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{{f5samples
{{f5samples
|id=FF:10011-101C2
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|name=bladder, adult, pool1
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|sample_cell_lot=NA
|sample_cell_catalog=NA
|sample_company=Ambion
|rna_lot_number=0910061 -2
|rna_catalog_number=Cat:AM6000 Lot:0910061 -2
|sample_species=Human (Homo sapiens)
|sample_strain=
|sample_dev_stage=55,58,79 years old adult
|sample_tissue=bladder
|sample_donor(cell lot)=3 pool
|sample_sex=mixed
|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=
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|profile_srnaseq=,,,
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|ancestors_in_disease_facet=
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|sample_description=
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|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:10011-101C2
|is_a=EFO:0002091;;FF:0000004;;FF:0000210;;FF:0010011
|is_a=EFO:0002091;;FF:0000004;;FF:0000210;;FF:0010011
|name=bladder, adult, pool1
|namespace=FANTOM5
|namespace=FANTOM5
|part_of=
|part_of=
|profile_cagescan=,,,
|profile_hcage=CNhs10616,LSID656,release008,COMPLETED
|profile_rnaseq=,,,
|profile_srnaseq=,,,
|rna_box=101
|rna_catalog_number=Cat:AM6000 Lot:0910061 -2
|rna_concentration=1
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-ToTALLY-RNA-v1.0
|rna_lot_number=0910061 -2
|rna_od260/230=
|rna_od260/280=
|rna_position=C2
|rna_rin=
|rna_sample_type=total RNA
|rna_tube_id=101C2
|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=55,58,79 years old adult
|sample_disease=normal
|sample_donor(cell lot)=3 pool
|sample_ethnicity=C
|sample_experimental_condition=
|sample_id=10011
|sample_note=
|sample_sex=mixed
|sample_species=Human (Homo sapiens)
|sample_strain=
|sample_tissue=bladder
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}}
}}

Revision as of 14:00, 21 March 2012


Name:bladder, 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
tissuebladder
dev stage55,58,79 years old adult
sexmixed
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 -2
catalog numberCat:AM6000 Lot:0910061 -2
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-0.0939
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-Whole0.0409
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: CNhs10616

Jaspar motifP-value
MA0002.20.104
MA0003.10.215
MA0004.10.0441
MA0006.10.557
MA0007.10.49
MA0009.10.351
MA0014.10.226
MA0017.10.54
MA0018.20.975
MA0019.10.0111
MA0024.10.00769
MA0025.10.526
MA0027.10.555
MA0028.11.04763e-8
MA0029.10.126
MA0030.11.99526e-4
MA0031.10.00289
MA0035.20.49
MA0038.10.837
MA0039.20.538
MA0040.10.297
MA0041.10.253
MA0042.10.471
MA0043.10.191
MA0046.10.0816
MA0047.20.0112
MA0048.10.0297
MA0050.10.993
MA0051.10.332
MA0052.15.69579e-4
MA0055.14.97869e-5
MA0057.10.983
MA0058.10.0105
MA0059.10.00138
MA0060.10.00367
MA0061.10.0175
MA0062.21.24457e-12
MA0065.20.189
MA0066.10.0407
MA0067.10.325
MA0068.10.00755
MA0069.10.761
MA0070.10.115
MA0071.10.0447
MA0072.10.11
MA0073.10.649
MA0074.10.715
MA0076.11.30832e-10
MA0077.10.217
MA0078.10.177
MA0079.20.528
MA0080.20.188
MA0081.10.127
MA0083.19.23297e-13
MA0084.10.59
MA0087.10.386
MA0088.10.0177
MA0090.10.0577
MA0091.10.221
MA0092.10.145
MA0093.10.0287
MA0099.23.57471e-11
MA0100.10.0567
MA0101.10.0362
MA0102.20.603
MA0103.10.722
MA0104.20.00114
MA0105.12.77797e-4
MA0106.10.19
MA0107.10.037
MA0108.22.2171e-21
MA0111.10.425
MA0112.20.389
MA0113.10.824
MA0114.10.0685
MA0115.10.0723
MA0116.10.00514
MA0117.10.649
MA0119.10.686
MA0122.10.408
MA0124.10.505
MA0125.10.951
MA0131.10.0902
MA0135.10.969
MA0136.10.00104
MA0137.20.171
MA0138.20.329
MA0139.10.287
MA0140.10.224
MA0141.10.0143
MA0142.10.224
MA0143.10.563
MA0144.10.298
MA0145.10.0389
MA0146.10.15
MA0147.16.18225e-4
MA0148.10.00611
MA0149.10.0414
MA0150.10.0143
MA0152.10.844
MA0153.10.194
MA0154.10.476
MA0155.10.617
MA0156.11.86021e-5
MA0157.10.147
MA0159.10.373
MA0160.10.108
MA0162.10.784
MA0163.13.65915e-6
MA0164.10.246
MA0258.10.112
MA0259.10.082



