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|DRA_sample_Accession=CAGE@SAMD00005680
|DRA_sample_Accession=CAGE@SAMD00005680
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|DRA_sample_Accession_RNASeq=RNA-Seq@SAMD00005680
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|profile_rnaseq=
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|refex=http://refex.dbcls.jp/genelist.php?lang
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Revision as of 19:28, 10 August 2017

Name:small cell lung carcinoma cell line:LK-2
Species:Human (Homo sapiens)
Library ID:CNhs11285
Sample type:cell lines
Genomic View: UCSC
RefEX:Specific genes
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuelung
dev stageNA
sexmale
age74
cell typeunclassifiable
cell lineLK-2
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  SAMD00005680
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11285 CAGE DRX008007 DRR008879
Accession ID Hg19

Library idBAMCTSS
CNhs11285 DRZ000304 DRZ001689
Accession ID Hg38

Library idBAMCTSS
CNhs11285 DRZ011654 DRZ013039
Download raw sequence, BAM & CTSS
Hg19
FastaBAMCTSS
downloaddownloaddonwload
Hg38
BAMCTSS
downloaddonwload

RNA-Seq Accession numbers
MethodSample accession id
RNA-Seq  SAMD00005680
Library accession numbers

Library idMethodExp. accession idRun accession id
RDhi10072 RNA-Seq DRX057129 DRR062888
Accession ID Hg19

Library idBAMCTSS
RDhi10072 DRZ007964


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-penis0.0769
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-lymphoma0.594
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
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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: CNhs11285

Jaspar motifP-value
MA0002.20.00211
MA0003.10.268
MA0004.10.395
MA0006.10.475
MA0007.10.363
MA0009.10.354
MA0014.10.91
MA0017.10.0429
MA0018.20.213
MA0019.10.214
MA0024.12.3465e-5
MA0025.10.0258
MA0027.10.993
MA0028.10.00184
MA0029.10.763
MA0030.10.149
MA0031.10.347
MA0035.20.338
MA0038.10.00183
MA0039.20.463
MA0040.10.606
MA0041.10.275
MA0042.10.825
MA0043.13.05185e-4
MA0046.10.201
MA0047.20.22
MA0048.10.479
MA0050.12.16279e-7
MA0051.15.94986e-5
MA0052.10.00554
MA0055.10.42
MA0057.10.0835
MA0058.10.459
MA0059.10.506
MA0060.18.76173e-8
MA0061.10.00627
MA0062.20.00252
MA0065.20.0863
MA0066.10.0158
MA0067.10.763
MA0068.19.82421e-5
MA0069.10.688
MA0070.10.767
MA0071.10.423
MA0072.10.87
MA0073.10.292
MA0074.10.25
MA0076.19.63932e-4
MA0077.10.00419
MA0078.10.759
MA0079.20.515
MA0080.26.67939e-7
MA0081.10.0761
MA0083.12.07996e-6
MA0084.10.626
MA0087.10.772
MA0088.10.908
MA0090.10.283
MA0091.10.00791
MA0092.10.118
MA0093.10.355
MA0099.26.77307e-10
MA0100.10.26
MA0101.10.0367
MA0102.20.485
MA0103.10.00326
MA0104.20.147
MA0105.10.00485
MA0106.10.884
MA0107.10.0052
MA0108.20.76
MA0111.10.701
MA0112.20.00146
MA0113.10.346
MA0114.10.225
MA0115.10.657
MA0116.10.0135
MA0117.10.479
MA0119.10.206
MA0122.10.794
MA0124.10.329
MA0125.10.00844
MA0131.10.313
MA0135.10.639
MA0136.17.85551e-4
MA0137.27.16127e-4
MA0138.20.0588
MA0139.10.83
MA0140.10.0798
MA0141.10.169
MA0142.17.71796e-4
MA0143.13.90304e-4
MA0144.10.00784
MA0145.10.115
MA0146.10.0303
MA0147.10.146
MA0148.10.205
MA0149.10.864
MA0150.10.118
MA0152.10.786
MA0153.10.831
MA0154.10.00813
MA0155.10.0297
MA0156.10.0807
MA0157.10.879
MA0159.10.692
MA0160.10.103
MA0162.10.207
MA0163.10.032
MA0164.10.287
MA0258.10.0126
MA0259.10.378



