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{{f5samples
{{f5samples
|DRA_sample_Accession=CAGE@DRS007789
|DRA_sample_Accession=CAGE@SAMD00005221
|accession_numbers=CAGE;DRX007894;DRR008766;DRZ000191;DRZ001576;DRZ011541;DRZ012926
|ancestors_in_anatomy_facet=
|ancestors_in_anatomy_facet=
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000548,CL:0000066,CL:0000255
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000548,CL:0000066,CL:0000255
Line 8: Line 9:
|created_by=
|created_by=
|creation_date=
|creation_date=
|datafreeze_phase=1
|data_phase=2
|datafreeze_phase=2
|def=
|def=
|expression_enrichment_score=chr1:203764633..203764674,+!p2@ZC3H11A!1.44!42.21!ZC3H11A;;chr6:1312325..1312340,+!p1@FOXQ1!1.31!31.12!FOXQ1;;chr13:73633131..73633149,+!p1@KLF5!1.30!197.50!KLF5;;chr6:126102292..126102329,+!p3@NCOA7!1.28!58.34!NCOA7;;chr19:45260775..45260838,+!p5@BCL3!1.26!22.18!BCL3;;chr11:34645791..34645836,+!p3@EHF!1.26!17.29!EHF;;chr11:65667884..65667895,-!p2@FOSL1!1.25!63.82!FOSL1;;chr17:46682321..46682362,-!p1@HOXB6!1.25!16.71!HOXB6;;chr19:1753498..1753519,+!p1@ONECUT3!1.22!15.56!ONECUT3;;chr3:141087339..141087387,+!p2@ZBTB38!1.15!134.84!ZBTB38;;chr5:134369905..134369972,-!p1@PITX1!1.14!19.59!PITX1;;chr11:34642612..34642646,+!p1@EHF!1.12!12.10!EHF;;chr3:169491171..169491205,+!p1@MYNN!1.10!200.81!MYNN;;chr11:65667846..65667868,-!p1@FOSL1!1.08!288.83!FOSL1;;chr2:70142232..70142251,+!p1@MXD1!1.08!62.09!MXD1;;chr5:72744594..72744609,-!p1@FOXD1!1.07!49.84!FOXD1;;chr1:43148855..43148908,+!p4@YBX1!1.07!17.00!YBX1;;chr3:141087393..141087426,+!p3@ZBTB38!1.06!42.21!ZBTB38;;chr13:45010939..45011033,-!p1@TSC22D1!1.04!662.22!TSC22D1;;chr6:126102254..126102289,+!p5@NCOA7!1.03!27.08!NCOA7;;chr1:158979851..158979865,+!p5@IFI16!1.02!21.32!IFI16;;chr17:46688334..46688385,-!p1@HOXB7!1.00!13.11!HOXB7;;chr8:128747757..128747800,+!p7@MYC!1.00!12.24!MYC;;chr17:46703942..46703964,-!p4@HOXB9!1.00!8.93!HOXB9;;chr1:246729544..246729572,-!p1@TFB2M!0.96!81.25!TFB2M;;chr1:161736038..161736056,+!p4@ATF6!0.93!18.29!ATF6;;chr3:147111198..147111225,+!p4@ZIC1!0.93!7.49!ZIC1;;chr2:157189180..157189290,-!p1@NR4A2!0.92!39.47!NR4A2;;chr17:46687959..46688007,-!p2@HOXB7!0.92!10.23!HOXB7;;chr5:76383133..76383186,-!p2@ZBED3!0.91!14.98!ZBED3;;chr5:138609782..138609826,+!p5@MATR3!0.90!47.11!MATR3;;chr10:96122682..96122730,-!p1@NOC3L!0.88!102.86!NOC3L;;chr1:158979792..158979814,+!p2@IFI16!0.88!67.13!IFI16;;chr17:38256822..38256851,-!p1@NR1D1!0.88!55.17!NR1D1;;chr1:158979872..158979898,+!p3@IFI16!0.88!21.46!IFI16;;chr22:38598057..38598071,+!p3@MAFF!0.87!15.56!MAFF;;chr11:31832658..31832681,-!p1@PAX6!0.87!6.34!PAX6;;chr19:45261550..45261641,+!p6@BCL3!0.86!10.66!BCL3;;chr1:246729483..246729538,-!p2@TFB2M!0.85!61.80!TFB2M;;chr12:10875351..10875422,-!p4@CSDA!0.83!11.67!CSDA;;chr15:96875657..96875760,+!p14@NR2F2!0.83!9.80!NR2F2;;chr13:45009301..45009320,-!p7@TSC22D1!0.82!5.62!TSC22D1;;chr8:128747729..128747748,+!p14@MYC!0.82!5.62!MYC;;chr2:70142189..70142223,+!p2@MXD1!0.81!42.06!MXD1;;chr1:8939265..8939367,-!p5@ENO1!0.81!11.81!ENO1;;chr10:96122645..96122675,-!p2@NOC3L!0.80!26.94!NOC3L;;chr10:35484053..35484076,+!p1@CREM!0.80!14.12!CREM;;chr8:128748470..128748487,+!p1@MYC!0.79!625.92!MYC;;chr13:36871902..36872023,-!p1@CCDC169-SOHLH2,p1@CCDC169,p1@SOHLH2!0.79!11.96!SOHLH2;;chr1:158985493..158985535,+!p4@IFI16!0.79!8.21!IFI16;;chr10:51572408..51572454,+!p3@NCOA4!0.78!32.12!NCOA4;;chr19:45579725..45579743,-!p1@ZNF296!0.78!24.35!ZNF296;;chr12:66218255..66218304,+!p3@HMGA2!0.78!14.55!HMGA2;;chr9:124991204..124991246,-!p1@LHX6!0.78!5.04!LHX6;;chr8:10697329..10697365,-!p2@PINX1,p2@SOX7!0.77!35.44!SOX7;;chr19:33864571..33864596,+!p2@CEBPG!0.77!12.68!CEBPG;;chr4:4291861..4291913,-!p1@LYAR!0.76!120.14!LYAR;;chr7:148581327..148581347,-!p2@EZH2!0.76!17.57!EZH2;;chr19:33865009..33865090,+!p3@CEBPG!0.76!6.48!CEBPG;;chr13:73636252..73636307,+!p2@KLF5!0.75!5.47!KLF5;;chr16:1031762..1031781,+!p1@SOX8!0.75!4.61!SOX8;;chr17:38256877..38256900,-!p2@NR1D1!0.74!15