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{{f5samples
{{f5samples
|id=FF:10408-106B3
|F5samples=
|name=lung adenocarcinoma cell line:PC-14
|ancestors_in_anatomy_facet=UBERON:0000061,UBERON:0000062,UBERON:0000077,UBERON:0000118,UBERON:0000119,UBERON:0000170,UBERON:0000171,UBERON:0000464,UBERON:0000465,UBERON:0000466,UBERON:0000467,UBERON:0000468,UBERON:0000475,UBERON:0000477,UBERON:0000479,UBERON:0000480,UBERON:0000481,UBERON:0000483,UBERON:0000915,UBERON:0000922,UBERON:0000923,UBERON:0000925,UBERON:0000926,UBERON:0001004,UBERON:0001007,UBERON:0001041,UBERON:0001048,UBERON:0001062,UBERON:0001555,UBERON:0002048,UBERON:0002050,UBERON:0002224,UBERON:0002532,UBERON:0003104,UBERON:0003258,UBERON:0004119,UBERON:0004120,UBERON:0004185,UBERON:0004921,UBERON:0005153,UBERON:0005178,UBERON:0005181,UBERON:0005423,UBERON:0005597,UBERON:0005911,UBERON:0007026,UBERON:0008947,UBERON:0009142
|sample_id=10408
|rna_tube_id=106B3
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|rna_position=B3
|sample_cell_lot=
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|sample_company=RIKEN Bioresource centre
|rna_lot_number=
|rna_catalog_number=
|sample_species=Human (Homo sapiens)
|sample_strain=
|sample_dev_stage=
|sample_tissue=lung
|sample_donor(cell lot)=
|sample_sex=unknown
|sample_age=unknown
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|rna_rin=9.6
|rna_od260/230=2.07
|rna_od260/280=2.09
|sample_cell_type=unclassifiable
|sample_cell_line=PC-14
|sample_collaboration=Yukio Nakamura (RIKEN BRC)
|sample_experimental_condition=
|sample_disease=lung adenocarcinoma
|rna_sample_type=total RNA
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0
|rna_weight_ug=45.90775
|rna_concentration=1.83631
|sample_note=machine failed, remainder reloaded, low amount
|profile_hcage=CNhs10726,LSID691,release008,COMPLETED
|profile_cagescan=,,,
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|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:0000118,UBERON:0000119,UBERON:0000170,UBERON:0000171,UBERON:0000464,UBERON:0000465,UBERON:0000466,UBERON:0000467,UBERON:0000468,UBERON:0000475,UBERON:0000477,UBERON:0000479,UBERON:0000480,UBERON:0000481,UBERON:0000483,UBERON:0000915,UBERON:0000922,UBERON:0000923,UBERON:0000925,UBERON:0000926,UBERON:0001004,UBERON:0001007,UBERON:0001041,UBERON:0001048,UBERON:0001062,UBERON:0001555,UBERON:0002048,UBERON:0002050,UBERON:0002224,UBERON:0002532,UBERON:0003104,UBERON:0003258,UBERON:0004119,UBERON:0004120,UBERON:0004185,UBERON:0004921,UBERON:0005153,UBERON:0005178,UBERON:0005181,UBERON:0005423,UBERON:0005597,UBERON:0005911,UBERON:0007026,UBERON:0008947,UBERON:0009142
|ancestors_in_disease_facet=DOID:0050687,DOID:14566,DOID:162,DOID:299,DOID:305,DOID:4,DOID:7
|ancestors_in_disease_facet=DOID:0050687,DOID:14566,DOID:162,DOID:299,DOID:305,DOID:4,DOID:7
|sample_description=
|comment=
|created_by=
|creation_date=
|def=
|fonse_cell_line=FF:0100353,FF:0101120
|fonse_cell_line=FF:0100353,FF:0101120
|fonse_cell_line_closure=FF:0100353,FF:0101120
|fonse_cell_line_closure=FF:0100353,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:10408-106B3
|is_a=EFO:0002091;;FF:0000003;;FF:0000210;;FF:0102877
|is_a=EFO:0002091;;FF:0000003;;FF:0000210;;FF:0102877
|name=lung adenocarcinoma cell line:PC-14
|namespace=FANTOM5
|namespace=FANTOM5
|part_of=
|part_of=
|profile_cagescan=,,,
|profile_hcage=CNhs10726,LSID691,release008,COMPLETED
|profile_rnaseq=,,,
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|rna_catalog_number=
|rna_concentration=1.83631
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0
|rna_lot_number=
|rna_od260/230=2.07
|rna_od260/280=2.09
|rna_position=B3
|rna_rin=9.6
|rna_sample_type=total RNA
|rna_tube_id=106B3
|rna_weight_ug=45.90775
|sample_age=unknown
|sample_cell_catalog=RCB0446
|sample_cell_line=PC-14
|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=lung adenocarcinoma
|sample_donor(cell lot)=
|sample_ethnicity=J
|sample_experimental_condition=
|sample_id=10408
|sample_note=machine failed, remainder reloaded, low amount
|sample_sex=unknown
|sample_species=Human (Homo sapiens)
|sample_strain=
|sample_tissue=lung
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}}
}}

