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{{f5samples
{{f5samples
|DRA_sample_Accession=CAGE@SAMD00005614
|DRA_sample_Accession=CAGE@SAMD00005614
|accession_numbers=CAGE;DRX007801;DRR008673;DRZ000098;DRZ001483
|accession_numbers=CAGE;DRX007801;DRR008673;DRZ000098;DRZ001483;DRZ011448;DRZ012833
|ancestors_in_anatomy_facet=
|ancestors_in_anatomy_facet=
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000988,CL:0000548,CL:0000763,CL:0002371,CL:0000255
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000988,CL:0000548,CL:0000763,CL:0002371,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/acute%2520myeloid%2520leukemia%2520%2528FAB%2520M0%2529%2520cell%2520line%253aKG-1.CNhs13053.10827-111C8.hg19.nobarcode.bam
|hg19ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.cell_line.hCAGE/acute%2520myeloid%2520leukemia%2520%2528FAB%2520M0%2529%2520cell%2520line%253aKG-1.CNhs13053.10827-111C8.hg19.ctss.bed.gz
|hg19fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.cell_line.hCAGE/acute%2520myeloid%2520leukemia%2520%2528FAB%2520M0%2529%2520cell%2520line%253aKG-1.CNhs13053.10827-111C8.hg19.nobarcode.rdna.fa.gz
|hg38bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/hg38_v2/basic/human.cell_line.hCAGE/acute%2520myeloid%2520leukemia%2520%2528FAB%2520M0%2529%2520cell%2520line%253aKG-1.CNhs13053.10827-111C8.hg38.nobarcode.bam
|hg38ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/hg38_v2/basic/human.cell_line.hCAGE/acute%2520myeloid%2520leukemia%2520%2528FAB%2520M0%2529%2520cell%2520line%253aKG-1.CNhs13053.10827-111C8.hg38.nobarcode.ctss.bed.gz
|id=FF:10827-111C8
|id=FF:10827-111C8
|is_a=EFO:0002091;;FF:0000210;;FF:0101883
|is_a=EFO:0002091;;FF:0000210;;FF:0101883
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|library_id=CNhs13053
|library_id=CNhs13053
|library_id_phase_based=2:CNhs13053
|library_id_phase_based=2:CNhs13053
|microRNAs=
|microRNAs_nn=
|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/human#cage;sample;10827
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/human#cage;sample;10827
|name=acute myeloid leukemia (FAB M0) cell line:KG-1
|name=acute myeloid leukemia (FAB M0) cell line:KG-1
|namespace=FANTOM5
|namespace=FANTOM5
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|profile_rnaseq=
|profile_rnaseq=
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|refex=http://refex.dbcls.jp/genelist.php?lang=en&db=human&roku_valid=1&rk[]=&order_key=score
|refex=http://refex.dbcls.jp/genelist.php?lang
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Line 91: Line 100:
|top_motifs=MYB:2.21701417088;E2F1..5:1.86707680521;YY1:1.76199269368;AIRE:1.70772420317;IKZF2:1.6438924376;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:1.57515877215;ZBTB16:1.56144577166;HAND1,2:1.49632836851;RXR{A,B,G}_{NR1H2,PPAR}dimers:1.45394918981;POU3F1..4:1.38847103381;ALX1:1.26734603778;DMAP1_NCOR{1,2}_SMARC:1.26047341298;STAT1,3:1.14166253823;ZNF143:1.13081023557;GATA6:1.12335965188;FOX{I1,J2}:1.1190229842;NKX2-2,8:1.10938720149;ELF1,2,4:1.0379299026;TOPORS:1.03367644296;RUNX1..3:1.01942115716;SPIB:1.00994269872;TEF:0.991317398057;PITX1..3:0.956512633069;NR5A1,2:0.822169457679;PAX4:0.774592178844;FOXA2:0.766632053074;ELK1,4_GABP{A,B1}:0.759515374215;CDX1,2,4:0.750108798469;HBP1_HMGB_SSRP1_UBTF:0.71295345849;SPI1:0.690094688843;NRF1:0.68982347884;ARID5B:0.679668794081;FOXP3:0.603250282871;BREu{core}:0.581988848186;NFY{A,B,C}:0.569593533925;GATA4:0.535444933894;ETS1,2:0.528492029655;POU1F1:0.464558531417;EVI1:0.460053125192;HOX{A6,A7,B6,B7}:0.447294645562;HES1:0.407177506518;CUX2:0.38379925284;RXR{A,B,G}:0.3819376304;MYOD1:0.342289765797;NKX6-1,2:0.340323