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{{f5samples
{{f5samples
|DRA_sample_Accession=CAGE@SAMD00005418
|DRA_sample_Accession=CAGE@SAMD00005418
|accession_numbers=CAGE;DRX007900;DRR008772;DRZ000197;DRZ001582
|accession_numbers=CAGE;DRX007900;DRR008772;DRZ000197;DRZ001582;DRZ011547;DRZ012932
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000955,UBERON:0004121,UBERON:0011216,UBERON:0000062,UBERON:0000061,UBERON:0000465,UBERON:0000477,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0010317,UBERON:0001017,UBERON:0001016
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000955,UBERON:0004121,UBERON:0011216,UBERON:0000062,UBERON:0000061,UBERON:0000465,UBERON:0000477,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0010317,UBERON:0001017,UBERON:0001016
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000548,CL:0002371,CL:0002319,CL:0000095,CL:0000243,CL:0000125,CL:0000255
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000548,CL:0002371,CL:0002319,CL:0000095,CL:0000243,CL:0000125,CL:0000255
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|fonse_treatment_closure=
|fonse_treatment_closure=
|has_quality=
|has_quality=
|hg19bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.cell_line.hCAGE/glioma%2520cell%2520line%253aGI-1.CNhs10731.10413-106B8.hg19.nobarcode.bam
|hg19ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.cell_line.hCAGE/glioma%2520cell%2520line%253aGI-1.CNhs10731.10413-106B8.hg19.ctss.bed.gz
|hg19fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.cell_line.hCAGE/glioma%2520cell%2520line%253aGI-1.CNhs10731.10413-106B8.hg19.nobarcode.rdna.fa.gz
|hg38bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/hg38_v2/basic/human.cell_line.hCAGE/glioma%2520cell%2520line%253aGI-1.CNhs10731.10413-106B8.hg38.nobarcode.bam
|hg38ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/hg38_v2/basic/human.cell_line.hCAGE/glioma%2520cell%2520line%253aGI-1.CNhs10731.10413-106B8.hg38.nobarcode.ctss.bed.gz
|id=FF:10413-106B8
|id=FF:10413-106B8
|is_a=EFO:0002091;;FF:0000210;;FF:0100711
|is_a=EFO:0002091;;FF:0000210;;FF:0100711
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|library_id=CNhs10731
|library_id=CNhs10731
|library_id_phase_based=2:CNhs10731
|library_id_phase_based=2:CNhs10731
|microRNAs=
|microRNAs_nn=
|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/human#cage;sample;10413
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/human#cage;sample;10413
|name=glioma cell line:GI-1
|name=glioma cell line:GI-1
|namespace=FANTOM5
|namespace=FANTOM5
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|profile_rnaseq=
|profile_rnaseq=
|profile_srnaseq=,,,
|profile_srnaseq=,,,
|refex=http://refex.dbcls.jp/genelist.php?lang
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Line 90: Line 100:
|top_motifs=ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:1.58007627964;bHLH_family:1.0245002728;HSF1,2:0.98668410731;GZF1:0.969708444572;RXR{A,B,G}:0.950545164449;PAX4:0.950043194185;NFY{A,B,C}:0.925198241649;NFIX:0.916060504273;TOPORS:0.894700061811;EN1,2:0.888695275885;ELK1,4_GABP{A,B1}:0.816457901734;HOX{A5,B5}:0.805087433072;GFI1:0.77300668311;ZNF143:0.764453805036;AHR_ARNT_ARNT2:0.745794212975;POU6F1:0.729276163404;NRF1:0.727298545332;NKX6-1,2:0.713151823803;SOX17:0.688655480606;ZNF384:0.686265039629;TLX1..3_NFIC{dimer}:0.667475965097;E2F1..5:0.662852068764;SREBF1,2:0.651503681943;LHX3,4:0.646293663262;PITX1..3:0.605904338514;HAND1,2:0.596920708146;YY1:0.595299606675;HBP1_HMGB_SSRP1_UBTF:0.547419759469;ONECUT1,2:0.544492898778;FOXD3:0.51933656157;MAFB:0.51883395245;SOX2:0.501840395131;MZF1:0.497420431007;CREB1:0.490108697806;TFAP2B:0.488199906361;PAX1,9:0.481984182363;ARID5B:0.465661544148;HOXA9_MEIS1:0.439624268464;ZNF238:0.434063503051;PAX5:0.420261914333;PATZ1:0.41701982452;GATA4:0.401627251044;MAZ:0.397132225566;NKX3-1:0.385457196025;TBX4,5:0.384289571744;ZIC1..3:0.382448289523;GTF2I:0.380741135759;CUX2:0.376503498031;RFX1:0.358560552091;CDX1,2,4:0.350221175991;BACH2:0.339667307541;EVI1:0.335372184469;PDX1:0.334749235719;FOXQ1:0.33388114755;HLF:0.326181410544;VSX1,2:0.311690074614;CRX:0.263613872059;NR3C1:0.262198060775;AIRE:0.246052179192;NKX3-2:0.245912893796;PRRX1,2:0.242659836474;FOSL2:0.236436800513;MYB:0.23110905671;ZBTB6:0.221108069004;TEAD1:0.220359003191;MYFfamily:0.213002090245;RXRA_VDR{dimer}:0.209904076476;SMAD1..7,9:0.193855771291;RREB1:0.188066316076;HMGA1,2:0.185888185898;ESRRA:0.179268866712;POU1F1:0.170926533243;PRDM1:0.166067128188;NFE2:0.15255570889;ATF5_CREB3:0.148423442099;TFDP1:0.141789519399;FOXM1:0.135436829818;CDC5L:0.13442594119;ZFP161:0.13337972705;IKZF1:0.124762129803;ATF4:0.121392832514;NFE2L2:0.107207554451;BREu{core}:0.106549093166;PBX1:0.102648566031;SRF:0.100417585297;FOXP1:0.0798910084014;NR1H4:0.0700637140046;GATA6:0.0447883013118;RUNX1..3:0.042386864958;RFX2..5_RFXANK_RFXAP:0.0394430392694;ADNP_IRX_SIX_ZHX:0.0321282420821;GTF2A1,2:0.0318972350478;ZBTB16:0.0205299782694;MYBL2:0.0184974884228;TAL1_TCF{3,4,12}:0.00603272583401;TFAP4:0.000983451711223;ELF1,2,4:-0.00432009623008;JUN:-0.00521766625633;FOXP3:-0.00684510962584;XCPE1{core}:-0.0112403589558;NFIL3:-0.012812236273;TFAP2{A,C}:-0.0139533864022;CEBPA,B_DDIT3:-0.0178645412669;ZNF423:-0.0314419968191;MEF2{A,B,C,D}:-0.0342871516294;HNF1A:-0.038699384317;FOS_FOS{B,L1}_JUN{B,D}:-0.0420183105488;NFATC1..3:-0.0456956509363;T:-0.0509256805424;RORA:-0.0688000548516;LEF1_TCF7_TCF7L1,2:-0.0709056463336;PAX3,7:-0.0722871261496;UFEwm:-0.0989744540969;SOX{8,9,10}:-0.103651001901;TFCP2:-0.124543061422;HOX{A4,D4}:-0.134188242395;FOXA2:-0.13459399137;RBPJ:-0.16393611846;BPTF:-0.167573075151;IRF7:-0.167689280215;XBP1:-0.170496946759;HIF1A:-0.17833333396;KLF4:-0.183281465236;PAX8:-0.19005012972;HMX1:-0.194356001153;EGR1..3:-0.196184150185;GFI1B:-0.19798994927;HNF4A_NR2F1,2:-0.200243599203;SPZ1:-0.2077305145;TEF:-0.209787517049;EBF1:-0.215154811895;REST:-0.224233838622;NKX2-1,4:-0.228075986111;ATF6:-0.242861728094;ESR1:-0.257454542566;STAT1,3:-0.265151763441;NFE2L1:-0.269114653176;PAX2:-0.269269210921;TLX2:-0.276824002438;SP1:-0.278680281164;FOX{D1,D2}:-0.288482046116;MTE{core}:-0.289391867744;HIC1:-0.29130475141;FOX{F1,F2,J1}:-0.295899880164;IRF1,2:-0.297953333918;NFKB1_REL_RELA:-0.30011905656;FOXN1:-0.333769556393;OCT4_SOX2{dimer}:-0.340122330841;NR6A1:-0.353794605741;DMAP1_NCOR{1,2}_SMARC:-0.368344861539;RXR{A,B,G}_{NR1H2,PPAR}dimers:-0.368581955843;NANOG:-0.383464678935;TBP:-0.389859114665;TP53:-0.394225537118;NKX2-2,8:-0.401092842561;LMO2:-0.413752167933;MED-1{core}:-0.413826303726;IKZF2:-0.414832854124;NHLH1,2:-0.433177502141;POU3F1..4:-0.434686071893;ALX4:-0.450440230321;DBP:-0.47061368742;NKX2-3_NKX2-5:-0.473391289221;SPIB:-0.475917478212;MYOD1:-0.482323075736;ATF2:-0.500062483376;FOX{I1,J2}:-0.502454011631;SPI1:-0.511480773203;STAT2,4,6:-0.515076050892;MTF1:-0.544979712573;HES1:-0.555232278736;POU5F1:-0.580808599796;NR5A1,2:-0.586776988024;ETS1,2:-0.608717993869;SNAI1..3:-0.615990193532;ZNF148:-0.640720897951;GLI1..3:-0.642864268572;GCM1,2:-0.647258276763;SOX5:-0.665294915975;PPARG:-0.704722763059;ALX1:-0.725924127972;ZEB1:-0.763655843157;EP300:-0.766746252279;NANOG{mouse}:-0.7882971492;AR:-0.789989173971;TGIF1:-0.860504568575;FOXO1,3,4:-0.909853091812;STAT5{A,B}:-0.94267440659;HOX{A6,A7,B6,B7}:-0.962443477229;PAX6:-1.23341566523;POU2F1..3:-1.5675776398;FOXL1:-1.62787901201
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|xref=
|xref=
|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_human;search_select_hide=table111:FF:10413-106B8;search_select_hide=table117:FF:10413-106B8
}}
}}

