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{{f5samples
{{f5samples
|DRA_sample_Accession=CAGE@SAMD00005172
|DRA_sample_Accession=CAGE@SAMD00005172
|accession_numbers=CAGE;DRX007931;DRR008803;DRZ000228;DRZ001613
|accession_numbers=CAGE;DRX007931;DRR008803;DRZ000228;DRZ001613;DRZ011578;DRZ012963
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0001003,UBERON:0002097,UBERON:0002199,UBERON:0000483,UBERON:0000479,UBERON:0004121,UBERON:0000062,UBERON:0000061,UBERON:0000465,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0000119,UBERON:0003102,UBERON:0007376,UBERON:0010371,UBERON:0010317,UBERON:0002416
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0001003,UBERON:0002097,UBERON:0002199,UBERON:0000483,UBERON:0000479,UBERON:0004121,UBERON:0000062,UBERON:0000061,UBERON:0000465,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0000119,UBERON:0003102,UBERON:0007376,UBERON:0010371,UBERON:0010317,UBERON:0002416
|ancestors_in_cell_lineage_facet=
|ancestors_in_cell_lineage_facet=
Line 41: Line 41:
|fonse_treatment_closure=
|fonse_treatment_closure=
|has_quality=
|has_quality=
|hg19bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.cell_line.hCAGE/melanoma%2520cell%2520line%253aG-361.CNhs11254.10465-106H6.hg19.nobarcode.bam
|hg19ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.cell_line.hCAGE/melanoma%2520cell%2520line%253aG-361.CNhs11254.10465-106H6.hg19.ctss.bed.gz
|hg19fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.cell_line.hCAGE/melanoma%2520cell%2520line%253aG-361.CNhs11254.10465-106H6.hg19.nobarcode.rdna.fa.gz
|hg38bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/hg38_v2/basic/human.cell_line.hCAGE/melanoma%2520cell%2520line%253aG-361.CNhs11254.10465-106H6.hg38.nobarcode.bam
|hg38ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/hg38_v2/basic/human.cell_line.hCAGE/melanoma%2520cell%2520line%253aG-361.CNhs11254.10465-106H6.hg38.nobarcode.ctss.bed.gz
|id=FF:10465-106H6
|id=FF:10465-106H6
|is_a=EFO:0002091;;FF:0000210;;FF:0101584
|is_a=EFO:0002091;;FF:0000210;;FF:0101584
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|library_id=CNhs11254
|library_id=CNhs11254
|library_id_phase_based=2:CNhs11254
|library_id_phase_based=2:CNhs11254
|microRNAs=
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|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/human#cage;sample;10465
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/human#cage;sample;10465
|name=melanoma cell line:G-361
|name=melanoma cell line:G-361
|namespace=FANTOM5
|namespace=FANTOM5
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|profile_hcage="CNhs11254,LSID757,release008,COMPLETED"
|profile_hcage=CNhs11254,LSID757,release008,COMPLETED
|profile_rnaseq=
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|refex=http://refex.dbcls.jp/genelist.php?lang
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Line 90: Line 100:
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|xref=
|xref=
|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_human;search_select_hide=table111:FF:10465-106H6;search_select_hide=table117:FF:10465-106H6
}}
}}

Latest revision as of 14:25, 3 June 2020

Name:melanoma cell line:G-361
Species:Human (Homo sapiens)
Library ID:CNhs11254
Sample type:cell lines
Genomic View: UCSC
RefEX:Specific genes
CAGEd-oPOSSUM:link
ZENBU report :link
Additional information
Sample information
strainNA
tissueskin
dev stageNA
sexmale
age31
cell typemelanocyte
cell lineG-361
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  SAMD00005172
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11254 CAGE DRX007931 DRR008803
Accession ID Hg19

Library idBAMCTSS
CNhs11254 DRZ000228 DRZ001613
Accession ID Hg38

Library idBAMCTSS
CNhs11254 DRZ011578 DRZ012963
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-penis0.149
C106-Hep2-epitheloid-placenta-cervical-rectal-anaplastic-glassy0
C107-Neutrophils-CD14-Eosinophils-Monocytederived-Whole-Peripheral-blood0
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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: CNhs11254

