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{{f5samples
{{f5samples
|id=FF:11689-122I6
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|name=Retinal Pigment Epithelial Cells, donor3
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|sample_experimental_condition=
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Line 66: Line 33:
|fonse_treatment=
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|comment=
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|creation_date=
|def=
|has_quality=
|has_quality=
|id=FF:11689-122I6
|is_a=EFO:0002091;;FF:0000002;;FF:0000158;;FF:0000210
|is_a=EFO:0002091;;FF:0000002;;FF:0000158;;FF:0000210
|name=Retinal Pigment Epithelial Cells, donor3
|namespace=FANTOM5
|namespace=FANTOM5
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|part_of=
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|rna_lot_number=4143
|rna_od260/230=
|rna_od260/280=
|rna_position=I6
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|rna_sample_type=total RNA
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|sample_age=
|sample_cell_catalog=
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|sample_cell_lot=
|sample_cell_type=retinal pigment epithelial cell
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|sample_company=Sciencell/3H
|sample_description=
|sample_dev_stage=
|sample_disease=
|sample_donor(cell lot)=
|sample_ethnicity=
|sample_experimental_condition=
|sample_id=11689
|sample_note=
|sample_sex=
|sample_species=Human (Homo sapiens)
|sample_strain=
|sample_tissue=eye
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}}
}}

Revision as of 15:00, 21 March 2012


Name:Retinal Pigment Epithelial Cells, donor3
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
sexNA
ageNA
cell typeretinal pigment epithelial cell
cell lineNA
companySciencell/3H
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot number4143
catalog numberSC6545
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-TRIzol-ethanol-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
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: CNhs12733

Jaspar motifP-value
MA0002.20.649
MA0003.10.461
MA0004.10.0127
MA0006.10.149
MA0007.10.784
MA0009.10.758
MA0014.10.902
MA0017.10.838
MA0018.20.406
MA0019.10.361
MA0024.10.869
MA0025.10.266
MA0027.10.702
MA0028.10.00523
MA0029.10.568
MA0030.10.359
MA0031.10.849
MA0035.20.285
MA0038.10.5
MA0039.20.48
MA0040.10.446
MA0041.10.413
MA0042.10.721
MA0043.10.392
MA0046.10.263
MA0047.20.498
MA0048.10.607
MA0050.19.66068e-11
MA0051.19.77357e-5
MA0052.10.117
MA0055.10.679
MA0057.10.377
MA0058.10.00688
MA0059.10.00383
MA0060.10.491
MA0061.13.25735e-4
MA0062.20.5
MA0065.20.00536
MA0066.10.31
MA0067.10.578
MA0068.10.236
MA0069.10.949
MA0070.10.0236
MA0071.10.514
MA0072.10.914
MA0073.10.621
MA0074.10.54
MA0076.10.0158
MA0077.10.0193
MA0078.10.296
MA0079.20.688
MA0080.25.11607e-10
MA0081.10.0174
MA0083.10.743
MA0084.10.187
MA0087.10.916
MA0088.10.471
MA0090.13.25768e-5
MA0091.10.182
MA0092.10.978
MA0093.10.0167
MA0099.20.735
MA0100.10.876
MA0101.10.00134
MA0102.20.445
MA0103.10.00567
MA0104.20.0295
MA0105.10.00999
MA0106.10.603
MA0107.13.59864e-4
MA0108.21.66151e-4
MA0111.10.935
MA0112.20.712
MA0113.10.394
MA0114.10.00808
MA0115.10.854
MA0116.10.332
MA0117.10.361
MA0119.10.7
MA0122.10.29
MA0124.10.374
MA0125.10.208
MA0131.10.0618
MA0135.10.694
MA0136.14.04241e-6
MA0137.20.198
MA0138.20.937
MA0139.10.0496
MA0140.10.936
MA0141.10.385
MA0142.10.847
MA0143.10.899
MA0144.10.0128
MA0145.10.0151
MA0146.10.628
MA0147.10.055
MA0148.10.412
MA0149.10.833
MA0150.16.39673e-4
MA0152.10.521
MA0153.10.109
MA0154.10.894
MA0155.10.0498
MA0156.11.76847e-5
MA0157.10.849
MA0159.14.71342e-4
MA0160.10.983
MA0162.10.189
MA0163.10.699
MA0164.10.312
MA0258.10.587
MA0259.10.768



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: CNhs12733

Novel motifP-value
10.622
100.00906
1000.308
1010.366
1020.723
1030.537
1040.922
1050.545
1060.0535
1070.864
1080.777
1090.123
110.455
1100.552
1110.0919
1120.133
1130.00982
1140.405
1150.284
1160.935
1170.153
1180.293
1190.069
120.696
1200.75
1210.9
1220.149
1235.88927e-4
1240.822
1250.262
1260.333
1270.456
1280.177
1290.782
130.588
1300.117
1310.506
1320.758
1330.98
1340.642
1350.0376
1360.442
1370.605
1380.0133
1390.524
140.502
1400.486
1410.183
1420.598
1430.298
1440.331
1450.963
1460.949
1470.7
1480.131
1490.0329
150.796
1500.269
1510.305
1520.0167
1530.21
1540.269
1550.079
1560.0688
1570.0412
1580.0123
1590.305
160.192
1600.976
1610.606
1620.294
1630.572
1640.351
1650.215
1660.881
1670.215
1680.695
1690.536
170.623
180.717
190.742
20.884
200.152
210.787
220.316
230.299
240.9
250.955
260.0983
270.607
280.49
290.746
30.0999
300.0715
310.774
320.175
330.314
340.718
350.547
360.827
370.14
380.301
390.338
40.985
400.0689
410.0713
420.11
430.242
440.705
450.144
460.192
470.801
480.688
490.225
50.483
500.964
510.712
520.944
530.259
540.425
550.904
560.793
570.9
580.185
590.504
60.814
600.12
610.527
620.232
630.319
640.895
650.442
660.603
670.865
680.94
690.115
70.385
700.672
710.591
720.307
730.0849
740.657
750.845
760.00585
770.362
780.208
790.438
80.713
800.954
810.44
820.4
830.0247
840.289
850.481
860.502
870.265
880.514
890.512
90.929
900.393
910.12
920.531
930.631
940.355
950.00491
960.881
970.371
980.0867
990.113



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: CNhs12733


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)
0000147 (pigment cell)
0000149 (visual pigment cell)
0000255 (eukaryotic cell)
0000325 (stuff accumulating cell)
0000548 (animal cell)
0002371 (somatic cell)
0002586 (retinal pigment epithelial cell)

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)
0000119 (cell layer)
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)
0000483 (epithelium)
0000922 (embryo)
0000923 (germ layer)
0000924 (ectoderm)
0000966 (retina)
0000970 (eye)
0001016 (nervous system)
0001032 (sensory system)
0001048 (primordium)
0001062 (anatomical entity)
0001444 (subdivision of head)
0001456 (face)
0001781 (layer of retina)
0001782 (pigmented layer of retina)
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)
0004923 (organ component layer)
0005085 (ectodermal placode)
0005291 (embryonic tissue)
0005388 (photoreceptor array)
0005423 (developing anatomical structure)
0005424 (presumptive retinal pigmented epithelium)
0006598 (presumptive structure)
0007284 (presumptive neural plate)
0007625 (pigment epithelium of eye)

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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