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Revision as of 18:52, 15 May 2017

Name:oral squamous cell carcinoma cell line:HO-1-u-1
Species:Human (Homo sapiens)
Library ID:CNhs11287
Sample type:cell lines
Genomic View: UCSC
RefEX:Specific genes
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuegum
dev stageNA
sexunknown
ageNA
cell typeunclassifiable
cell lineHO-1-u-1
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  SAMD00005382
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11287 CAGE DRX007973 DRR008845
Accession ID Hg19

Library idBAMCTSS
CNhs11287 DRZ000270 DRZ001655
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-penis0.0841
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-lymphoma0.492
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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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: CNhs11287

Jaspar motifP-value
MA0002.20.0012
MA0003.10.218
MA0004.10.186
MA0006.10.402
MA0007.10.764
MA0009.10.297
MA0014.10.0428
MA0017.10.343
MA0018.20.0162
MA0019.10.732
MA0024.12.66232e-4
MA0025.10.555
MA0027.10.119
MA0028.10.037
MA0029.10.0756
MA0030.10.297
MA0031.10.118
MA0035.20.0745
MA0038.12.32456e-4
MA0039.23.71953e-4
MA0040.10.516
MA0041.10.647
MA0042.10.694
MA0043.10.00253
MA0046.10.577
MA0047.20.112
MA0048.10.189
MA0050.11.27532e-7
MA0051.15.30532e-5
MA0052.10.117
MA0055.18.56634e-5
MA0057.10.734
MA0058.10.277
MA0059.10.289
MA0060.11.02741e-19
MA0061.10.0749
MA0062.20.0349
MA0065.20.905
MA0066.10.122
MA0067.10.494
MA0068.10.386
MA0069.10.719
MA0070.10.17
MA0071.10.618
MA0072.10.604
MA0073.10.409
MA0074.10.689
MA0076.10.0225
MA0077.10.206
MA0078.10.295
MA0079.20.804
MA0080.21.76726e-8
MA0081.10.101
MA0083.10.225
MA0084.10.378
MA0087.10.694
MA0088.10.471
MA0090.10.648
MA0091.10.00203
MA0092.10.148
MA0093.10.174
MA0099.20.599
MA0100.10.503
MA0101.10.789
MA0102.20.765
MA0103.13.48759e-5
MA0104.20.00201
MA0105.10.00405
MA0106.10.173
MA0107.10.355
MA0108.20.28
MA0111.10.99
MA0112.20.0359
MA0113.10.114
MA0114.10.968
MA0115.10.78
MA0116.10.0155
MA0117.10.56
MA0119.10.224
MA0122.10.603
MA0124.10.928
MA0125.10.0365
MA0131.10.453
MA0135.10.726
MA0136.11.04228e-4
MA0137.20.274
MA0138.20.303
MA0139.10.679
MA0140.10.067
MA0141.10.835
MA0142.10.0738
MA0143.10.869
MA0144.10.425
MA0145.10.364
MA0146.10.888
MA0147.10.004
MA0148.10.0565
MA0149.10.0687
MA0150.10.368
MA0152.10.817
MA0153.10.346
MA0154.10.022
MA0155.10.132
MA0156.10.0484
MA0157.10.284
MA0159.10.945
MA0160.10.573
MA0162.10.784
MA0163.10.0619
MA0164.10.43
MA0258.10.0962
MA0259.10.0321



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: CNhs11287

Novel motifP-value
10.504
100.515
1000.147
1010.713
1020.477
1030.337
1040.447
1050.0913
1060.00109
1070.174
1080.972
1090.627
110.175
1100.511
1110.548
1120.0458
1130.558
1140.201
1150.98
1160.118
1170.901
1180.465
1190.166
120.687
1200.364
1210.65
1220.242
1230.762
1240.832
1250.829
1260.636
1270.953
1280.0253
1290.598
130.0442
1300.277
1310.38
1320.623
1330.00265
1340.367
1350.236
1360.0268
1370.153
1380.388
1390.0827
140.523
1400.316
1410.25
1420.739
1430.43
1440.327
1450.399
1460.403
1470.905
1480.221
1490.0294
150.528
1500.591
1510.38
1520.296
1530.561
1540.102
1550.747
1560.807
1570.883
1580.944
1590.43
160.483
1600.517
1610.559
1620.9
1630.195
1640.339
1650.636
1660.422
1670.144
1680.513
1690.124
170.656
180.117
190.0557
20.133
200.209
210.494
220.185
230.144
240.51
250.974
260.422
270.165
280.549
290.842
30.44
300.755
310.468
320.00113
330.413
340.267
350.175
360.212
370.323
380.665
390.963
40.224
400.0767
410.361
420.81
430.129
440.501
450.708
460.0788
470.642
480.901
490.493
50.298
500.641
510.243
520.476
530.493
540.315
550.266
560.633
570.778
580.536
590.0245
60.737
600.281
610.539
620.115
630.558
640.882
650.0834
662.28466e-5
670.672
680.3
690.604
70.823
700.0534
710.635
720.325
730.284
740.0947
750.877
760.849
770.0611
780.449
790.0231
80.41
800.0432
810.126
820.00214
830.189
840.844
850.00345
860.274
870.187
880.943
890.0751
90.015
900.308
910.0252
920.0236
930.712
940.0514
950.607
960.132
970.741
980.569
990.551



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: CNhs11287


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)
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)
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)
0004785 (respiratory system mucosa)
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)
0000166 (oral opening)

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)

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:0010316 (germ layer / neural crest)

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