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{{f5samples
{{f5samples
|DRA_sample_Accession=CAGE@SAMD00005525
|DRA_sample_Accession=CAGE@SAMD00005525
|accession_numbers=CAGE;DRX007975;DRR008847;DRZ000272;DRZ001657
|accession_numbers=CAGE;DRX007975;DRR008847;DRZ000272;DRZ001657;DRZ011622;DRZ013007
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0001723,UBERON:0003343,UBERON:0000033,UBERON:0000974,UBERON:0001007,UBERON:0000344,UBERON:0004121,UBERON:0000064,UBERON:0004119,UBERON:0010314,UBERON:0000062,UBERON:0004111,UBERON:0000475,UBERON:0000061,UBERON:0000465,UBERON:0000481,UBERON:0004923,UBERON:0000161,UBERON:0001444,UBERON:0000477,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0000020,UBERON:0004785,UBERON:0001032,UBERON:0003729,UBERON:0010317,UBERON:0001555,UBERON:0001004,UBERON:0000153,UBERON:0007811,UBERON:0000165,UBERON:0004456,UBERON:0000166,UBERON:0001033
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0001723,UBERON:0003343,UBERON:0000033,UBERON:0000974,UBERON:0001007,UBERON:0000344,UBERON:0004121,UBERON:0000064,UBERON:0004119,UBERON:0010314,UBERON:0000062,UBERON:0004111,UBERON:0000475,UBERON:0000061,UBERON:0000465,UBERON:0000481,UBERON:0004923,UBERON:0000161,UBERON:0001444,UBERON:0000477,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0000020,UBERON:0004785,UBERON:0001032,UBERON:0003729,UBERON:0010317,UBERON:0001555,UBERON:0001004,UBERON:0000153,UBERON:0007811,UBERON:0000165,UBERON:0004456,UBERON:0000166,UBERON:0001033
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000548,CL:0000066,CL:0002371,CL:0000076,CL:0000255,CL:0002076,CL:0002251
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000548,CL:0000066,CL:0002371,CL:0000076,CL:0000255,CL:0002076,CL:0002251
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|library_id=CNhs11810
|library_id=CNhs11810
|library_id_phase_based=2:CNhs11810
|library_id_phase_based=2:CNhs11810
|microRNAs=
|microRNAs_nn=
|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/human#cage;sample;10544
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/human#cage;sample;10544
|name=oral squamous cell carcinoma cell line:SAS
|name=oral squamous cell carcinoma cell line:SAS
|namespace=FANTOM5
|namespace=FANTOM5
Line 58: Line 62:
|profile_rnaseq=
|profile_rnaseq=
|profile_srnaseq=,,,
|profile_srnaseq=,,,
|refex=http://refex.dbcls.jp/genelist.php?lang=en&db=human&roku_valid=1&rk[]=&order_key=score
|refex=http://refex.dbcls.jp/genelist.php?lang
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Line 96: Line 100:
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|xref=
|xref=
|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_human;search_select_hide=table111:FF:10544-107H4;search_select_hide=table117:FF:10544-107H4
}}
}}

Latest revision as of 14:28, 3 June 2020

Name:oral squamous cell carcinoma cell line:SAS
Species:Human (Homo sapiens)
Library ID:CNhs11810
Sample type:cell lines
Genomic View: UCSC
RefEX:Specific genes
CAGEd-oPOSSUM:link
ZENBU report :link
Additional information
Sample information
strainNA
tissuetongue
dev stageNA
sexunknown
ageNA
cell typeunclassifiable
cell lineSAS
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

CAGE Accession numbers
MethodSample accession id
CAGE  SAMD00005525
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11810 CAGE DRX007975 DRR008847
Accession ID Hg19

Library idBAMCTSS
CNhs11810 DRZ000272 DRZ001657
Accession ID Hg38

Library idBAMCTSS
CNhs11810 DRZ011622 DRZ013007
Download raw sequence, BAM & CTSS
Hg19
FastaBAMCTSS
downloaddownloaddonwload
Hg38
BAMCTSS
downloaddonwload


