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{{f5samples
{{f5samples
|DRA_sample_Accession=CAGE@SAMD00005261
|DRA_sample_Accession=CAGE@SAMD00005261
|accession_numbers=CAGE;DRX007991;DRR008863;DRZ000288;DRZ001673
|accession_numbers=CAGE;DRX007991;DRR008863;DRZ000288;DRZ001673;DRZ011638;DRZ013023
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0002113,UBERON:0002100,UBERON:0000062,UBERON:0000475,UBERON:0006554,UBERON:0000061,UBERON:0000465,UBERON:0000477,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0003103,UBERON:0009569,UBERON:0000489,UBERON:0005177,UBERON:0005172,UBERON:0005173,UBERON:0011143,UBERON:0001008,UBERON:0002417,UBERON:0000916
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0002113,UBERON:0002100,UBERON:0000062,UBERON:0000475,UBERON:0006554,UBERON:0000061,UBERON:0000465,UBERON:0000477,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0003103,UBERON:0009569,UBERON:0000489,UBERON:0005177,UBERON:0005172,UBERON:0005173,UBERON:0011143,UBERON:0001008,UBERON:0002417,UBERON:0000916
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000548,CL:0000066,CL:0002371,CL:0000255,CL:1000497,CL:0002518
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000548,CL:0000066,CL:0002371,CL:0000255,CL:1000497,CL:0002518
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/renal%2520cell%2520carcinoma%2520cell%2520line%253aTUHR10TKB.CNhs11257.10471-106I3.hg19.nobarcode.bam
|hg19ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.cell_line.hCAGE/renal%2520cell%2520carcinoma%2520cell%2520line%253aTUHR10TKB.CNhs11257.10471-106I3.hg19.ctss.bed.gz
|hg19fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.cell_line.hCAGE/renal%2520cell%2520carcinoma%2520cell%2520line%253aTUHR10TKB.CNhs11257.10471-106I3.hg19.nobarcode.rdna.fa.gz
|hg38bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/hg38_v2/basic/human.cell_line.hCAGE/renal%2520cell%2520carcinoma%2520cell%2520line%253aTUHR10TKB.CNhs11257.10471-106I3.hg38.nobarcode.bam
|hg38ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/hg38_v2/basic/human.cell_line.hCAGE/renal%2520cell%2520carcinoma%2520cell%2520line%253aTUHR10TKB.CNhs11257.10471-106I3.hg38.nobarcode.ctss.bed.gz
|id=FF:10471-106I3
|id=FF:10471-106I3
|is_a=EFO:0002091;;FF:0000210;;FF:0103732
|is_a=EFO:0002091;;FF:0000210;;FF:0103732
Line 46: Line 51:
|library_id=CNhs11257
|library_id=CNhs11257
|library_id_phase_based=2:CNhs11257
|library_id_phase_based=2:CNhs11257
|microRNAs=
|microRNAs_nn=
|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/human#cage;sample;10471
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/human#cage;sample;10471
|name=renal cell carcinoma cell line:TUHR10TKB
|name=renal cell carcinoma cell line:TUHR10TKB
|namespace=FANTOM5
|namespace=FANTOM5
|part_of=
|part_of=
|profile_cagescan=,,,
|profile_cagescan=,,,
|profile_hcage="CNhs11257,LSID757,release008,COMPLETED"
|profile_hcage=CNhs11257,LSID757,release008,COMPLETED
|profile_rnaseq=
|profile_rnaseq=
|profile_srnaseq=",,,"
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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:10471-106I3;search_select_hide=table117:FF:10471-106I3
}}
}}

Latest revision as of 14:25, 3 June 2020

Name:renal cell carcinoma cell line:TUHR10TKB
Species:Human (Homo sapiens)
Library ID:CNhs11257
Sample type:cell lines
Genomic View: UCSC
RefEX:Specific genes
CAGEd-oPOSSUM:link
ZENBU report :link
Additional information
Sample information
strainNA
tissuekidney
dev stageNA
sexmale
age69
cell typeunclassifiable
cell lineTUHR10TKB
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  SAMD00005261
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11257 CAGE DRX007991 DRR008863
Accession ID Hg19

Library idBAMCTSS
CNhs11257 DRZ000288 DRZ001673
Accession ID Hg38

Library idBAMCTSS
CNhs11257 DRZ011638 DRZ013023
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-penis0.12
C106-Hep2-epitheloid-placenta-cervical-rectal-anaplastic-glassy0
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C89-small-retinoblastoma-medulloblastoma-iPS-acantholytic-eye-bronchogenic0
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: CNhs11257

