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{{f5samples
{{f5samples
|F5samples=
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|ancestors_in_anatomy_facet=UBERON:0000061,UBERON:0000062,UBERON:0000063,UBERON:0000064,UBERON:0000065,UBERON:0000072,UBERON:0000077,UBERON:0000119,UBERON:0000465,UBERON:0000467,UBERON:0000468,UBERON:0000479,UBERON:0000480,UBERON:0000481,UBERON:0000483,UBERON:0000490,UBERON:0000922,UBERON:0000923,UBERON:0000925,UBERON:0000926,UBERON:0000949,UBERON:0001004,UBERON:0001007,UBERON:0001041,UBERON:0001042,UBERON:0001048,UBERON:0001062,UBERON:0001555,UBERON:0001557,UBERON:0002046,UBERON:0002050,UBERON:0002368,UBERON:0002530,UBERON:0002532,UBERON:0003091,UBERON:0003104,UBERON:0004117,UBERON:0004119,UBERON:0004120,UBERON:0004185,UBERON:0004921,UBERON:0005291,UBERON:0005423,UBERON:0005911,UBERON:0006562,UBERON:0007026,UBERON:0007123,UBERON:0007689,UBERON:0007690,UBERON:0008814,UBERON:0009142,UBERON:0009145
|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
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|creation_date=
|creation_date=
|def=
|def=
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|fonse_cell_line=FF:0101120,FF:0101610
|fonse_cell_line=FF:0101120,FF:0101610
|fonse_cell_line_closure=FF:0101120,FF:0101610
|fonse_cell_line_closure=FF:0101120,FF:0101610

Revision as of 16:49, 29 March 2012


Name:papillary adenocarcinoma cell line:8505C
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuethyroid
dev stageNA
sexunknown
ageNA
cell typeunclassifiable
cell line8505C
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]


Relative expression to median (log10)

Transcription factors with enriched expression in this sampleRanked list of transcription factor promoter expression in this sample relative to the median expression in the FANTOM5 collection is shown. Value is log10 transformed.



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-penis0.105
C106-Hep2-epitheloid-placenta-cervical-rectal-anaplastic-glassy0
C107-Neutrophils-CD14-Eosinophils-Monocytederived-Whole-Peripheral-blood0
C108-breast-hepatoblastoma-MCF7-parotid-salivary-submaxillary-prostate0
C109-Reticulocytes-non-acute-Hodgkin-Burkitt-retinoblastoma-lymphoma0.335
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
C110-leukemia-chronic-Eosinophils-acute-Whole-CD34-Lymphatic0
C111-medulla-lung-trachea-testis-caudate-epididymis-throat0
C112-gastric-pancreas-temporal-duodenum-small-extraskeletal-adrenal0
C113-thyroid-throat-lung-lymph-small-colon-trachea0
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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: CNhs11716

Jaspar motifP-value
MA0002.20.0382
MA0003.10.0794
MA0004.10.357
MA0006.10.994
MA0007.10.216
MA0009.10.827
MA0014.10.786
MA0017.10.0305
MA0018.20.0103
MA0019.10.568
MA0024.12.18956e-4
MA0025.10.0013
MA0027.10.761
MA0028.10.0115
MA0029.10.916
MA0030.10.398
MA0031.10.28
MA0035.20.0517
MA0038.10.0294
MA0039.20.677
MA0040.10.895
MA0041.10.517
MA0042.10.61
MA0043.10.00186
MA0046.10.00375
MA0047.20.632
MA0048.10.406
MA0050.10.243
MA0051.10.014
MA0052.10.0101
MA0055.10.0479
MA0057.10.521
MA0058.10.705
MA0059.10.0651
MA0060.10.233
MA0061.10.0253
MA0062.20.177
MA0065.20.784
MA0066.10.85
MA0067.10.0471
MA0068.10.0424
MA0069.10.984
MA0070.10.487
MA0071.10.258
MA0072.10.464
MA0073.10.909
MA0074.10.956
MA0076.10.0943
MA0077.10.543
MA0078.10.367
MA0079.27.79814e-5
MA0080.21.27889e-5
MA0081.10.166
MA0083.10.428
MA0084.10.156
MA0087.10.261
MA0088.10.266
MA0090.10.00357
MA0091.10.0898
MA0092.10.645
MA0093.10.402
MA0099.20.456
MA0100.10.605
MA0101.10.139
MA0102.20.05
MA0103.10.106
MA0104.20.0535
MA0105.10.358
MA0106.10.462
MA0107.10.051
MA0108.20.0556
MA0111.10.467
MA0112.20.452
MA0113.10.0503
MA0114.10.289
MA0115.10.515
MA0116.10.257
MA0117.10.0577
MA0119.10.0594
MA0122.10.827
MA0124.10.0244
MA0125.10.45
MA0131.10.389
MA0135.10.0199
MA0136.10.00788
MA0137.20.119
MA0138.20.217
MA0139.10.825
MA0140.10.297
MA0141.10.515
MA0142.10.192
MA0143.10.127
MA0144.10.346
MA0145.10.0478
MA0146.10.0546
MA0147.10.00714
MA0148.10.446
MA0149.10.044
MA0150.10.0758
MA0152.10.783
MA0153.10.11
MA0154.10.366
MA0155.10.167
MA0156.10.627
MA0157.10.481
MA0159.10.0179
MA0160.10.0323
MA0162.10.0242
MA0163.10.357
MA0164.10.442
MA0258.10.131
MA0259.10.0359



