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|DRA_sample_Accession=CAGE@SAMD00005178
|DRA_sample_Accession=CAGE@SAMD00005178
|DRA_sample_Accession_RNASeq=RNA-Seq@SAMD00005178
|DRA_sample_Accession_RNASeq=RNA-Seq@SAMD00005178
|accession_numbers=CAGE;DRX007829;DRR008701;DRZ000126;DRZ001511
|accession_numbers=CAGE;DRX007829;DRR008701;DRZ000126;DRZ001511;DRZ011476;DRZ012861
|accession_numbers_RNASeq=RNA-Seq;DRX057130;DRR062889;DRZ007965
|accession_numbers_RNASeq=RNA-Seq;DRX057130;DRR062889;DRZ007965
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|profile_rnaseq=
|profile_rnaseq=
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|refex=http://refex.dbcls.jp/genelist.php?lang
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Revision as of 19:30, 10 August 2017

Name:argyrophil small cell carcinoma cell line:TC-YIK
Species:Human (Homo sapiens)
Library ID:CNhs11725
Sample type:cell lines
Genomic View: UCSC
RefEX:Specific genes
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuecervix
dev stageNA
sexfemale
age31
cell typeunclassifiable
cell lineTC-YIK
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  SAMD00005178
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11725 CAGE DRX007829 DRR008701
Accession ID Hg19

Library idBAMCTSS
CNhs11725 DRZ000126 DRZ001511
Accession ID Hg38

Library idBAMCTSS
CNhs11725 DRZ011476 DRZ012861
Download raw sequence, BAM & CTSS
Hg19
FastaBAMCTSS
downloaddownloaddonwload
Hg38
BAMCTSS
downloaddonwload

RNA-Seq Accession numbers
MethodSample accession id
RNA-Seq  SAMD00005178
Library accession numbers

Library idMethodExp. accession idRun accession id
RDhi10073 RNA-Seq DRX057130 DRR062889
Accession ID Hg19

Library idBAMCTSS
RDhi10073 DRZ007965


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-penis0.13
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-lymphoma0.299
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
C110-leukemia-chronic-Eosinophils-acute-Whole-CD34-Lymphatic0
C111-medulla-lung-trachea-testis-caudate-epididymis-throat0.0976
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: CNhs11725

Jaspar motifP-value
MA0002.23.08261e-5
MA0003.10.539
MA0004.10.0583
MA0006.10.235
MA0007.10.448
MA0009.10.728
MA0014.10.337
MA0017.10.341
MA0018.20.164
MA0019.10.899
MA0024.14.06331e-5
MA0025.10.221
MA0027.10.394
MA0028.10.0938
MA0029.10.498
MA0030.10.0558
MA0031.10.0748
MA0035.20.578
MA0038.10.128
MA0039.20.365
MA0040.10.809
MA0041.10.463
MA0042.10.607
MA0043.10.92
MA0046.11.11552e-42
MA0047.20.00921
MA0048.10.494
MA0050.12.66862e-5
MA0051.10.00591
MA0052.10.0121
MA0055.10.207
MA0057.10.223
MA0058.10.012
MA0059.10.00856
MA0060.19.26993e-4
MA0061.16.51271e-5
MA0062.20.0687
MA0065.20.771
MA0066.10.327
MA0067.10.582
MA0068.10.546
MA0069.10.492
MA0070.10.335
MA0071.10.736
MA0072.10.713
MA0073.10.538
MA0074.10.344
MA0076.10.0337
MA0077.10.891
MA0078.10.407
MA0079.20.802
MA0080.25.45416e-9
MA0081.10.00192
MA0083.18.21898e-4
MA0084.10.589
MA0087.10.726
MA0088.10.0955
MA0090.18.21113e-4
MA0091.10.716
MA0092.10.1
MA0093.10.0427
MA0099.22.03989e-17
MA0100.10.11
MA0101.16.96638e-5
MA0102.20.0253
MA0103.13.06817e-6
MA0104.20.00187
MA0105.17.65195e-4
MA0106.10.364
MA0107.15.88325e-6
MA0108.20.817
MA0111.10.712
MA0112.20.00403
MA0113.10.302
MA0114.10.0443
MA0115.10.00106
MA0116.10.0227
MA0117.10.639
MA0119.10.113
MA0122.10.384
MA0124.10.235
MA0125.10.0262
MA0131.10.551
MA0135.10.578
MA0136.11.02136e-6
MA0137.20.0717
MA0138.20.489
MA0139.10.674
MA0140.10.564
MA0141.10.585
MA0142.10.673
MA0143.10.0251
MA0144.10.0134
MA0145.10.0531
MA0146.10.573
MA0147.10.00245
MA0148.10.168
MA0149.10.872
MA0150.18.63331e-5
MA0152.10.906
MA0153.11.30226e-26
MA0154.10.071
MA0155.10.485
MA0156.12.69252e-4
MA0157.10.215
MA0159.10.542
MA0160.10.369
MA0162.10.288
MA0163.10.0188
MA0164.10.314
MA0258.10.0697
MA0259.10.0141



