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{{f5samples
{{f5samples
|F5samples=
|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_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 16:32, 29 March 2012


Name:anaplastic carcinoma cell line:8305C
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 line8305C
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-penis-0.0569
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-lymphoma-0.177
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
C110-leukemia-chronic-Eosinophils-acute-Whole-CD34-Lymphatic0
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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: CNhs10745

Jaspar motifP-value
MA0002.20.0593
MA0003.10.0963
MA0004.10.976
MA0006.10.851
MA0007.10.0708
MA0009.10.477
MA0014.10.776
MA0017.15.2888e-4
MA0018.20.00571
MA0019.10.19
MA0024.10.534
MA0025.10.921
MA0027.10.77
MA0028.10.00372
MA0029.10.451
MA0030.10.247
MA0031.10.0364
MA0035.20.486
MA0038.10.473
MA0039.20.252
MA0040.10.898
MA0041.10.387
MA0042.10.761
MA0043.10.566
MA0046.10.5
MA0047.20.0559
MA0048.10.255
MA0050.14.22286e-8
MA0051.11.10064e-6
MA0052.10.0458
MA0055.10.931
MA0057.10.153
MA0058.10.741
MA0059.10.415
MA0060.10.33
MA0061.10.971
MA0062.20.0838
MA0065.22.61773e-4
MA0066.10.043
MA0067.10.0356
MA0068.10.395
MA0069.10.445
MA0070.10.13
MA0071.10.0125
MA0072.10.18
MA0073.10.261
MA0074.10.998
MA0076.10.00398
MA0077.10.453
MA0078.10.726
MA0079.20.416
MA0080.21.00156e-4
MA0081.10.567
MA0083.10.424
MA0084.10.237
MA0087.10.297
MA0088.10.297
MA0090.10.0237
MA0091.10.0641
MA0092.10.18
MA0093.10.844
MA0099.25.15885e-5
MA0100.10.628
MA0101.10.181
MA0102.20.115
MA0103.10.0469
MA0104.20.752
MA0105.10.12
MA0106.10.288
MA0107.10.072
MA0108.20.27
MA0111.10.439
MA0112.21.00023e-4
MA0113.10.257
MA0114.10.00632
MA0115.10.0136
MA0116.10.00467
MA0117.10.494
MA0119.10.966
MA0122.10.78
MA0124.10.661
MA0125.10.498
MA0131.10.128
MA0135.10.128
MA0136.10.356
MA0137.20.554
MA0138.20.0888
MA0139.10.526
MA0140.10.8
MA0141.18.40797e-4
MA0142.10.0182
MA0143.10.658
MA0144.10.382
MA0145.10.0565
MA0146.10.00364
MA0147.10.66
MA0148.10.287
MA0149.10.834
MA0150.10.251
MA0152.10.0315
MA0153.10.611
MA0154.10.0135
MA0155.10.356
MA0156.10.152
MA0157.10.362
MA0159.10.211
MA0160.10.014
MA0162.10.373
MA0163.19.25566e-4
MA0164.10.0637
MA0258.10.00123
MA0259.10.827



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: CNhs10745

Novel motifP-value
10.115
100.313
1000.98
1010.573
1020.119
1030.176
1040.471
1050.124
1060.584
1070.641
1080.495
1090.0768
110.243
1100.705
1110.352
1120.00396
1130.107
1140.083
1150.239
1160.526
1170.419
1180.925
1190.32
120.655
1200.715
1210.558
1220.0238
1230.617
1240.409
1250.789
1260.446
1270.188
1280.379
1290.158
130.213
1300.685
1310.535
1320.993
1330.737
1340.691
1350.652
1360.397
1370.851
1380.501
1390.941
140.224
1400.012
1410.0308
1420.122
1430.832
1440.908
1450.969
1460.931
1470.71
1480.0647
1490.474
150.813
1500.789
1510.408
1520.18
1530.555
1540.844
1550.173
1560.536
1570.907
1580.345
1590.604
160.257
1600.0969
1610.749
1620.581
1630.109
1640.374
1650.955
1660.613
1670.533
1680.0427
1690.00728
170.166
180.784
190.212
20.455
200.387
210.713
220.0598
230.949
240.395
250.225
260.418
270.135
280.893
290.286
30.66
300.671
310.255
320.00641
330.903
340.0584
350.748
360.454
370.198
380.165
390.799
40.384
400.0861
410.0103
420.901
430.156
440.034
450.61
460.394
470.128
480.329
490.0929
50.863
500.978
510.124
520.204
530.634
540.296
550.162
560.317
570.688
580.108
590.0101
60.65
600.0752
610.293
620.0388
630.589
640.526
650.26
660.945
670.911
680.94
690.526
70.0466
700.164
710.189
720.372
730.0822
740.269
750.294
760.397
770.052
780.153
790.576
80.215
800.205
810.397
820.0595
830.315
840.684
850.194
860.885
870.425
880.873
890.0342
90.279
900.766
910.52
920.283
930.819
940.585
950.0534
960.0968
970.638
980.00228
990.366



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: CNhs10745


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)
305 (carcinoma)
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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