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: CNhs11716

Novel motifP-value
10.701
100.184
1000.0488
1010.753
1020.927
1030.293
1040.734
1050.0154
1060.507
1070.923
1080.676
1090.259
110.714
1100.706
1110.525
1120.794
1130.0423
1140.547
1150.641
1160.95
1170.566
1180.0326
1190.852
120.0793
1200.0829
1210.861
1220.55
1230.886
1240.0865
1250.388
1260.989
1270.599
1280.00731
1290.805
130.0568
1300.256
1310.731
1320.593
1330.191
1340.0122
1350.856
1360.0913
1370.102
1380.688
1390.0291
140.248
1400.787
1410.983
1420.955
1430.0504
1440.788
1450.833
1460.46
1470.11
1480.573
1490.795
150.921
1500.311
1510.45
1520.0329
1530.302
1540.773
1550.355
1560.448
1570.525
1580.0246
1590.645
160.663
1600.196
1610.33
1620.868
1630.663
1640.0387
1650.329
1660.866
1670.0662
1680.6
1690.856
170.825
180.193
190.58
20.175
200.0388
210.00255
220.085
230.531
240.649
250.232
260.348
270.793
280.554
290.115
30.846
300.294
310.555
320.912
330.0425
340.0569
350.895
360.541
370.902
380.872
390.677
40.158
400.504
410.647
420.84
430.316
440.0536
450.229
460.749
470.987
480.913
490.0739
50.421
500.906
510.618
520.0795
530.142
540.746
550.995
560.665
570.176
580.605
590.557
60.784
600.175
610.773
620.661
630.506
640.572
650.464
660.94
670.554
680.926
690.335
70.62
700.0681
710.347
720.331
730.515
740.531
750.761
760.132
770.809
780.844
790.15
80.144
800.00308
810.948
820.1
830.967
840.182
850.3
860.236
870.159
880.867
890.909
90.176
900.595
910.798
920.992
930.109
940.509
950.466
960.118
970.715
980.963
990.0742



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: CNhs11716


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)
3112 (papillary adenocarcinoma)
4 (disease)
7 (disease of anatomical entity)

UBERON: Anatomy
0000061 (anatomical structure)
0000062 (organ)
0000063 (organ segment)
0000064 (organ part)
0000065 (respiratory tract)
0000072 (segment of respiratory tract)
0000077 (mixed endoderm/mesoderm-derived structure)
0000119 (cell layer)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000479 (tissue)
0000480 (anatomical group)
0000481 (multi-tissue structure)
0000483 (epithelium)
0000490 (unilaminar epithelium)
0000922 (embryo)
0000923 (germ layer)
0000925 (endoderm)
0000926 (mesoderm)
0000949 (endocrine system)
0001004 (respiratory system)
0001007 (digestive system)
0001041 (foregut)
0001042 (chordate pharynx)
0001048 (primordium)
0001062 (anatomical entity)
0001555 (digestive tract)
0001557 (upper respiratory tract)
0002046 (thyroid gland)
0002050 (embryonic structure)
0002368 (endocrine gland)
0002530 (gland)
0002532 (epiblast (generic))
0003091 (thyroid primordium)
0003104 (mesenchyme)
0004117 (pharyngeal pouch)
0004119 (endoderm-derived structure)
0004120 (mesoderm-derived structure)
0004185 (endodermal part of digestive tract)
0004921 (subdivision of digestive tract)
0005291 (embryonic tissue)
0005423 (developing anatomical structure)
0005911 (endo-epithelium)
0006562 (pharynx)
0007026 (primitive gut)
0007123 (pharyngeal pouch 2)
0007689 (thyroid diverticulum)
0007690 (early pharyngeal endoderm)
0008814 (pharyngeal arch system)
0009142 (entire embryonic mesenchyme)
0009145 (pharyngeal region of foregut)

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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