Latest revision as of 13:59, 3 June 2020

Name:glioma cell line:GI-1
Species:Human (Homo sapiens)
Library ID:CNhs10731
Sample type:cell lines
Genomic View: UCSC
RefEX:Specific genes
CAGEd-oPOSSUM:link
ZENBU report :link
Additional information
Sample information
strainNA
tissuebrain
dev stage61 year old adult
sexmale
age61
cell typeglioblast
cell lineGI-1
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  SAMD00005418
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs10731 CAGE DRX007900 DRR008772
Accession ID Hg19

Library idBAMCTSS
CNhs10731 DRZ000197 DRZ001582
Accession ID Hg38

Library idBAMCTSS
CNhs10731 DRZ011547 DRZ012932
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
C106-Hep2-epitheloid-placenta-cervical-rectal-anaplastic-glassy0
C107-Neutrophils-CD14-Eosinophils-Monocytederived-Whole-Peripheral-blood0
C108-breast-hepatoblastoma-MCF7-parotid-salivary-submaxillary-prostate0
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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: CNhs10731

Jaspar motifP-value
MA0002.20.281
MA0003.10.244
MA0004.10.113
MA0006.10.411
MA0007.10.0122
MA0009.10.188
MA0014.10.605
MA0017.10.0738
MA0018.20.747
MA0019.10.141
MA0024.10.00938
MA0025.10.679
MA0027.10.483
MA0028.18.30508e-4
MA0029.10.478
MA0030.10.685
MA0031.10.383
MA0035.20.646
MA0038.10.00531
MA0039.20.0206
MA0040.10.595
MA0041.10.293
MA0042.10.763
MA0043.10.0674
MA0046.10.311
MA0047.20.716
MA0048.10.048
MA0050.10.28
MA0051.10.209
MA0052.10.169
MA0055.10.311
MA0057.10.422
MA0058.10.0063
MA0059.10.553
MA0060.16.57458e-8
MA0061.10.00213
MA0062.20.0139
MA0065.20.127
MA0066.10.327
MA0067.10.689
MA0068.10.0225
MA0069.10.574
MA0070.10.00162
MA0071.10.773
MA0072.10.957
MA0073.10.768
MA0074.10.634
MA0076.12.42947e-4
MA0077.10.837
MA0078.10.436
MA0079.20.958
MA0080.21.37652e-13
MA0081.10.0323
MA0083.10.147
MA0084.10.763
MA0087.10.292
MA0088.10.648
MA0090.10.473
MA0091.10.303
MA0092.10.0761
MA0093.10.0317
MA0099.21.58421e-5
MA0100.10.305
MA0101.10.0861
MA0102.20.05
MA0103.10.00151
MA0104.20.199
MA0105.10.0016
MA0106.10.598
MA0107.10.024
MA0108.20.019
MA0111.10.563
MA0112.25.44259e-4
MA0113.10.687
MA0114.10.501
MA0115.10.197
MA0116.10.00764
MA0117.10.74
MA0119.10.817
MA0122.10.59
MA0124.10.0788
MA0125.10.657
MA0131.10.846
MA0135.10.528
MA0136.11.34134e-10
MA0137.20.016
MA0138.20.0374
MA0139.10.87
MA0140.10.445
MA0141.10.215
MA0142.10.0332
MA0143.10.876
MA0144.19.42131e-4
MA0145.10.381
MA0146.10.532
MA0147.10.488
MA0148.10.455
MA0149.10.732
MA0150.10.341
MA0152.10.683
MA0153.10.518
MA0154.10.012
MA0155.10.307
MA0156.10.00244
MA0157.10.0932
MA0159.10.0859
MA0160.10.262
MA0162.10.254
MA0163.10.0887
MA0164.10.353
MA0258.10.0377
MA0259.10.843