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: CNhs11285

Novel motifP-value
10.151
100.381
1000.865
1010.925
1020.756
1030.0753
1040.582
1050.974
1060.0371
1070.364
1080.996
1090.0879
110.0504
1100.465
1110.107
1120.02
1130.308
1140.0235
1150.636
1160.621
1170.443
1180.217
1190.0917
120.581
1200.933
1210.205
1220.61
1230.592
1240.814
1250.288
1260.196
1270.0615
1280.094
1290.607
130.779
1300.352
1310.97
1320.871
1330.29
1340.831
1350.187
1360.132
1370.261
1380.213
1390.0807
140.714
1400.87
1410.233
1420.664
1430.041
1440.194
1450.184
1460.939
1470.571
1480.468
1490.0129
150.412
1500.484
1510.197
1520.122
1530.845
1540.692
1550.756
1560.717
1570.363
1580.702
1590.562
160.218
1600.401
1610.717
1620.86
1630.722
1640.936
1650.72
1660.981
1670.414
1680.256
1690.0106
170.276
180.427
190.0516
20.338
200.598
210.377
220.0542
230.0123
240.392
250.632
260.598
270.124
280.965
290.968
30.149
300.364
310.365
320.00345
330.75
340.181
350.638
360.916
370.211
380.389
390.622
40.896
400.262
410.0702
420.503
430.0578
440.253
450.403
460.197
470.436
480.349
490.182
50.319
500.706
510.295
520.495
530.482
540.0924
550.254
560.535
570.91
580.477
590.0195
60.362
600.0982
610.909
620.164
630.23
640.633
650.0633
660.385
670.531
680.211
690.401
70.755
700.0889
710.136
720.37
730.0877
740.924
750.683
760.863
770.101
780.823
790.054
80.285
800.282
810.559
820.00139
830.797
840.636
850.00309
860.692
870.962
880.948
890.0633
90.129
900.673
910.337
920.0241
930.848
940.144
950.349
960.444
970.81
980.314
990.6



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: CNhs11285


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)
0000082 (epithelial cell of lung)
0000255 (eukaryotic cell)

DOID: Disease
4 (disease)
0050686 (organ system cancer)
0050615 (respiratory system cancer)
162 (cancer)
14566 (disease of cellular proliferation)
0050687 (cell type cancer)
1324 (lung cancer)
305 (carcinoma)
1325 (bronchus cancer)
3905 (lung carcinoma)
5409 (lung small cell carcinoma)
3904 (bronchogenic carcinoma)

UBERON: Anatomy
0000468 (multi-cellular organism)
0002048 (lung)
0002100 (trunk)
0000483 (epithelium)
0000479 (tissue)
0000064 (organ part)
0004119 (endoderm-derived structure)
0000466 (immaterial anatomical entity)
0000062 (organ)
0004111 (anatomical conduit)
0000475 (organism subdivision)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000063 (organ segment)
0004802 (respiratory tract epithelium)
0000025 (tube)
0005911 (endo-epithelium)
0000477 (anatomical cluster)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0000119 (cell layer)
0009569 (subdivision of trunk)
0005178 (thoracic cavity element)
0000072 (segment of respiratory tract)
0005177 (trunk region element)
0004807 (respiratory system epithelium)
0000117 (respiratory tube)
0000171 (respiration organ)
0000115 (lung epithelium)
0000464 (anatomical space)
0005181 (thoracic segment organ)
0010317 (germ layer / neural crest derived structure)
0000065 (respiratory tract)
0000170 (pair of lungs)
0001004 (respiratory system)
0002224 (thoracic cavity)
0000915 (thoracic segment of trunk)

FF: FANTOM5
0000102 (sample by type)
0000003 (cell line sample)
0000210 (human sample)
0000101 (sample by species)
0000001 (sample)
0100297 (carcinoma cell line sample)
0100353 (lung cell line sample)
0102061 (bronchogenic carcinoma cell sample)
0101120 (epithelial cell line sample)
0100762 (lung cancer cell line sample)
0102206 (small cell lung cancer cell line sample)
0100189 (small cell lung cancer 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
UBERON:0001041 (foregut)
UBERON:0008947 (respiratory primordium)
UBERON:0002532 (epiblast (generic))
UBERON:0006595 (presumptive endoderm)
UBERON:0010316 (germ layer / neural crest)

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