.70!NR1D1;;chr2:46524897..46524911,+!p2@EPAS1!0.74!13.69!EPAS1;;chr13:73636516..73636532,+!p3@KLF5!0.74!5.19!KLF5;;chr5:134369879..134369898,-!p2@PITX1!0.73!4.32!PITX1;;chr19:45908292..45908374,-!p1@PPP1R13L!0.72!42.64!PPP1R13L;;chr13:79177703..79177729,-!p2@POU4F1!0.71!4.18!POU4F1;;chr5:16465902..16465917,-!p1@ZNF622!0.70!108.62!ZNF622;;chr13:27998831..27998851,+!p2@GTF3A!0.70!27.37!GTF3A;;chr5:72744445..72744466,-!p2@FOXD1!0.70!7.06!FOXD1;;chr8:10588010..10588030,-!p1@SOX7!0.70!4.03!SOX7;;chr6:34204642..34204664,+!p2@HMGA1!0.69!599.70!HMGA1;;chr19:57791328..57791377,+!p2@ZNF460!0.69!54.45!ZNF460;;chr13:41593425..41593480,-!p1@ELF1!0.69!28.23!ELF1;;chr7:64838786..64838809,+!p2@ZNF92!0.69!24.92!ZNF92;;chr4:4291837..4291859,-!p2@LYAR!0.69!14.26!LYAR;;chr2:70167296..70167306,+!p3@MXD1!0.69!6.34!MXD1;;chr12:57914286..57914304,-!p1@DDIT3!0.67!155.87!DDIT3;;chr13:45011349..45011391,-!p4@TSC22D1!0.67!9.94!TSC22D1;;chr8:128750175..128750201,+!p8@MYC!0.67!6.91!MYC;;chr8:128752771..128752843,+!p9@MYC!0.67!5.62!MYC;;chr5:72744562..72744573,-!p3@FOXD1!0.66!4.61!FOXD1;;chr17:46687935..46687950,-!p3@HOXB7!0.66!3.60!HOXB7;;chr11:65668011..65668020,-!p3@FOSL1!0.66!3.60!FOSL1;;chr10:60145155..60145206,+!p1@TFAM!0.65!176.61!TFAM;;chr5:76383070..76383117,-!p3@ZBED3!0.65!7.63!ZBED3;;chr12:51157837..51157892,+!p1@ATF1!0.64!85.42!ATF1;;chr9:110252035..110252057,-!p1@KLF4!0.64!63.82!KLF4;;chr6:20402102..20402152,+!p1@E2F3!0.64!15.85!E2F3;;chr12:72057747..72057854,+!p4@THAP2!0.64!10.23!THAP2;;chr6:10412600..10412637,-!p1@TFAP2A!0.64!6.05!TFAP2A;;chr12:6798731..6798751,-!p4@ZNF384!0.64!5.47!ZNF384;;chr3:148804275..148804346,-!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Line 38: Line 40:
|fonse_treatment_closure=
|fonse_treatment_closure=
|has_quality=
|has_quality=
|hg19bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.cell_line.hCAGE/giant%2520cell%2520carcinoma%2520cell%2520line%253aLU65.CNhs11274.10487-107B1.hg19.nobarcode.bam
|hg19ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.cell_line.hCAGE/giant%2520cell%2520carcinoma%2520cell%2520line%253aLU65.CNhs11274.10487-107B1.hg19.ctss.bed.gz
|hg19fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.cell_line.hCAGE/giant%2520cell%2520carcinoma%2520cell%2520line%253aLU65.CNhs11274.10487-107B1.hg19.nobarcode.rdna.fa.gz
|hg38bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/hg38_v2/basic/human.cell_line.hCAGE/giant%2520cell%2520carcinoma%2520cell%2520line%253aLU65.CNhs11274.10487-107B1.hg38.nobarcode.bam
|hg38ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/hg38_v2/basic/human.cell_line.hCAGE/giant%2520cell%2520carcinoma%2520cell%2520line%253aLU65.CNhs11274.10487-107B1.hg38.nobarcode.ctss.bed.gz
|id=FF:10487-107B1
|id=FF:10487-107B1
|is_a=EFO:0002091;;FF:0000210;;FF:0102411
|is_a=EFO:0002091;;FF:0000210;;FF:0102411
|is_obsolete=
|is_obsolete=
|library_ids=CNhs11274
|library_id=CNhs11274
|library_id_phase_based=2:CNhs11274
|microRNAs=
|microRNAs_nn=
|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/human#cage;sample;10487
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/human#cage;sample;10487
|name=giant cell carcinoma cell line:LU65
|name=giant cell carcinoma cell line:LU65
|namespace=FANTOM5
|namespace=FANTOM5
Line 47: Line 59:
|profile_cagescan=,,,
|profile_cagescan=,,,
|profile_hcage=CNhs11274,LSID758,release008,COMPLETED
|profile_hcage=CNhs11274,LSID758,release008,COMPLETED
|profile_rnaseq=,,,
|profile_rnaseq=
|profile_srnaseq=,,,
|profile_srnaseq=,,,
|refex=http://refex.dbcls.jp/genelist.php?lang
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Line 86: Line 99:
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|xref=
|xref=
}} {{DRAAccessionNumbers
|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_human;search_select_hide=table111:FF:10487-107B1;search_select_hide=table117:FF:10487-107B1
|DRA_sample_Accession=CAGE@DRS007789
|accession_numbers=DRX007894;DRR008766;DRZ000191;DRZ001576;CAGE
|library_id=CNhs11274
}}
}}

