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{{f5samples
{{f5samples
|id=FF:10475-106I7
|F5samples=
|name=retinoblastoma cell line:Y79
|ancestors_in_anatomy_facet=UBERON:0000019,UBERON:0000020,UBERON:0000033,UBERON:0000047,UBERON:0000061,UBERON:0000062,UBERON:0000063,UBERON:0000064,UBERON:0000073,UBERON:0000153,UBERON:0000465,UBERON:0000467,UBERON:0000468,UBERON:0000475,UBERON:0000479,UBERON:0000480,UBERON:0000481,UBERON:0000922,UBERON:0000923,UBERON:0000924,UBERON:0000955,UBERON:0000966,UBERON:0000970,UBERON:0001016,UBERON:0001017,UBERON:0001032,UBERON:0001048,UBERON:0001062,UBERON:0001444,UBERON:0001456,UBERON:0001802,UBERON:0002050,UBERON:0002104,UBERON:0002346,UBERON:0002532,UBERON:0003056,UBERON:0003071,UBERON:0003072,UBERON:0003075,UBERON:0004121,UBERON:0004128,UBERON:0004456,UBERON:0005085,UBERON:0005291,UBERON:0005388,UBERON:0005423,UBERON:0005743,UBERON:0006598,UBERON:0007284
|sample_id=10475
|rna_tube_id=106I7
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|sample_cell_lot=
|sample_cell_catalog=RCB1645
|sample_company=RIKEN Bioresource centre
|rna_lot_number=
|rna_catalog_number=
|sample_species=Human (Homo sapiens)
|sample_strain=
|sample_dev_stage=
|sample_tissue=eye
|sample_donor(cell lot)=
|sample_sex=female
|sample_age=2.5
|sample_ethnicity=unknown
|rna_rin=
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|rna_od260/280=2.11
|sample_cell_type=unclassifiable
|sample_cell_line=Y79
|sample_collaboration=Yukio Nakamura (RIKEN BRC)
|sample_experimental_condition=
|sample_disease=retinoblastoma
|rna_sample_type=total RNA
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0
|rna_weight_ug=36.803
|rna_concentration=1.47212
|sample_note=
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|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000004,CL:0000012,CL:0000030,CL:0000055,CL:0000095,CL:0000123,CL:0000125,CL:0000133,CL:0000144,CL:0000219,CL:0000220,CL:0000221,CL:0000243,CL:0000255,CL:0000333,CL:0000339,CL:0000548,CL:0002319,CL:0002321,CL:0002371
|ancestors_in_anatomy_facet=UBERON:0000019,UBERON:0000020,UBERON:0000033,UBERON:0000047,UBERON:0000061,UBERON:0000062,UBERON:0000063,UBERON:0000064,UBERON:0000073,UBERON:0000153,UBERON:0000465,UBERON:0000467,UBERON:0000468,UBERON:0000475,UBERON:0000479,UBERON:0000480,UBERON:0000481,UBERON:0000922,UBERON:0000923,UBERON:0000924,UBERON:0000955,UBERON:0000966,UBERON:0000970,UBERON:0001016,UBERON:0001017,UBERON:0001032,UBERON:0001048,UBERON:0001062,UBERON:0001444,UBERON:0001456,UBERON:0001802,UBERON:0002050,UBERON:0002104,UBERON:0002346,UBERON:0002532,UBERON:0003056,UBERON:0003071,UBERON:0003072,UBERON:0003075,UBERON:0004121,UBERON:0004128,UBERON:0004456,UBERON:0005085,UBERON:0005291,UBERON:0005388,UBERON:0005423,UBERON:0005743,UBERON:0006598,UBERON:0007284
|ancestors_in_disease_facet=DOID:0050686,DOID:14566,DOID:162,DOID:3093,DOID:4
|ancestors_in_disease_facet=DOID:0050686,DOID:14566,DOID:162,DOID:3093,DOID:4
|sample_description=
|comment=
|created_by=
|creation_date=
|def=
|fonse_cell_line=FF:0100255
|fonse_cell_line=FF:0100255
|fonse_cell_line_closure=FF:0100255
|fonse_cell_line_closure=FF:0100255
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:10475-106I7
|is_a=EFO:0002091;;FF:0000003;;FF:0000210;;FF:0102920
|is_a=EFO:0002091;;FF:0000003;;FF:0000210;;FF:0102920
|name=retinoblastoma cell line:Y79
|namespace=FANTOM5
|namespace=FANTOM5
|part_of=
|part_of=
|profile_cagescan=,,,
|profile_hcage=CNhs11267,LSID758,release008,COMPLETED
|profile_rnaseq=,,,
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|rna_box=106
|rna_catalog_number=
|rna_concentration=1.47212
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0
|rna_lot_number=
|rna_od260/230=1.18
|rna_od260/280=2.11
|rna_position=I7
|rna_rin=
|rna_sample_type=total RNA
|rna_tube_id=106I7
|rna_weight_ug=36.803
|sample_age=2.5
|sample_cell_catalog=RCB1645
|sample_cell_line=Y79
|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=retinoblastoma
|sample_donor(cell lot)=
|sample_ethnicity=unknown
|sample_experimental_condition=
|sample_id=10475
|sample_note=
|sample_sex=female
|sample_species=Human (Homo sapiens)
|sample_strain=
|sample_tissue=eye
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}}
}}

