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{{f5samples
{{f5samples
|F5samples=
|ancestors_in_anatomy_facet=UBERON:0000061,UBERON:0000062,UBERON:0000077,UBERON:0000118,UBERON:0000119,UBERON:0000170,UBERON:0000171,UBERON:0000464,UBERON:0000465,UBERON:0000466,UBERON:0000467,UBERON:0000468,UBERON:0000475,UBERON:0000477,UBERON:0000479,UBERON:0000480,UBERON:0000481,UBERON:0000483,UBERON:0000915,UBERON:0000922,UBERON:0000923,UBERON:0000925,UBERON:0000926,UBERON:0001004,UBERON:0001007,UBERON:0001041,UBERON:0001048,UBERON:0001062,UBERON:0001555,UBERON:0002048,UBERON:0002050,UBERON:0002224,UBERON:0002532,UBERON:0003104,UBERON:0003258,UBERON:0004119,UBERON:0004120,UBERON:0004185,UBERON:0004921,UBERON:0005153,UBERON:0005178,UBERON:0005181,UBERON:0005423,UBERON:0005597,UBERON:0005911,UBERON:0007026,UBERON:0008947,UBERON:0009142
|ancestors_in_anatomy_facet=UBERON:0000061,UBERON:0000062,UBERON:0000077,UBERON:0000118,UBERON:0000119,UBERON:0000170,UBERON:0000171,UBERON:0000464,UBERON:0000465,UBERON:0000466,UBERON:0000467,UBERON:0000468,UBERON:0000475,UBERON:0000477,UBERON:0000479,UBERON:0000480,UBERON:0000481,UBERON:0000483,UBERON:0000915,UBERON:0000922,UBERON:0000923,UBERON:0000925,UBERON:0000926,UBERON:0001004,UBERON:0001007,UBERON:0001041,UBERON:0001048,UBERON:0001062,UBERON:0001555,UBERON:0002048,UBERON:0002050,UBERON:0002224,UBERON:0002532,UBERON:0003104,UBERON:0003258,UBERON:0004119,UBERON:0004120,UBERON:0004185,UBERON:0004921,UBERON:0005153,UBERON:0005178,UBERON:0005181,UBERON:0005423,UBERON:0005597,UBERON:0005911,UBERON:0007026,UBERON:0008947,UBERON:0009142
|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:0100353,FF:0101120
|fonse_cell_line=FF:0100353,FF:0101120
|fonse_cell_line_closure=FF:0100353,FF:0101120
|fonse_cell_line_closure=FF:0100353,FF:0101120

Revision as of 16:55, 29 March 2012


Name:large cell non-keratinizing squamous carcinoma cell line:SKG-II-SF
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuecervix
dev stageNA
sexfemale
age50
cell typeunclassifiable
cell lineSKG-II-SF
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-penis0.0335
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-lymphoma0.435
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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: CNhs11825

Jaspar motifP-value
MA0002.20.00609
MA0003.10.333
MA0004.10.942
MA0006.10.796
MA0007.10.53
MA0009.10.8
MA0014.10.136
MA0017.10.0223
MA0018.20.317
MA0019.10.451
MA0024.10.001
MA0025.10.168
MA0027.10.293
MA0028.10.101
MA0029.10.041
MA0030.10.194
MA0031.10.456
MA0035.20.585
MA0038.10.00559
MA0039.20.013
MA0040.10.74
MA0041.10.504
MA0042.10.442
MA0043.10.0452
MA0046.10.954
MA0047.20.994
MA0048.10.843
MA0050.10.35
MA0051.10.909
MA0052.10.382
MA0055.10.0733
MA0057.10.931
MA0058.10.595
MA0059.10.362
MA0060.12.79108e-9
MA0061.10.0138
MA0062.20.14
MA0065.20.0484
MA0066.10.00381
MA0067.10.815
MA0068.10.576
MA0069.10.487
MA0070.10.719
MA0071.10.0754
MA0072.10.225
MA0073.10.965
MA0074.10.158
MA0076.10.0521
MA0077.10.782
MA0078.10.349
MA0079.20.296
MA0080.27.15372e-9
MA0081.10.266
MA0083.10.921
MA0084.10.886
MA0087.10.956
MA0088.10.399
MA0090.10.0262
MA0091.10.0279
MA0092.10.168
MA0093.10.991
MA0099.20.0299
MA0100.10.931
MA0101.10.347
MA0102.20.793
MA0103.10.0336
MA0104.20.531
MA0105.11.59175e-6
MA0106.10.0539
MA0107.10.206
MA0108.20.0419
MA0111.10.487
MA0112.29.67941e-5
MA0113.10.0558
MA0114.10.161
MA0115.10.893
MA0116.13.21131e-4
MA0117.10.555
MA0119.10.159
MA0122.10.538
MA0124.10.827
MA0125.10.135
MA0131.10.536
MA0135.10.549
MA0136.19.35734e-5
MA0137.20.665
MA0138.20.0292
MA0139.10.266
MA0140.10.978
MA0141.10.0238
MA0142.10.487
MA0143.10.366
MA0144.10.415
MA0145.10.266
MA0146.10.446
MA0147.10.509
MA0148.10.897
MA0149.10.517
MA0150.10.485
MA0152.10.547
MA0153.10.913
MA0154.10.00435
MA0155.10.216
MA0156.10.433
MA0157.10.392
MA0159.10.183
MA0160.10.241
MA0162.10.52
MA0163.11.68337e-5
MA0164.10.696
MA0258.13.59877e-4
MA0259.10.98