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
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C81-trachea-salivary-throat-aorta-eye-submaxillary-parotid0
C82-Basophils-CD14-Eosinophils-Natural-Peripheral-immature-CD340
C83-choriocarcinoma-pancreatic-placenta-chorionic-HES3GFP-testicular-amniotic0
C84-choriocarcinoma-pancreatic-Wilms-Mallassezderived-thymus-salivary-colon0
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



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: CNhs11810

Jaspar motifP-value
MA0002.20.0206
MA0003.10.58
MA0004.10.455
MA0006.10.567
MA0007.10.102
MA0009.10.416
MA0014.10.288
MA0017.10.51
MA0018.20.507
MA0019.10.824
MA0024.11.09721e-4
MA0025.10.985
MA0027.10.272
MA0028.10.0184
MA0029.10.45
MA0030.10.285
MA0031.10.496
MA0035.20.995
MA0038.10.137
MA0039.20.824
MA0040.10.504
MA0041.10.383
MA0042.10.64
MA0043.10.997
MA0046.10.816
MA0047.20.882
MA0048.10.0949
MA0050.10.661
MA0051.10.216
MA0052.10.715
MA0055.10.039
MA0057.11
MA0058.10.956
MA0059.10.11
MA0060.10.0573
MA0061.10.0733
MA0062.20.098
MA0065.20.663
MA0066.10.693
MA0067.10.16
MA0068.10.767
MA0069.10.874
MA0070.10.93
MA0071.10.751
MA0072.10.406
MA0073.10.733
MA0074.10.316
MA0076.10.0362
MA0077.10.487
MA0078.10.111
MA0079.20.87
MA0080.29.36374e-7
MA0081.10.0466
MA0083.10.558
MA0084.10.0967
MA0087.10.0928
MA0088.10.413
MA0090.10.00107
MA0091.10.0846
MA0092.10.505
MA0093.10.506
MA0099.29.33013e-10
MA0100.10.574
MA0101.10.24
MA0102.20.817
MA0103.14.78792e-7
MA0104.20.03
MA0105.10.00202
MA0106.18.8997e-6
MA0107.10.0983
MA0108.20.784
MA0111.10.956
MA0112.20.222
MA0113.10.0653
MA0114.10.48
MA0115.10.131
MA0116.10.00819
MA0117.10.0797
MA0119.10.593
MA0122.10.448
MA0124.10.0893
MA0125.10.628
MA0131.10.311
MA0135.10.771
MA0136.10.038
MA0137.20.0279
MA0138.20.339
MA0139.10.696
MA0140.10.784
MA0141.10.687
MA0142.10.0858
MA0143.10.786
MA0144.10.329
MA0145.10.435
MA0146.10.48
MA0147.10.00536
MA0148.10.281
MA0149.10.298
MA0150.10.658
MA0152.10.775
MA0153.10.642
MA0154.10.0651
MA0155.10.228
MA0156.10.273
MA0157.10.402
MA0159.10.35
MA0160.10.671
MA0162.10.0586
MA0163.17.84473e-5
MA0164.10.246
MA0258.10.0788
MA0259.10.424