Revision as of 14:08, 21 March 2012


Name:retinoblastoma cell line:Y79
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueeye
dev stageNA
sexfemale
age2.5
cell typeunclassifiable
cell lineY79
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
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C85-neuroblastoma-carcinoid-retinoblastoma-small-pineal-rhabdomyosarcoma-medulloblastoma0
C86-colon-carcinoid-small-neuroectodermal-giant-large-neuroepithelioma0
C87-retinoblastoma-left-nonsmall-heart-small-diaphragm-bronchogenic0.949
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: CNhs11267

Jaspar motifP-value
MA0002.29.99127e-4
MA0003.10.225
MA0004.10.159
MA0006.10.106
MA0007.10.279
MA0009.10.571
MA0014.10.775
MA0017.10.0196
MA0018.20.129
MA0019.10.242
MA0024.18.50216e-10
MA0025.10.515
MA0027.10.569
MA0028.10.162
MA0029.10.28
MA0030.10.801
MA0031.10.989
MA0035.20.951
MA0038.10.00309
MA0039.20.991
MA0040.10.0899
MA0041.10.234
MA0042.10.4
MA0043.10.244
MA0046.10.0844
MA0047.20.17
MA0048.10.235
MA0050.11.23767e-12
MA0051.18.71117e-7
MA0052.10.0802
MA0055.10.02
MA0057.10.125
MA0058.10.116
MA0059.10.095
MA0060.15.88556e-20
MA0061.10.00821
MA0062.20.595
MA0065.20.0583
MA0066.10.154
MA0067.10.786
MA0068.10.583
MA0069.10.744
MA0070.10.609
MA0071.10.913
MA0072.10.303
MA0073.10.616
MA0074.10.193
MA0076.10.0335
MA0077.10.267
MA0078.10.954
MA0079.20.188
MA0080.27.71717e-12
MA0081.10.0539
MA0083.19.32455e-4
MA0084.10.31
MA0087.10.36
MA0088.10.319
MA0090.10.0124
MA0091.10.42
MA0092.10.266
MA0093.10.115
MA0099.29.1745e-18
MA0100.10.125
MA0101.10.0328
MA0102.20.0297
MA0103.10.737
MA0104.20.0141
MA0105.10.0543
MA0106.10.25
MA0107.10.00549
MA0108.23.33224e-5
MA0111.10.771
MA0112.20.00267
MA0113.10.0835
MA0114.10.157
MA0115.10.534
MA0116.10.131
MA0117.10.624
MA0119.10.47
MA0122.10.526
MA0124.10.566
MA0125.10.062
MA0131.10.153
MA0135.10.114
MA0136.12.36182e-9
MA0137.20.00184
MA0138.20.44
MA0139.10.408
MA0140.10.893
MA0141.10.243
MA0142.10.873
MA0143.10.795
MA0144.18.16775e-5
MA0145.10.0162
MA0146.10.289
MA0147.10.0184
MA0148.10.173
MA0149.10.834
MA0150.11.36416e-4
MA0152.10.999
MA0153.10.172
MA0154.10.0825
MA0155.10.374
MA0156.19.00392e-7
MA0157.10.456
MA0159.10.0563
MA0160.10.26
MA0162.10.243
MA0163.10.00951
MA0164.10.828
MA0258.10.14
MA0259.10.0528