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: CNhs11825

Novel motifP-value
10.052
100.201
1000.739
1010.547
1020.568
1030.225
1040.633
1050.549
1060.112
1070.722
1080.7
1090.942
110.0565
1100.299
1110.198
1120.148
1130.201
1140.0157
1150.712
1160.47
1170.264
1180.638
1190.0901
120.995
1200.394
1210.211
1220.262
1230.993
1240.00563
1250.15
1260.645
1270.616
1280.00936
1290.177
130.873
1300.259
1310.949
1320.632
1330.231
1340.164
1350.0104
1360.0884
1370.355
1380.802
1390.00265
140.499
1400.265
1410.6
1420.263
1430.012
1440.163
1450.15
1460.917
1470.846
1480.0424
1490.0167
150.227
1500.85
1510.435
1520.875
1530.352
1540.77
1550.695
1560.513
1570.233
1580.325
1590.594
160.369
1600.155
1610.667
1620.823
1630.846
1640.625
1650.947
1660.835
1670.891
1680.385
1690.0474
170.231
180.138
190.103
20.548
200.2
210.746
220.131
230.377
240.784
250.491
260.198
270.0604
280.841
290.372
30.046
300.739
310.352
320.00445
330.692
340.402
350.0243
360.922
370.0976
380.509
390.59
40.758
400.476
410.0562
420.312
430.0765
440.014
450.701
460.0209
470.193
480.222
490.143
50.0689
500.771
510.271
520.679
530.6
540.404
550.616
560.584
570.639
580.273
590.0896
60.725
600.229
610.859
620.0501
630.44
640.306
650.215
660.159
670.593
680.334
690.264
70.49
700.0963
710.133
720.438
730.559
740.0348
750.209
760.832
770.181
780.941
790.00195
80.0432
800.669
810.142
820.0314
830.315
840.939
850.00106
860.283
870.207
880.912
890.11
90.177
900.00987
910.157
920.0377
930.104
940.025
950.729
960.11
970.755
980.0664
990.975



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: CNhs11825


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
0000061 (anatomical structure)
0000062 (organ)
0000077 (mixed endoderm/mesoderm-derived structure)
0000118 (lung bud)
0000119 (cell layer)
0000170 (pair of lungs)
0000171 (respiration organ)
0000464 (anatomical space)
0000465 (material anatomical entity)
0000466 (immaterial anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000475 (organism subdivision)
0000477 (anatomical cluster)
0000479 (tissue)
0000480 (anatomical group)
0000481 (multi-tissue structure)
0000483 (epithelium)
0000915 (thoracic segment of trunk)
0000922 (embryo)
0000923 (germ layer)
0000925 (endoderm)
0000926 (mesoderm)
0001004 (respiratory system)
0001007 (digestive system)
0001041 (foregut)
0001048 (primordium)
0001062 (anatomical entity)
0001555 (digestive tract)
0002048 (lung)
0002050 (embryonic structure)
0002224 (thoracic cavity)
0002532 (epiblast (generic))
0003104 (mesenchyme)
0003258 (endoderm of foregut)
0004119 (endoderm-derived structure)
0004120 (mesoderm-derived structure)
0004185 (endodermal part of digestive tract)
0004921 (subdivision of digestive tract)
0005153 (epithelial bud)
0005178 (thoracic cavity element)
0005181 (thoracic segment organ)
0005423 (developing anatomical structure)
0005597 (lung primordium)
0005911 (endo-epithelium)
0007026 (primitive gut)
0008947 (respiratory primordium)
0009142 (entire embryonic mesenchyme)

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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