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{{f5samples
{{f5samples
|F5samples=
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|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000004,CL:0000012,CL:0000063,CL:0000066,CL:0000076,CL:0000255,CL:0000548
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000004,CL:0000012,CL:0000063,CL:0000066,CL:0000076,CL:0000255,CL:0000548
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|creation_date=
|creation_date=
|def=
|def=
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|fonse_cell_line=FF:0101120,FF:0102027
|fonse_cell_line=FF:0101120,FF:0102027
|fonse_cell_line_closure=FF:0101120,FF:0102027
|fonse_cell_line_closure=FF:0101120,FF:0102027

Revision as of 16:49, 29 March 2012


Name:oral squamous cell carcinoma cell line:HSC-3
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuetongue
dev stageNA
sexmale
age64
cell typeunclassifiable
cell lineHSC-3
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-penis0.195
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-lymphoma0.277
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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: CNhs11717

Jaspar motifP-value
MA0002.20.289
MA0003.10.864
MA0004.10.829
MA0006.10.171
MA0007.10.437
MA0009.10.0449
MA0014.10.883
MA0017.10.416
MA0018.22.20961e-5
MA0019.10.647
MA0024.10.283
MA0025.10.432
MA0027.10.438
MA0028.10.788
MA0029.10.46
MA0030.10.0761
MA0031.10.169
MA0035.20.711
MA0038.10.00323
MA0039.20.933
MA0040.10.0965
MA0041.10.434
MA0042.10.207
MA0043.11.77572e-4
MA0046.10.162
MA0047.20.336
MA0048.10.622
MA0050.10.00389
MA0051.10.0624
MA0052.10.0021
MA0055.10.406
MA0057.10.421
MA0058.10.735
MA0059.10.553
MA0060.15.36407e-5
MA0061.10.536
MA0062.20.0938
MA0065.20.0042
MA0066.10.0584
MA0067.10.00323
MA0068.10.00397
MA0069.10.263
MA0070.10.336
MA0071.10.478
MA0072.10.252
MA0073.10.398
MA0074.10.477
MA0076.10.271
MA0077.10.468
MA0078.10.761
MA0079.20.24
MA0080.25.28315e-6
MA0081.10.0212
MA0083.10.00216
MA0084.10.321
MA0087.10.604
MA0088.10.322
MA0090.10.0285
MA0091.10.371
MA0092.11
MA0093.10.79
MA0099.20.119
MA0100.10.326
MA0101.10.162
MA0102.20.13
MA0103.16.49669e-6
MA0104.20.646
MA0105.13.52174e-4
MA0106.14.57307e-7
MA0107.10.171
MA0108.20.0021
MA0111.10.21
MA0112.20.00185
MA0113.10.565
MA0114.10.145
MA0115.10.943
MA0116.10.00163
MA0117.10.564
MA0119.10.0246
MA0122.10.648
MA0124.10.0157
MA0125.10.623
MA0131.10.469
MA0135.10.333
MA0136.13.67249e-4
MA0137.20.0363
MA0138.20.595
MA0139.10.143
MA0140.10.831
MA0141.10.474
MA0142.15.67593e-4
MA0143.10.342
MA0144.10.971
MA0145.10.162
MA0146.10.401
MA0147.10.653
MA0148.10.27
MA0149.10.0773
MA0150.10.769
MA0152.10.314
MA0153.10.614
MA0154.10.0156
MA0155.10.987
MA0156.10.00892
MA0157.10.621
MA0159.10.0638
MA0160.10.834
MA0162.10.219
MA0163.12.46752e-6
MA0164.10.909
MA0258.10.196
MA0259.10.912



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: CNhs11717

Novel motifP-value
10.159
100.148
1000.23
1010.641
1020.297
1030.0862
1040.605
1050.587
1060.0251
1070.00702
1080.191
1090.0153
110.224
1100.0337
1110.628
1120.0708
1130.104
1140.0917
1150.753
1160.572
1170.0213
1180.312
1190.264
120.182
1200.0246
1210.402
1220.965
1230.447
1240.0793
1250.418
1260.551
1270.654
1280.568
1290.087
130.0442
1300.972
1310.251
1320.308
1330.024
1340.0157
1350.89
1360.133
1370.227
1380.0304
1390.862
140.906
1400.934
1410.0455
1420.93
1430.0531
1440.96
1450.152
1460.57
1470.434
1480.868
1490.203
150.489
1500.279
1510.408
1520.463
1530.947
1540.988
1550.49
1560.701
1570.875
1580.25
1590.625
160.0249
1600.0885
1610.0591
1620.159
1630.717
1640.0877
1650.0941
1660.66
1670.152
1680.171
1690.0119
170.102
180.235
190.683
20.267
200.998
210.11
220.803
230.775
240.0783
250.455
260.182
270.531
280.496
290.0332
30.205
300.596
310.758
320.605
330.219
340.469
350.431
360.581
370.52
380.354
390.586
40.973
400.351
410.273
420.539
430.477
440.00292
450.372
460.0865
470.138
480.175
490.79
50.832
500.778
510.604
520.364
530.889
540.675
550.167
560.418
570.0425
580.277
590.125
60.783
600.0731
610.914
620.273
630.191
640.396
650.326
660.836
670.728
680.127
690.137
70.161
700.024
710.0197
720.444
730.407
740.274
750.0516
760.491
770.225
780.0112
790.644
80.119
800.061
810.384
820.942
830.708
840.257
850.619
860.344
870.0839
880.431
890.0371
90.713
900.74
910.708
920.42
930.542
940.913
950.63
960.891
970.94
980.953
990.309



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: CNhs11717


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)
0000076 (squamous epithelial cell)
0000255 (eukaryotic cell)
0000548 (animal cell)

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

UBERON: Anatomy
0000033 (head)
0000061 (anatomical structure)
0000062 (organ)
0000064 (organ part)
0000153 (anterior region of body)
0000161 (orifice)
0000165 (mouth)
0000166 (oral opening)
0000344 (mucosa)
0000464 (anatomical space)
0000465 (material anatomical entity)
0000466 (immaterial anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000475 (organism subdivision)
0000477 (anatomical cluster)
0000480 (anatomical group)
0000481 (multi-tissue structure)
0000922 (embryo)
0000923 (germ layer)
0000925 (endoderm)
0000930 (stomodeum)
0000974 (neck)
0001004 (respiratory system)
0001007 (digestive system)
0001062 (anatomical entity)
0001444 (subdivision of head)
0001555 (digestive tract)
0002050 (embryonic structure)
0002532 (epiblast (generic))
0003343 (mucosa of oral region)
0003729 (mouth mucosa)
0004111 (anatomical conduit)
0004119 (endoderm-derived structure)
0004785 (respiratory system mucosa)
0004923 (organ component layer)
0005423 (developing anatomical structure)
0007026 (primitive gut)

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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