030078;NKX2-3_NKX2-5:0.331947109603;ZNF384:0.283126987604;FOXP1:0.252738606171;FOXD3:0.242929696656;NKX3-2:0.211924742701;NKX3-1:0.197782037663;NANOG{mouse}:0.190368581654;PDX1:0.178961274471;FOXM1:0.163733665884;PRRX1,2:0.162139505451;RBPJ:0.158822234933;CRX:0.157566395936;RXRA_VDR{dimer}:0.139253182796;HOX{A4,D4}:0.115179829174;IRF1,2:0.0977174818411;KLF4:0.0908359871172;HNF4A_NR2F1,2:0.0885785687876;VSX1,2:0.0669652022297;FOXQ1:0.0646957451154;OCT4_SOX2{dimer}:0.0567607617058;TGIF1:0.0555953825728;BPTF:0.0551385645864;PBX1:0.0365899796441;UFEwm:0.0362905779989;PAX8:0.0341975352051;POU5F1:0.0184437150881;SNAI1..3:0.0181158218685;PAX6:-0.0152749412018;FOX{F1,F2,J1}:-0.0427113897886;GCM1,2:-0.0700123298805;ONECUT1,2:-0.0754935273476;CREB1:-0.0831729424615;ATF5_CREB3:-0.0947500365465;TFDP1:-0.0983362729035;STAT5{A,B}:-0.100595025727;NFIL3:-0.114845153441;HSF1,2:-0.143724425695;HOXA9_MEIS1:-0.178717683237;ESR1:-0.192786060766;PAX3,7:-0.208162441723;POU2F1..3:-0.217006326638;RREB1:-0.220768041504;HMGA1,2:-0.230938913604;ALX4:-0.231196832239;HNF1A:-0.232937298758;TLX2:-0.233541832024;ZEB1:-0.244492512299;NFKB1_REL_RELA:-0.248388534933;CDC5L:-0.256108103572;NKX2-1,4:-0.272268054694;EN1,2:-0.27556323285;REST:-0.277859269058;NR6A1:-0.284470180304;RORA:-0.335558731617;NFE2L1:-0.336723148116;PPARG:-0.356981976005;bHLH_family:-0.360346736893;SOX{8,9,10}:-0.376619193816;POU6F1:-0.376679784716;ZIC1..3:-0.395748602791;NR1H4:-0.396017193945;ZNF423:-0.402266071686;AR:-0.410948097131;GFI1:-0.412481255149;NANOG:-0.427756386473;HIF1A:-0.428661200982;ZNF238:-0.429033707888;EP300:-0.440084457554;ZNF148:-0.474797358548;SOX17:-0.500027300866;RFX2..5_RFXANK_RFXAP:-0.513875151043;GZF1:-0.515159548689;TFAP4:-0.515306011847;AHR_ARNT_ARNT2:-0.528855023604;LHX3,4:-0.549581926299;NFE2:-0.55230670012;DBP:-0.554367637329;CEBPA,B_DDIT3:-0.555506589035;FOSL2:-0.555869917518;IRF7:-0.561440890851;FOS_FOS{B,L1}_JUN{B,D}:-0.611932152041;XBP1:-0.62969457476;MEF2{A,B,C,D}:-0.649020292953;BACH2:-0.657772356892;PAX2:-0.659109870268;PRDM1:-0.667495961206;SOX5:-0.67500181808;MYBL2:-0.68957717169;FOXO1,3,4:-0.712587447451;ESRRA:-0.712659988627;ZFP161:-0.718756813407;PAX5:-0.719989635003;MZF1:-0.800037459565;ATF4:-0.811578900233;HLF:-0.813199916273;MYFfamily:-0.875066826785;SMAD1..7,9:-0.8886004523;HIC1:-0.889095009545;RFX1:-0.897169883275;NFATC1..3:-0.917914309136;T:-0.938672717022;TAL1_TCF{3,4,12}:-0.980818085219;SRF:-0.997322779171;LEF1_TCF7_TCF7L1,2:-0.999184692174;HOX{A5,B5}:-1.00665821768;GTF2A1,2:-1.02605809909;SREBF1,2:-1.02703711545;IKZF1:-1.02837647946;STAT2,4,6:-1.02899260664;PATZ1:-1.05803387182;NFE2L2:-1.05922720806;ATF2:-1.07338682409;FOXN1:-1.08930869178;SOX2:-1.10778355538;SPZ1:-1.12472604943;NHLH1,2:-1.12689839308;GTF2I:-1.13688314022;LMO2:-1.14586104396;HMX1:-1.15789165025;EBF1:-1.16746652945;TP53:-1.22901386992;MAFB:-1.23824449024;TFAP2B:-1.26070680783;NFIX:-1.26859150441;GLI1..3:-1.27302210617;ZBTB6:-1.27651830927;FOXL1:-1.30352281687;PAX1,9:-1.34089232015;JUN:-1.34549847419;ATF6:-1.35448820842;TEAD1:-1.36494914914;TFAP2{A,C}:-1.37460334158;MED-1{core}:-1.38928582471;GFI1B:-1.39100025938;EGR1..3:-1.48941975163;TBP:-1.49240409851;MTF1:-1.52908550436;ADNP_IRX_SIX_ZHX:-1.56946985164;FOX{D1,D2}:-1.59163032007;TBX4,5:-1.65830058019;MAZ:-1.67940710889;NR3C1:-1.74092705013;XCPE1{core}:-1.79636078818;TLX1..3_NFIC{dimer}:-1.87020815705;TFCP2:-1.9450601993;MTE{core}:-2.12010335288;SP1:-2.12865473632
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|xref=
|xref=
|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_human;search_select_hide=table111:FF:10827-111C8;search_select_hide=table117:FF:10827-111C8
}}
}}