Latest revision as of 14:26, 3 June 2020

Name:giant cell carcinoma cell line:LU65
Species:Human (Homo sapiens)
Library ID:CNhs11274
Sample type:cell lines
Genomic View: UCSC
RefEX:Specific genes
CAGEd-oPOSSUM:link
ZENBU report :link
Additional information
Sample information
strainNA
tissuelung
dev stageNA
sexunknown
ageunknown
cell typeunclassifiable
cell lineLU65
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  SAMD00005221
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11274 CAGE DRX007894 DRR008766
Accession ID Hg19

Library idBAMCTSS
CNhs11274 DRZ000191 DRZ001576
Accession ID Hg38

Library idBAMCTSS
CNhs11274 DRZ011541 DRZ012926
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
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C84-choriocarcinoma-pancreatic-Wilms-Mallassezderived-thymus-salivary-colon0
C85-neuroblastoma-carcinoid-retinoblastoma-small-pineal-rhabdomyosarcoma-medulloblastoma0
C86-colon-carcinoid-small-neuroectodermal-giant-large-neuroepithelioma0
C87-retinoblastoma-left-nonsmall-heart-small-diaphragm-bronchogenic0
C88-Melanocyte-melanoma-Macrophage-Mesenchymal-migratory-Dendritic-Monocytederived0
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: CNhs11274