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: CNhs10616

Novel motifP-value
10.0519
100.0728
1000.064
1010.764
1020.235
1030.369
1040.742
1050.599
1060.514
1070.0297
1080.513
1090.0243
110.149
1100.218
1110.035
1120.947
1130.267
1140.0681
1150.312
1160.856
1170.028
1180.0443
1190.769
120.415
1200.00775
1210.911
1220.927
1238.85005e-4
1240.593
1250.327
1260.559
1270.48
1280.168
1290.319
130.0331
1300.773
1310.0587
1320.0838
1330.0024
1340.0714
1350.0102
1360.253
1370.512
1380.842
1390.815
140.884
1400.561
1410.598
1420.963
1430.124
1440.936
1450.834
1460.947
1470.454
1480.703
1490.183
150.0425
1500.828
1510.939
1520.866
1530.219
1540.798
1550.381
1560.519
1570.954
1580.662
1590.917
160.513
1600.971
1610.23
1620.88
1630.761
1640.00435
1650.686
1660.188
1670.0536
1680.227
1690.791
170.863
180.154
190.189
20.0149
200.0235
210.375
220.65
230.112
240.495
250.34
260.0331
270.603
280.486
290.00241
30.285
300.0229
310.826
320.611
330.0928
340.338
350.331
360.0125
370.181
380.691
390.166
40.0498
400.0277
410.112
420.296
430.509
440.988
450.149
460.389
470.131
480.253
490.366
50.715
500.516
510.799
520.0927
530.898
540.856
550.765
560.876
570.156
580.918
590.726
60.373
600.596
610.465
620.697
630.61
640.29
650.934
660.00545
670.482
680.389
690.759
70.277
700.312
710.0842
720.703
730.0311
740.895
750.00718
760.0268
770.173
780.374
790.499
80.32
800.432
810.806
820.996
830.21
840.857
850.459
860.777
870.0316
880.778
890.623
90.307
900.219
910.0234
920.412
930.0109
940.0685
954.73561e-4
960.835
970.905
980.112
990.429



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: CNhs10616


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)
0000161 (orifice)
0000162 (cloaca)
0000163 (embryonic cloaca)
0000164 (primitive urogenital sinus)
0000464 (anatomical space)
0000465 (material anatomical entity)
0000466 (immaterial anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000475 (organism subdivision)
0000477 (anatomical cluster)
0000479 (tissue)
0000480 (anatomical group)
0000481 (multi-tissue structure)
0000489 (cavitated compound organ)
0000922 (embryo)
0000923 (germ layer)
0000925 (endoderm)
0000926 (mesoderm)
0001007 (digestive system)
0001008 (renal system)
0001046 (hindgut)
0001062 (anatomical entity)
0001255 (urinary bladder)
0001353 (anal region)
0001555 (digestive tract)
0001556 (lower urinary tract)
0002050 (embryonic structure)
0002075 (viscus)
0002100 (trunk)
0002323 (body cavity)
0002532 (epiblast (generic))
0002553 (anatomical cavity)
0003064 (intermediate mesoderm)
0003103 (compound organ)
0003104 (mesenchyme)
0004111 (anatomical conduit)
0004119 (endoderm-derived structure)
0004120 (mesoderm-derived structure)
0004122 (genitourinary system)
0004185 (endodermal part of digestive tract)
0004458 (body cavity or lining)
0004921 (subdivision of digestive tract)
0005177 (trunk region element)
0005423 (developing anatomical structure)
0006554 (urinary system structure)
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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