Jaspar motifP-value
MA0002.20.00399
MA0003.10.0194
MA0004.17.45182e-4
MA0006.10.131
MA0007.10.39
MA0009.10.189
MA0014.10.319
MA0017.10.0816
MA0018.20.0755
MA0019.10.835
MA0024.10.474
MA0025.10.874
MA0027.10.745
MA0028.14.93708e-5
MA0029.10.544
MA0030.10.919
MA0031.10.571
MA0035.20.807
MA0038.10.222
MA0039.20.482
MA0040.10.0991
MA0041.10.0762
MA0042.10.124
MA0043.10.893
MA0046.10.0444
MA0047.20.855
MA0048.10.0843
MA0050.10.00246
MA0051.10.249
MA0052.10.0133
MA0055.10.0235
MA0057.10.97
MA0058.12.13197e-5
MA0059.15.75602e-5
MA0060.10.233
MA0061.19.99253e-4
MA0062.23.27342e-7
MA0065.20.813
MA0066.10.436
MA0067.10.354
MA0068.10.0504
MA0069.10.992
MA0070.10.155
MA0071.10.74
MA0072.10.631
MA0073.10.907
MA0074.10.521
MA0076.12.91774e-7
MA0077.10.884
MA0078.10.449
MA0079.20.198
MA0080.27.69283e-10
MA0081.10.834
MA0083.17.42404e-5
MA0084.10.967
MA0087.10.875
MA0088.10.0623
MA0090.10.154
MA0091.10.156
MA0092.10.231
MA0093.11.3117e-4
MA0099.24.74729e-9
MA0100.10.745
MA0101.10.0149
MA0102.20.00112
MA0103.10.149
MA0104.25.79303e-6
MA0105.15.16167e-4
MA0106.10.129
MA0107.17.65465e-4
MA0108.25.87856e-7
MA0111.10.798
MA0112.20.0314
MA0113.10.156
MA0114.10.278
MA0115.10.781
MA0116.10.008
MA0117.10.0988
MA0119.10.665
MA0122.10.0445
MA0124.10.663
MA0125.10.613
MA0131.10.107
MA0135.10.0874
MA0136.15.24631e-6
MA0137.20.166
MA0138.20.913
MA0139.10.525
MA0140.10.377
MA0141.10.114
MA0142.10.0823
MA0143.10.968
MA0144.10.0199
MA0145.10.111
MA0146.10.71
MA0147.12.29074e-6
MA0148.10.956
MA0149.10.5
MA0150.13.10234e-4
MA0152.10.972
MA0153.10.653
MA0154.10.0555
MA0155.10.154
MA0156.10.0423
MA0157.10.961
MA0159.10.626
MA0160.10.622
MA0162.10.0118
MA0163.10.228
MA0164.10.753
MA0258.10.223
MA0259.16.70991e-4



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: CNhs11254

Novel motifP-value
10.929
100.922
1000.546
1010.854
1020.233
1030.974
1040.311
1050.0668
1060.0641
1070.093
1080.228
1090.772
110.551
1100.594
1110.919
1120.94
1130.0754
1140.489
1150.822
1160.649
1170.833
1180.325
1190.214
120.0858
1200.672
1210.0954
1220.999
1230.483
1240.743
1250.927
1260.759
1270.193
1280.743
1290.267
130.619
1300.54
1310.0208
1320.984
1330.591
1340.474
1350.118
1360.0102
1370.582
1380.773
1390.558
140.605
1400.182
1410.393
1420.0934
1430.865
1440.868
1450.42
1460.333
1470.847
1480.5
1490.178
150.91
1500.767
1510.574
1520.117
1530.853
1540.799
1550.345
1560.518
1570.992
1580.245
1590.236
160.894
1600.174
1610.337
1620.535
1630.406
1640.787
1650.087
1660.213
1670.0229
1680.743
1690.0604
170.658
180.442
190.112
20.0274
200.0646
210.65
220.419
230.0888
240.837
250.159
260.85
270.193
280.859
290.478
30.817
300.103
310.42
320.0166
330.925
340.24
350.952
360.632
370.59
380.427
390.936
40.802
400.175
410.194
420.52
430.256
440.399
450.0978
460.448
470.839
480.778
490.365
50.334
500.399
510.39
520.0796
530.433
540.672
550.987
560.525
570.235
580.068
590.167
60.171
600.0643
610.432
620.0633
630.679
640.95
650.258
660.219
670.575
680.439
690.956
70.293
700.865
710.721
720.362
730.408
740.916
750.553
760.267
770.0854
780.266
790.407
80.809
800.0457
810.717
820.596
830.974
840.0396
850.317
860.131
870.492
880.456
890.0193
90.262
900.171
910.484
920.173
930.203
940.781
950.735
960.17
970.732
980.964
990.899



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: CNhs11254


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

DOID: Disease
4 (disease)
162 (cancer)
14566 (disease of cellular proliferation)
0050687 (cell type cancer)
1909 (melanoma)

UBERON: Anatomy
0000468 (multi-cellular organism)
0001003 (skin epidermis)
0002097 (skin of body)
0002199 (integument)
0000483 (epithelium)
0000479 (tissue)
0004121 (ectoderm-derived structure)
0000062 (organ)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0000119 (cell layer)
0003102 (surface structure)
0007376 (outer epithelium)
0010371 (ecto-epithelium)
0010317 (germ layer / neural crest derived structure)
0002416 (integumental system)

FF: FANTOM5
0000102 (sample by type)
0000003 (cell line sample)
0000210 (human sample)
0000101 (sample by species)
0000001 (sample)
0100849 (melanoma cell line sample)
0101584 (G-361 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:0002532 (epiblast (generic))
UBERON:0006601 (presumptive ectoderm)
UBERON:0010316 (germ layer / neural crest)

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