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: CNhs11725

Novel motifP-value
10.806
100.466
1000.354
1010.978
1020.628
1030.158
1040.375
1050.58
1062.74761e-5
1070.0104
1080.997
1090.536
110.37
1100.434
1110.509
1120.419
1130.832
1140.128
1150.814
1160.448
1170.724
1180.73
1190.24
120.967
1200.816
1210.656
1220.0818
1230.385
1240.495
1250.92
1260.97
1270.112
1280.0177
1290.395
130.356
1300.385
1310.573
1320.325
1330.358
1340.612
1350.0858
1360.489
1370.355
1380.982
1390.487
140.615
1400.985
1410.552
1420.579
1435.59403e-4
1440.103
1450.239
1460.595
1470.419
1480.337
1490.114
150.431
1500.242
1510.25
1520.0111
1530.629
1540.564
1550.325
1560.958
1570.589
1580.996
1590.268
160.51
1600.815
1610.923
1620.596
1630.124
1640.577
1650.256
1660.394
1670.454
1680.193
1690.026
170.397
180.014
190.169
20.502
200.427
210.478
220.0612
230.00241
240.136
250.669
260.683
270.498
280.964
290.615
30.429
300.256
310.589
320.0116
330.796
340.262
350.587
360.45
370.171
380.358
390.202
40.816
400.907
410.0543
420.515
430.118
440.395
450.216
460.233
470.727
480.842
490.292
50.248
500.543
510.366
520.102
530.768
540.304
550.0845
560.889
570.962
580.693
590.0548
60.693
600.0145
610.989
620.345
630.151
640.761
650.0797
660.811
670.403
680.79
690.909
70.679
700.0854
710.267
720.153
730.0745
740.169
750.716
760.734
770.311
780.486
790.2
80.781
800.218
810.189
820.684
830.0512
840.96
850.0137
860.319
870.691
880.474
890.192
90.0581
900.167
910.156
920.316
930.469
940.0685
950.614
960.354
970.874
980.524
990.877



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: CNhs11725


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)
0000255 (eukaryotic cell)
0002535 (epithelial cell of cervix)

DOID: Disease
4 (disease)
0050686 (organ system cancer)
162 (cancer)
14566 (disease of cellular proliferation)
0050687 (cell type cancer)
193 (reproductive organ cancer)
305 (carcinoma)
120 (female reproductive organ cancer)
4362 (cervical cancer)

UBERON: Anatomy
0000468 (multi-cellular organism)
0000002 (uterine cervix)
0000995 (uterus)
0000483 (epithelium)
0003134 (female reproductive organ)
0000479 (tissue)
0001560 (neck of organ)
0005156 (reproductive structure)
0000064 (organ part)
0000062 (organ)
0004120 (mesoderm-derived structure)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000990 (reproductive system)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0000119 (cell layer)
0003133 (reproductive organ)
0003975 (internal female genitalia)
0004175 (internal genitalia)
0010317 (germ layer / neural crest derived structure)
0006955 (uterine epithelium)
0004801 (cervix epithelium)
0003100 (female organism)
0000474 (female reproductive system)

FF: FANTOM5
0000102 (sample by type)
0000003 (cell line sample)
0000210 (human sample)
0000101 (sample by species)
0000001 (sample)
0100297 (carcinoma cell line sample)
0101120 (epithelial cell line sample)
0101967 (cervical cancer 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
UBERON:0002532 (epiblast (generic))
UBERON:0006603 (presumptive mesoderm)
UBERON:0010316 (germ layer / neural crest)

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