Revision as of 14:06, 21 March 2012


Name:lung adenocarcinoma cell line:PC-14
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuelung
dev stageNA
sexunknown
ageunknown
cell typeunclassifiable
cell linePC-14
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
C102-neuroblastoma-testicular-pituitary-carcinosarcoma-rectum-acantholytic-iPS0
C103-CD4-CD8-Natural-Peripheral-Whole-Neutrophils-Basophils0
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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: CNhs10726

Jaspar motifP-value
MA0002.20.751
MA0003.10.723
MA0004.10.644
MA0006.10.0617
MA0007.10.171
MA0009.10.105
MA0014.10.191
MA0017.10.0828
MA0018.20.01
MA0019.10.84
MA0024.10.0833
MA0025.10.91
MA0027.10.943
MA0028.11.62918e-4
MA0029.10.596
MA0030.11.30441e-4
MA0031.10.00476
MA0035.20.0847
MA0038.10.146
MA0039.26.42551e-4
MA0040.10.751
MA0041.10.0282
MA0042.10.437
MA0043.10.342
MA0046.10.119
MA0047.20.00168
MA0048.10.386
MA0050.10.0322
MA0051.10.327
MA0052.10.0249
MA0055.10.00203
MA0057.10.339
MA0058.10.507
MA0059.10.0658
MA0060.10.00212
MA0061.10.00499
MA0062.27.18284e-5
MA0065.20.027
MA0066.10.424
MA0067.10.0135
MA0068.10.324
MA0069.10.56
MA0070.10.294
MA0071.10.77
MA0072.10.509
MA0073.10.606
MA0074.10.789
MA0076.14.14025e-5
MA0077.10.0364
MA0078.10.633
MA0079.20.0793
MA0080.20.118
MA0081.10.0718
MA0083.10.0024
MA0084.10.353
MA0087.10.375
MA0088.10.729
MA0090.10.0752
MA0091.10.0797
MA0092.10.514
MA0093.10.712
MA0099.21.60762e-4
MA0100.10.599
MA0101.10.0657
MA0102.20.408
MA0103.11.90872e-8
MA0104.20.06
MA0105.16.23632e-4
MA0106.10.567
MA0107.10.0581
MA0108.20.00337
MA0111.10.231
MA0112.20.296
MA0113.10.369
MA0114.10.00692
MA0115.10.166
MA0116.10.0278
MA0117.10.0241
MA0119.10.959
MA0122.10.236
MA0124.10.46
MA0125.10.363
MA0131.10.648
MA0135.10.165
MA0136.10.431
MA0137.20.138
MA0138.20.8
MA0139.10.176
MA0140.10.33
MA0141.10.569
MA0142.10.223
MA0143.10.303
MA0144.10.104
MA0145.10.0535
MA0146.10.268
MA0147.10.106
MA0148.17.59018e-6
MA0149.10.591
MA0150.10.00158
MA0152.10.184
MA0153.10.245
MA0154.10.248
MA0155.10.908
MA0156.10.0339
MA0157.10.0494
MA0159.10.327
MA0160.10.101
MA0162.10.838
MA0163.10.0131
MA0164.10.159
MA0258.10.765
MA0259.10.213