Jaspar motifP-value
MA0002.20.978
MA0003.10.749
MA0004.10.00299
MA0006.10.319
MA0007.10.95
MA0009.10.687
MA0014.10.688
MA0017.10.204
MA0018.20.439
MA0019.10.077
MA0024.10.23
MA0025.10.374
MA0027.10.903
MA0028.13.79894e-7
MA0029.10.289
MA0030.10.221
MA0031.10.943
MA0035.20.226
MA0038.10.45
MA0039.20.598
MA0040.10.91
MA0041.10.232
MA0042.10.588
MA0043.10.13
MA0046.10.823
MA0047.20.194
MA0048.10.145
MA0050.10.00126
MA0051.10.182
MA0052.10.865
MA0055.10.00212
MA0057.10.919
MA0058.10.00198
MA0059.12.69713e-5
MA0060.10.00401
MA0061.10.486
MA0062.21.77027e-7
MA0065.20.0131
MA0066.10.416
MA0067.10.726
MA0068.10.102
MA0069.10.973
MA0070.10.136
MA0071.10.205
MA0072.10.269
MA0073.10.964
MA0074.10.718
MA0076.18.69851e-9
MA0077.10.066
MA0078.10.408
MA0079.20.0131
MA0080.20.0159
MA0081.10.58
MA0083.10.019
MA0084.10.0852
MA0087.10.269
MA0088.10.0336
MA0090.10.261
MA0091.10.209
MA0092.10.987
MA0093.10.00345
MA0099.23.16534e-9
MA0100.10.578
MA0101.10.53
MA0102.20.907
MA0103.10.00493
MA0104.23.94585e-6
MA0105.10.00774
MA0106.10.191
MA0107.10.747
MA0108.22.25089e-4
MA0111.10.555
MA0112.20.0246
MA0113.10.821
MA0114.10.0222
MA0115.10.115
MA0116.10.00724
MA0117.10.792
MA0119.10.0546
MA0122.10.539
MA0124.10.285
MA0125.10.876
MA0131.10.209
MA0135.10.2
MA0136.10.0471
MA0137.20.618
MA0138.20.764
MA0139.10.0997
MA0140.10.101
MA0141.10.014
MA0142.10.705
MA0143.10.561
MA0144.10.464
MA0145.10.92
MA0146.10.936
MA0147.17.56597e-7
MA0148.10.0562
MA0149.10.0189
MA0150.10.00358
MA0152.10.262
MA0153.10.404
MA0154.10.329
MA0155.10.33
MA0156.14.76619e-4
MA0157.10.983
MA0159.10.0702
MA0160.10.0338
MA0162.10.437
MA0163.19.91107e-10
MA0164.10.7
MA0258.10.139
MA0259.10.0146



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: CNhs11274

Novel motifP-value
10.0155
100.0319
1000.0232
1010.919
1020.515
1030.447
1040.64
1050.958
1060.297
1070.221
1080.478
1090.0143
110.357
1100.115
1110.0251
1120.488
1130.144
1140.0251
1150.991
1160.486
1170.0371
1180.169
1190.339
120.932
1200.0379
1210.314
1220.352
1230.0349
1240.56
1250.88
1260.694
1270.744
1280.0658
1290.933
136.6495e-4
1300.717
1310.493
1320.458
1330.502
1340.333
1350.486
1360.127
1370.379
1380.436
1390.0131
140.946
1400.133
1410.136
1420.639
1430.899
1440.717
1450.475
1460.843
1470.365
1480.00652
1490.681
150.0765
1500.967
1510.688
1520.0619
1530.152
1540.955
1550.739
1560.352
1570.56
1580.4
1590.509
160.432
1600.769
1610.993
1620.793
1630.39
1640.137
1650.349
1660.395
1670.00588
1680.786
1690.277
170.771
180.368
190.95
20.237
200.0372
210.192
220.6
230.977
240.223
250.458
260.254
270.442
280.825
290.0619
30.097
300.14
310.579
320.345
330.0585
340.199
350.284
360.0109
370.308
380.638
390.558
40.962
400.0362
410.948
420.183
430.284
440.765
450.516
460.415
470.137
480.215
490.158
50.538
500.938
510.959
520.195
530.963
540.944
550.797
560.857
570.0652
580.264
590.946
60.549
600.819
610.316
620.255
630.182
640.367
650.865
660.166
670.522
680.0267
690.614
70.0603
700.0411
710.0184
720.558
730.695
740.648
750.0789
760.0709
770.915
780.00589
790.0787
80.262
800.185
810.6
820.712
830.517
840.377
850.447
860.756
870.636
880.799
890.589
90.289
900.393
910.261
920.656
930.487
940.487
950.23
960.355
970.995
980.0206
990.297



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: CNhs11274


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)
0000255 (eukaryotic cell)

DOID: Disease
4 (disease)
162 (cancer)
14566 (disease of cellular proliferation)
0050687 (cell type cancer)
305 (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)
0101120 (epithelial cell line sample)
0102411 (giant cell carcinoma 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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