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{{f5samples
{{f5samples
|DRA_sample_Accession=CAGE@SAMD00005899
|DRA_sample_Accession=CAGE@SAMD00005899
|accession_numbers=CAGE;DRX007839;DRR008711;DRZ000136;DRZ001521
|accession_numbers=CAGE;DRX007839;DRR008711;DRZ000136;DRZ001521;DRZ011486;DRZ012871
|ancestors_in_anatomy_facet=
|ancestors_in_anatomy_facet=
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000548,CL:0000066,CL:0000076,CL:0000255
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000548,CL:0000066,CL:0000076,CL:0000255
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|profile_rnaseq=
|profile_rnaseq=
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|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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Revision as of 19:44, 10 August 2017

Name:bronchial squamous cell carcinoma cell line:KNS-62
Species:Human (Homo sapiens)
Library ID:CNhs11862
Sample type:cell lines
Genomic View: UCSC
RefEX:Specific genes
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuelung
dev stageNA
sexmale
age49
cell typeunclassifiable
cell lineKNS-62
companyJAPAN HEALTH SCIENCES FOUNDATION - Health Science Research Resources Bank
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
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  SAMD00005899
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11862 CAGE DRX007839 DRR008711
Accession ID Hg19

Library idBAMCTSS
CNhs11862 DRZ000136 DRZ001521
Accession ID Hg38

Library idBAMCTSS
CNhs11862 DRZ011486 DRZ012871
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
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-penis0.405
C106-Hep2-epitheloid-placenta-cervical-rectal-anaplastic-glassy0
C107-Neutrophils-CD14-Eosinophils-Monocytederived-Whole-Peripheral-blood0
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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: CNhs11862

Jaspar motifP-value
MA0002.24.2408e-4
MA0003.10.31
MA0004.10.0251
MA0006.10.662
MA0007.10.856
MA0009.10.27
MA0014.10.0393
MA0017.10.662
MA0018.20.0514
MA0019.10.202
MA0024.12.69515e-4
MA0025.10.432
MA0027.10.818
MA0028.10.0101
MA0029.10.732
MA0030.10.906
MA0031.10.134
MA0035.20.854
MA0038.10.357
MA0039.20.0039
MA0040.10.158
MA0041.10.354
MA0042.10.382
MA0043.10.0961
MA0046.10.235
MA0047.20.562
MA0048.10.0709
MA0050.15.67161e-4
MA0051.10.0372
MA0052.10.0602
MA0055.10.00434
MA0057.10.281
MA0058.10.0327
MA0059.10.0052
MA0060.10.22
MA0061.10.0196
MA0062.20.0113
MA0065.20.172
MA0066.10.411
MA0067.10.142
MA0068.10.0481
MA0069.10.845
MA0070.10.632
MA0071.10.51
MA0072.10.398
MA0073.10.848
MA0074.10.94
MA0076.10.0211
MA0077.10.335
MA0078.10.566
MA0079.20.841
MA0080.22.19936e-6
MA0081.10.0307
MA0083.12.84605e-4
MA0084.10.0906
MA0087.10.614
MA0088.10.197
MA0090.10.721
MA0091.10.00259
MA0092.10.5
MA0093.10.0415
MA0099.20.0692
MA0100.10.664
MA0101.10.0162
MA0102.20.0812
MA0103.13.02377e-7
MA0104.21.77527e-4
MA0105.13.35683e-4
MA0106.13.77863e-4
MA0107.10.0122
MA0108.20.0239
MA0111.10.224
MA0112.20.235
MA0113.10.149
MA0114.10.304
MA0115.10.0154
MA0116.10.0446
MA0117.10.0536
MA0119.10.624
MA0122.10.981
MA0124.10.229
MA0125.10.788
MA0131.10.239
MA0135.10.899
MA0136.14.57915e-4
MA0137.20.00941
MA0138.20.758
MA0139.10.542
MA0140.10.33
MA0141.10.515
MA0142.10.0706
MA0143.10.62
MA0144.10.221
MA0145.10.839
MA0146.10.807
MA0147.11.912e-4
MA0148.10.0815
MA0149.10.0444
MA0150.10.755
MA0152.10.129
MA0153.10.792
MA0154.10.00946
MA0155.10.0806
MA0156.10.0565
MA0157.10.273
MA0159.10.175
MA0160.10.967
MA0162.10.793
MA0163.10.0767
MA0164.10.435
MA0258.10.336
MA0259.10.00982



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: CNhs11862

Novel motifP-value
10.585
100.996
1000.0991
1010.619
1020.328
1030.606
1040.792
1050.783
1060.915
1070.351
1080.256
1090.127
110.939
1100.186
1110.418
1120.29
1130.443
1140.669
1150.0332
1160.852
1170.921
1181
1190.2
120.459
1200.638
1210.727
1220.873
1230.0182
1240.482
1250.957
1260.787
1270.579
1280.347
1290.618
130.0865
1300.835
1310.108
1320.147
1330.0129
1340.0321
1350.0209
1360.00694
1370.0176
1380.63
1390.696
140.716
1400.283
1410.951
1420.551
1430.0342
1440.234
1450.687
1460.911
1470.392
1480.811
1490.43
150.365
1500.405
1510.507
1520.315
1530.371
1540.722
1550.454
1560.327
1570.968
1580.231
1590.516
160.791
1600.736
1610.601
1620.469
1630.274
1640.283
1650.842
1660.209
1670.38
1680.45
1690.819
170.839
180.193
190.0399
20.686
200.471
210.484
220.139
230.0186
240.891
250.678
260.801
270.756
280.645
290.412
30.982
300.96
310.321
320.00823
330.552
340.144
350.138
360.932
370.865
380.825
390.786
40.619
400.786
410.0395
420.92
430.0627
440.169
450.935
460.711
470.39
480.223
490.086
50.129
500.683
510.519
520.495
530.949
540.422
550.281
560.779
570.31
580.551
590.173
60.828
600.611
610.829
620.167
630.451
640.599
650.536
660.327
670.864
680.237
690.314
70.828
700.787
710.844
720.29
730.378
740.0661
750.592
760.393
770.439
780.225
790.226
80.644
805.78864e-4
810.171
820.024
830.166
840.466
850.0285
860.149
870.0796
880.268
890.784
90.0941
900.262
910.0876
920.164
930.59
940.286
950.201
960.0238
970.57
980.925
990.221



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: CNhs11862


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

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

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)

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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