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: CNhs10726

Novel motifP-value
10.684
100.377
1000.681
1010.428
1020.609
1030.515
1040.871
1050.0426
1060.00722
1070.553
1080.38
1090.0375
110.392
1100.981
1110.615
1120.242
1130.235
1140.393
1150.356
1160.0491
1170.482
1180.563
1190.773
120.943
1200.652
1210.762
1220.00687
1230.379
1240.6
1250.126
1260.493
1270.971
1280.161
1290.0203
130.296
1300.169
1310.0521
1320.566
1330.0264
1340.349
1350.12
1360.0184
1370.256
1380.957
1390.464
140.844
1400.611
1410.809
1420.946
1430.0218
1440.015
1450.626
1460.0918
1470.251
1480.33
1490.478
150.413
1500.906
1510.868
1520.54
1530.177
1540.0265
1550.623
1560.837
1570.922
1580.866
1590.732
160.621
1600.905
1610.85
1620.432
1630.581
1640.307
1650.517
1660.0352
1670.333
1680.772
1690.274
170.434
180.0572
190.432
20.761
200.788
210.532
220.304
230.831
240.181
250.827
260.604
270.674
280.486
290.428
30.776
300.0656
310.676
320.00732
330.511
340.738
350.0204
360.787
370.122
380.393
390.582
40.786
400.31
410.0555
420.463
430.296
440.475
450.0354
460.514
470.865
480.776
490.152
50.895
500.416
510.96
520.83
530.89
540.624
550.923
560.38
570.795
580.793
590.789
60.25
600.457
610.132
620.423
630.59
640.916
650.905
660.0735
670.499
681.41171e-4
690.923
70.476
700.557
710.931
720.78
730.976
740.157
750.896
760.989
770.0857
780.455
790.00144
80.411
800.694
810.0712
820.00779
830.317
840.987
850.04
860.25
870.0915
880.58
890.991
90.994
900.757
910.843
920.1
930.97
940.295
950.971
960.28
970.0812
980.236
990.465



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: CNhs10726


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)
299 (adenocarcinoma)
305 (carcinoma)
4 (disease)
7 (disease of anatomical entity)

UBERON: Anatomy
0000061 (anatomical structure)
0000062 (organ)
0000077 (mixed endoderm/mesoderm-derived structure)
0000118 (lung bud)
0000119 (cell layer)
0000170 (pair of lungs)
0000171 (respiration organ)
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)
0000483 (epithelium)
0000915 (thoracic segment of trunk)
0000922 (embryo)
0000923 (germ layer)
0000925 (endoderm)
0000926 (mesoderm)
0001004 (respiratory system)
0001007 (digestive system)
0001041 (foregut)
0001048 (primordium)
0001062 (anatomical entity)
0001555 (digestive tract)
0002048 (lung)
0002050 (embryonic structure)
0002224 (thoracic cavity)
0002532 (epiblast (generic))
0003104 (mesenchyme)
0003258 (endoderm of foregut)
0004119 (endoderm-derived structure)
0004120 (mesoderm-derived structure)
0004185 (endodermal part of digestive tract)
0004921 (subdivision of digestive tract)
0005153 (epithelial bud)
0005178 (thoracic cavity element)
0005181 (thoracic segment organ)
0005423 (developing anatomical structure)
0005597 (lung primordium)
0005911 (endo-epithelium)
0007026 (primitive gut)
0008947 (respiratory primordium)
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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