Jaspar motifP-value
MA0002.20.0948
MA0003.10.864
MA0004.10.324
MA0006.10.0813
MA0007.10.117
MA0009.10.047
MA0014.10.26
MA0017.10.348
MA0018.20.128
MA0019.10.7
MA0024.10.575
MA0025.10.563
MA0027.10.87
MA0028.10.0137
MA0029.10.481
MA0030.10.799
MA0031.10.152
MA0035.20.487
MA0038.10.456
MA0039.20.00146
MA0040.10.489
MA0041.10.3
MA0042.10.532
MA0043.10.316
MA0046.12.49638e-7
MA0047.20.801
MA0048.10.144
MA0050.15.66318e-16
MA0051.13.09366e-10
MA0052.10.0438
MA0055.10.00271
MA0057.10.243
MA0058.10.162
MA0059.10.0555
MA0060.10.0875
MA0061.12.83753e-4
MA0062.20.164
MA0065.20.0828
MA0066.10.751
MA0067.10.814
MA0068.10.0171
MA0069.10.43
MA0070.10.498
MA0071.10.606
MA0072.10.301
MA0073.10.418
MA0074.10.528
MA0076.10.0221
MA0077.10.387
MA0078.10.0146
MA0079.20.435
MA0080.22.77783e-10
MA0081.10.00706
MA0083.10.00137
MA0084.10.226
MA0087.10.215
MA0088.10.16
MA0090.10.415
MA0091.10.021
MA0092.10.276
MA0093.10.323
MA0099.20.122
MA0100.10.906
MA0101.18.98368e-4
MA0102.20.333
MA0103.10.0083
MA0104.20.0544
MA0105.14.12581e-4
MA0106.10.00221
MA0107.10.00196
MA0108.22.02888e-7
MA0111.10.611
MA0112.20.225
MA0113.10.351
MA0114.10.00318
MA0115.10.553
MA0116.10.0658
MA0117.10.939
MA0119.10.512
MA0122.10.518
MA0124.10.305
MA0125.10.131
MA0131.10.513
MA0135.10.533
MA0136.12.17602e-7
MA0137.20.927
MA0138.20.283
MA0139.10.392
MA0140.10.111
MA0141.10.53
MA0142.10.0354
MA0143.10.202
MA0144.10.354
MA0145.10.362
MA0146.10.0819
MA0147.10.0183
MA0148.10.108
MA0149.10.275
MA0150.10.959
MA0152.10.851
MA0153.11.49262e-6
MA0154.10.4
MA0155.10.577
MA0156.16.28339e-4
MA0157.10.129
MA0159.10.0638
MA0160.10.857
MA0162.10.472
MA0163.10.151
MA0164.10.928
MA0258.10.36
MA0259.10.00143



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: CNhs11257

Novel motifP-value
10.25
100.0763
1000.00731
1010.132
1020.826
1030.314
1040.622
1050.752
1060.113
1070.364
1080.747
1090.189
110.969
1100.0372
1110.153
1120.379
1130.276
1140.684
1150.797
1160.882
1170.0179
1180.00138
1190.385
120.115
1200.655
1210.834
1220.0631
1230.428
1240.585
1250.452
1260.498
1270.77
1280.0823
1290.447
133.63333e-4
1300.122
1310.762
1320.47
1330.161
1340.192
1350.0119
1360.712
1370.546
1380.913
1390.76
140.66
1400.144
1410.896
1420.133
1430.247
1440.804
1450.606
1460.205
1470.418
1480.554
1490.607
150.328
1500.743
1510.934
1520.71
1530.446
1540.954
1550.469
1560.984
1570.405
1580.39
1590.264
160.957
1600.0819
1610.346
1620.528
1630.191
1640.0139
1650.436
1660.146
1670.381
1680.0976
1690.379
170.528
180.0866
190.86
20.441
200.00777
210.347
220.961
230.302
240.809
250.633
260.0853
270.23
280.868
290.00781
30.0607
300.38
310.479
320.0887
330.348
340.203
350.439
360.0565
370.34
380.68
390.703
40.791
400.0349
410.0604
420.607
430.611
440.191
450.535
460.904
470.752
480.755
490.58
50.749
500.91
510.721
520.245
530.846
540.287
550.535
560.556
570.216
580.264
590.75
60.164
600.756
610.141
620.945
630.971
640.945
650.878
660.974
670.491
680.773
690.13
70.696
700.268
710.00489
720.999
730.541
740.272
750.0694
760.0159
770.468
780.0788
790.759
80.499
800.00321
810.821
820.871
830.996
840.725
850.794
860.776
870.258
880.636
890.366
90.0325
900.349
910.973
920.805
930.989
940.982
950.173
960.558
970.723
980.85
990.587



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: CNhs11257


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)
1000497 (kidney cell)
0002518 (kidney epithelial cell)

DOID: Disease
4 (disease)
162 (cancer)
14566 (disease of cellular proliferation)
0050687 (cell type cancer)
7 (disease of anatomical entity)
305 (carcinoma)

UBERON: Anatomy
0000468 (multi-cellular organism)
0002113 (kidney)
0002100 (trunk)
0000062 (organ)
0000475 (organism subdivision)
0006554 (urinary system structure)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000477 (anatomical cluster)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0003103 (compound organ)
0009569 (subdivision of trunk)
0000489 (cavitated compound organ)
0005177 (trunk region element)
0005172 (abdomen element)
0005173 (abdominal segment element)
0011143 (upper urinary tract)
0001008 (renal system)
0002417 (abdominal segment of trunk)
0000916 (abdomen)

FF: FANTOM5
0000102 (sample by type)
0000003 (cell line sample)
0000210 (human sample)
0000101 (sample by species)
0000001 (sample)
0100297 (carcinoma cell line sample)
0100067 (kidney cell line sample)
0101120 (epithelial cell line sample)
0103192 (renal cancer cell line sample)
0100383 (renal cell carcinoma cell line sample)
0103732 (TUHR-10TKB 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:0003104 (mesenchyme)
UBERON:0003918 (kidney mesenchyme)
UBERON:0007687 (kidney field)

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