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: CNhs11810

Novel motifP-value
10.881
100.842
1000.684
1010.198
1020.304
1030.376
1040.29
1050.848
1060.237
1070.0601
1080.361
1090.314
110.427
1100.266
1110.925
1120.574
1130.016
1140.455
1150.414
1160.0856
1170.601
1180.327
1190.623
120.531
1200.0428
1210.672
1220.246
1230.564
1240.00655
1250.727
1260.643
1270.439
1280.0868
1290.186
130.142
1300.752
1310.0993
1320.648
1330.0141
1349.5436e-4
1350.0162
1360.0264
1370.121
1380.82
1390.0649
140.881
1400.722
1410.754
1420.662
1430.0645
1440.595
1450.986
1460.825
1470.321
1480.889
1490.518
150.542
1500.13
1510.671
1520.255
1530.724
1540.383
1550.892
1560.948
1570.993
1580.186
1590.394
160.349
1600.78
1610.792
1620.476
1630.594
1640.104
1650.885
1660.0633
1670.331
1680.536
1690.828
170.355
180.497
190.0357
20.841
200.261
210.529
220.648
230.274
240.749
250.887
260.709
270.599
280.521
290.274
30.898
300.43
310.219
320.0013
330.143
340.069
350.197
360.651
370.555
380.953
390.528
40.515
400.586
410.114
420.932
430.0365
440.447
450.59
460.426
470.657
480.651
490.0362
50.0593
500.565
510.776
520.535
530.146
540.69
550.833
560.58
570.219
580.84
590.173
60.497
600.47
610.246
620.631
630.797
640.81
650.961
660.267
670.747
680.13
690.362
70.797
700.24
710.471
720.574
730.387
740.576
750.143
760.11
770.685
780.108
790.0793
80.97
800.192
810.0685
820.00331
830.502
840.703
850.00833
860.966
870.0662
880.773
890.342
90.396
900.17
910.141
920.371
930.542
940.192
950.158
960.194
970.679
980.22
990.948



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: CNhs11810


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)
0000548 (animal cell)
0000066 (epithelial cell)
0002371 (somatic cell)
0000076 (squamous epithelial cell)
0000255 (eukaryotic cell)
0002076 (endo-epithelial cell)
0002251 (epithelial cell of alimentary canal)

DOID: Disease
4 (disease)
162 (cancer)
14566 (disease of cellular proliferation)
0050687 (cell type cancer)
7 (disease of anatomical entity)
305 (carcinoma)
1749 (squamous cell carcinoma)

UBERON: Anatomy
0000468 (multi-cellular organism)
0001723 (tongue)
0003343 (mucosa of oral region)
0000033 (head)
0000974 (neck)
0001007 (digestive system)
0000344 (mucosa)
0004121 (ectoderm-derived structure)
0000064 (organ part)
0004119 (endoderm-derived structure)
0010314 (structure with developmental contribution from neural crest)
0000062 (organ)
0004111 (anatomical conduit)
0000475 (organism subdivision)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000481 (multi-tissue structure)
0004923 (organ component layer)
0000161 (orifice)
0001444 (subdivision of head)
0000477 (anatomical cluster)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0000020 (sense organ)
0004785 (respiratory system mucosa)
0001032 (sensory system)
0003729 (mouth mucosa)
0010317 (germ layer / neural crest derived structure)
0001555 (digestive tract)
0001004 (respiratory system)
0000153 (anterior region of body)
0007811 (craniocervical region)
0000165 (mouth)
0004456 (entire sense organ system)
0000166 (oral opening)
0001033 (gustatory system)

FF: FANTOM5
0000102 (sample by type)
0000003 (cell line sample)
0000210 (human sample)
0000101 (sample by species)
0000001 (sample)
0100297 (carcinoma cell line sample)
0102024 (squamous cell carcinoma cell line sample)
0101120 (epithelial cell line sample)
0102211 (oral squamous cell carcinoma cell line sample)
0102027 (oral cancer cell line sample)
0102709 (head and neck squamous cell carcinoma cell line sample)
0100786 (tongue cancer cell line sample)
0103980 (tongue squamous cell carcinoma cell line sample)
0103981 (SAS cell sample)

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
CL:0000223 (endodermal cell)
UBERON:0002532 (epiblast (generic))
UBERON:0006601 (presumptive ectoderm)
UBERON:0006595 (presumptive endoderm)
UBERON:0008814 (pharyngeal arch system)
UBERON:0010056 (future tongue)
UBERON:0010316 (germ layer / neural crest)

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