=
|def=
|fonse_cell_line=
|fonse_cell_line=
|fonse_cell_line_closure=
|fonse_cell_line_closure=
Line 66: Line 33:
|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:10022-101D4
|is_a=EFO:0002091;;FF:0000004;;FF:0000210;;FF:0010022
|is_a=EFO:0002091;;FF:0000004;;FF:0000210;;FF:0010022
|name=prostate, adult, pool1
|namespace=FANTOM5
|namespace=FANTOM5
|part_of=
|part_of=
|profile_cagescan=NCig10021,,,
|profile_hcage=CNhs10628,LSID657,release008,COMPLETED
|profile_rnaseq=,,,
|profile_srnaseq=,,,
|rna_box=101
|rna_catalog_number=Cat:AM6000 Lot:0910061 -13
|rna_concentration=1
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-ToTALLY-RNA-v1.0
|rna_lot_number=0910061 -13
|rna_od260/230=
|rna_od260/280=
|rna_position=D4
|rna_rin=
|rna_sample_type=total RNA
|rna_tube_id=101D4
|rna_weight_ug=10
|sample_age=
|sample_cell_catalog=NA
|sample_cell_line=
|sample_cell_lot=NA
|sample_cell_type=CELL MIXTURE - tissue sample
|sample_collaboration=FANTOM5 OSC CORE (contact: Al Forrest)
|sample_company=Ambion
|sample_description=
|sample_dev_stage=73,79,93 years old adult
|sample_disease=normal
|sample_donor(cell lot)=3 pool
|sample_ethnicity=C
|sample_experimental_condition=
|sample_id=10022
|sample_note=
|sample_sex=male
|sample_species=Human (Homo sapiens)
|sample_strain=
|sample_tissue=prostate
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}}
}}

Revision as of 14:00, 21 March 2012


Name:prostate, adult, pool1
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 stage73,79,93 years old adult
sexmale
ageNA
cell typeCELL MIXTURE - tissue sample
cell lineNA
companyAmbion
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot number0910061 -13
catalog numberCat:AM6000 Lot:0910061 -13
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-ToTALLY-RNA-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
C104-Mast-Basophils-immature-CD14-CD34-eye-Natural0
C105-heart-skeletal-occipital-hippocampus-acute-Sebocyte-penis-0.115
C106-Hep2-epitheloid-placenta-cervical-rectal-anaplastic-glassy0
C107-Neutrophils-CD14-Eosinophils-Monocytederived-Whole-Peripheral-blood0
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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-Whole0.0328
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: CNhs10628

Jaspar motifP-value
MA0002.20.0113
MA0003.10.222
MA0004.10.0941
MA0006.10.547
MA0007.10.484
MA0009.10.51
MA0014.10.787
MA0017.10.238
MA0018.20.778
MA0019.10.0576
MA0024.10.227
MA0025.10.362
MA0027.10.706
MA0028.10.0035
MA0029.10.151
MA0030.14.84061e-7
MA0031.10.00629
MA0035.20.866
MA0038.10.553
MA0039.20.471
MA0040.10.133
MA0041.10.0517
MA0042.10.116
MA0043.10.424
MA0046.13.68883e-4
MA0047.24.50346e-4
MA0048.10.105
MA0050.10.0554
MA0051.10.285
MA0052.10.0018
MA0055.10.012
MA0057.10.978
MA0058.10.0541
MA0059.10.00161
MA0060.10.569
MA0061.10.00966
MA0062.22.19853e-4
MA0065.20.022
MA0066.10.00564
MA0067.10.153
MA0068.10.00223
MA0069.10.713
MA0070.10.533
MA0071.10.0607
MA0072.10.264
MA0073.10.654
MA0074.10.904
MA0076.10.00596
MA0077.10.937
MA0078.10.138
MA0079.20.176
MA0080.20.354
MA0081.10.348
MA0083.13.59605e-5
MA0084.10.907
MA0087.10.221
MA0088.10.0722
MA0090.10.114
MA0091.10.806
MA0092.10.926
MA0093.10.111
MA0099.24.07904e-10
MA0100.10.181
MA0101.10.0399
MA0102.20.729
MA0103.10.593
MA0104.20.00279
MA0105.11.17025e-7
MA0106.10.305
MA0107.10.0535
MA0108.21.45947e-18
MA0111.10.387
MA0112.20.0179
MA0113.10.906
MA0114.10.0495
MA0115.10.0192
MA0116.11.28087e-4
MA0117.10.401
MA0119.10.226
MA0122.10.407
MA0124.10.388
MA0125.10.267
MA0131.10.488
MA0135.10.253
MA0136.10.0404
MA0137.20.0162
MA0138.20.307
MA0139.10.346
MA0140.10.357
MA0141.10.00944
MA0142.10.154
MA0143.10.673
MA0144.10.47
MA0145.10.293
MA0146.10.388
MA0147.18.46635e-4
MA0148.10.00364
MA0149.10.0199
MA0150.10.0012
MA0152.10.656
MA0153.18.20404e-4
MA0154.10.0616
MA0155.10.814
MA0156.10.0193
MA0157.10.284
MA0159.10.0697
MA0160.10.0508
MA0162.10.512
MA0163.12.57426e-10
MA0164.10.333
MA0258.10.0159
MA0259.10.0656



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: CNhs10628

Novel motifP-value
10.0122
100.0271
1000.111
1010.908
1020.596
1030.15
1040.529
1050.638
1060.413
1070.866
1080.525
1090.0206
110.035
1100.0683
1110.00237
1120.681
1130.461
1140.00355
1150.925
1160.65
1170.0139
1180.0661
1190.254
120.73
1200.0442
1210.489
1220.72
1230.0104
1240.707
1250.0791
1260.789
1270.572
1280.932
1290.443
130.062
1300.375
1310.161
1320.235
1330.135
1340.121
1350.239
1360.401
1370.34
1380.611
1390.0724
140.984
1400.169
1410.28
1420.71
1430.0175
1440.999
1450.405
1460.881
1470.641
1480.0664
1490.874
150.0369
1500.485
1510.729
1520.714
1530.636
1540.682
1550.202
1560.463
1570.947
1580.331
1590.738
160.0945
1600.649
1610.287
1620.615
1630.929
1640.0187
1650.782
1660.559
1670.0225
1680.555
1690.221
170.395
180.0307
190.856
20.186
200.0809
210.139
220.93
230.873
240.584
250.329
260.0134
270.958
280.689
290.0101
30.148
300.0617
310.87
320.222
330.15
340.571
350.168
360.0131
370.126
380.566
390.434
40.36
400.0699
410.0464
420.333
430.128
440.276
450.352
460.0575
470.0573
480.153
490.0625
50.389
500.63
510.623
520.421
530.97
540.879
550.406
560.808
570.105
580.569
590.647
60.461
600.696
610.254
620.232
630.475
640.169
650.573
660.117
670.321
680.851
690.478
70.234
700.0489
710.0334
720.977
730.113
740.274
750.00685
760.043
770.738
780.114
790.25
80.0917
800.702
810.335
820.399
830.454
840.824
850.415
860.672
870.128
880.906
890.528
90.523
900.0206
910.703
920.642
930.0624
940.0269
950.0114
960.666
970.897
980.0997
990.468



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: CNhs10628


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

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)
0007023 (adult organism)
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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