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: CNhs10731

Novel motifP-value
10.453
100.74
1000.965
1010.623
1020.624
1030.252
1040.394
1050.634
1062.36851e-4
1070.193
1080.497
1090.109
110.312
1100.589
1110.588
1120.0645
1130.071
1140.0179
1150.631
1160.805
1170.389
1180.906
1190.0399
120.312
1200.799
1210.929
1220.169
1230.396
1240.925
1250.401
1260.217
1270.66
1280.0139
1290.0148
130.894
1300.148
1310.369
1320.207
1330.0874
1340.988
1350.134
1360.351
1370.534
1380.167
1390.0595
140.997
1400.977
1410.351
1420.997
1430.0112
1440.891
1450.219
1460.564
1470.858
1480.0898
1490.18
150.294
1500.562
1510.551
1520.138
1530.997
1540.808
1550.668
1560.739
1570.712
1580.316
1590.614
160.263
1600.124
1610.214
1620.492
1630.956
1640.417
1650.0136
1660.753
1670.248
1680.933
1690.209
170.492
180.75
190.237
20.441
200.811
210.883
220.435
230.0164
240.99
250.128
260.33
270.211
280.897
290.985
30.714
300.67
310.224
320.153
330.432
340.418
350.803
360.102
370.706
380.125
390.429
40.905
400.139
410.0509
420.879
430.104
440.191
450.352
460.217
470.995
480.331
490.188
50.37
500.878
510.817
520.0776
530.757
540.616
550.945
560.882
570.715
580.0648
590.0436
60.348
600.0263
610.857
620.00157
630.236
640.901
650.0209
660.0555
670.84
680.832
690.442
70.229
700.02
710.691
720.576
730.383
740.66
750.923
760.853
770.486
780.0709
790.368
80.383
800.528
810.631
820.0193
830.852
840.704
850.115
860.91
870.338
880.78
890.0608
90.665
900.327
910.364
920.0759
930.205
940.143
950.439
960.198
970.234
980.0136
990.909



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: CNhs10731


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)
0002371 (somatic cell)
0002319 (neural cell)
0000095 (neuron associated cell)
0000243 (glial cell (sensu Vertebrata))
0000125 (glial cell)
0000255 (eukaryotic cell)

DOID: Disease
4 (disease)
0050686 (organ system cancer)
162 (cancer)
14566 (disease of cellular proliferation)
3093 (nervous system cancer)

UBERON: Anatomy
0000468 (multi-cellular organism)
0000955 (brain)
0004121 (ectoderm-derived structure)
0011216 (organ system subdivision)
0000062 (organ)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000477 (anatomical cluster)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0010317 (germ layer / neural crest derived structure)
0001017 (central nervous system)
0001016 (nervous system)

FF: FANTOM5
0000102 (sample by type)
0000003 (cell line sample)
0000210 (human sample)
0000101 (sample by species)
0000001 (sample)
0100711 (glioma cell line sample)
0100255 (brain cell line sample)
0100690 (brain cancer cell line sample)
0101531 (glial 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
CL:0000133 (neurectodermal cell)
CL:0000339 (glioblast (sensu Vertebrata))
CL:0000221 (ectodermal cell)
UBERON:0002532 (epiblast (generic))
UBERON:0006601 (presumptive ectoderm)
UBERON:0006238 (future brain)
UBERON:0010316 (germ layer / neural crest)

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