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: CNhs11267

Novel motifP-value
10.995
100.424
1000.331
1010.7
1020.419
1030.0382
1040.531
1050.841
1060.0011
1070.0105
1080.781
1090.48
110.482
1100.866
1110.818
1120.149
1130.916
1140.108
1150.654
1160.465
1170.678
1180.772
1190.467
120.862
1200.147
1210.952
1220.917
1230.204
1240.683
1250.264
1260.616
1270.534
1280.106
1290.433
130.792
1300.758
1310.414
1320.877
1330.642
1340.703
1350.0622
1360.971
1370.164
1380.102
1390.0279
140.892
1400.674
1410.992
1420.485
1430.39
1440.424
1450.406
1460.305
1470.357
1480.118
1490.133
150.268
1500.372
1510.302
1520.0158
1530.653
1540.921
1550.43
1560.98
1570.415
1580.0846
1590.00587
160.166
1600.548
1610.662
1620.841
1630.185
1640.453
1650.219
1660.697
1670.491
1680.0943
1690.0166
170.313
180.22
190.121
20.148
200.42
210.961
220.0989
238.4699e-4
240.496
250.399
260.899
270.112
280.914
290.566
30.243
300.194
310.397
320.0498
330.379
340.394
350.91
360.963
370.16
380.43
390.325
40.228
400.687
410.129
420.611
430.156
440.431
450.238
460.438
470.727
480.908
490.691
50.233
500.364
510.45
520.126
530.899
540.279
550.0492
560.353
570.741
580.244
590.0355
60.775
600.00755
610.953
620.121
630.124
640.925
650.097
660.0451
670.993
680.588
690.494
70.319
700.0186
710.359
720.0371
730.0124
740.271
750.431
760.701
770.0396
780.971
790.183
80.406
800.042
810.372
820.163
830.447
840.463
850.0333
860.56
870.319
880.694
890.0312
90.151
900.588
910.362
920.0263
930.91
940.304
950.367
960.281
970.495
980.304
990.433



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: CNhs11267


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)
0000030 (glioblast)
0000055 (non-terminally differentiated cell)
0000095 (neuron associated cell)
0000123 (neuron associated cell (sensu Vertebrata))
0000125 (glial cell)
0000133 (neurectodermal cell)
0000219 (motile cell)
0000221 (ectodermal cell)
0000243 (glial cell (sensu Vertebrata))
0000255 (eukaryotic cell)
0000333 (migratory neural crest cell)
0000339 (glioblast (sensu Vertebrata))
0000548 (animal cell)
0002319 (neural cell)
0002321 (embryonic cell)
0002371 (somatic cell)

DOID: Disease
0050686 (organ system cancer)
14566 (disease of cellular proliferation)
162 (cancer)
3093 (nervous system cancer)
4 (disease)

UBERON: Anatomy
0000019 (camera-type eye)
0000020 (sense organ)
0000033 (head)
0000047 (simple eye)
0000061 (anatomical structure)
0000062 (organ)
0000063 (organ segment)
0000064 (organ part)
0000073 (regional part of nervous system)
0000153 (anterior region of body)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000475 (organism subdivision)
0000479 (tissue)
0000480 (anatomical group)
0000481 (multi-tissue structure)
0000922 (embryo)
0000923 (germ layer)
0000924 (ectoderm)
0000955 (brain)
0000966 (retina)
0000970 (eye)
0001016 (nervous system)
0001017 (central nervous system)
0001032 (sensory system)
0001048 (primordium)
0001062 (anatomical entity)
0001444 (subdivision of head)
0001456 (face)
0001802 (posterior segment of eyeball)
0002050 (embryonic structure)
0002104 (visual system)
0002346 (neurectoderm)
0002532 (epiblast (generic))
0003056 (pre-chordal neural plate)
0003071 (eye primordium)
0003072 (optic cup)
0003075 (neural plate)
0004121 (ectoderm-derived structure)
0004128 (optic vesicle)
0004456 (entire sense organ system)
0005085 (ectodermal placode)
0005291 (embryonic tissue)
0005388 (photoreceptor array)
0005423 (developing anatomical structure)
0006598 (presumptive structure)
0007284 (presumptive neural plate)

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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