Latest revision as of 15:07, 3 June 2020

Name:acute myeloid leukemia (FAB M0) cell line:KG-1
Species:Human (Homo sapiens)
Library ID:CNhs13053
Sample type:cell lines
Genomic View: UCSC
RefEX:Specific genes
CAGEd-oPOSSUM:link
ZENBU report :link
Additional information
Sample information
strainNA
tissueblood
dev stageNA
sexmale
age59
cell typemyeloid progenitor cell
cell lineKG-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  SAMD00005614
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs13053 CAGE DRX007801 DRR008673
Accession ID Hg19

Library idBAMCTSS
CNhs13053 DRZ000098 DRZ001483
Accession ID Hg38

Library idBAMCTSS
CNhs13053 DRZ011448 DRZ012833
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
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C83-choriocarcinoma-pancreatic-placenta-chorionic-HES3GFP-testicular-amniotic0
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: CNhs13053

Jaspar motifP-value
MA0002.23.28285e-4
MA0003.10.763
MA0004.10.102
MA0006.10.201
MA0007.10.863
MA0009.10.323
MA0014.10.307
MA0017.10.0613
MA0018.20.00943
MA0019.10.121
MA0024.17.91362e-6
MA0025.10.184
MA0027.10.06
MA0028.10.00147
MA0029.10.628
MA0030.10.00597
MA0031.10.244
MA0035.20.0504
MA0038.10.0167
MA0039.20.155
MA0040.10.618
MA0041.10.188
MA0042.10.719
MA0043.10.0424
MA0046.10.483
MA0047.20.463
MA0048.10.122
MA0050.10.392
MA0051.10.596
MA0052.18.52805e-5
MA0055.10.0693
MA0057.10.655
MA0058.10.054
MA0059.12.18127e-4
MA0060.10.223
MA0061.10.673
MA0062.25.93532e-7
MA0065.20.00733
MA0066.10.306
MA0067.10.457
MA0068.10.0587
MA0069.10.0484
MA0070.10.666
MA0071.10.0756
MA0072.10.652
MA0073.10.594
MA0074.10.964
MA0076.16.66663e-4
MA0077.10.118
MA0078.10.925
MA0079.20.218
MA0080.21.15821e-8
MA0081.10.00546
MA0083.11.18798e-4
MA0084.10.974
MA0087.10.214
MA0088.16.40716e-4
MA0090.11.32002e-4
MA0091.10.497
MA0092.10.666
MA0093.10.0899
MA0099.21.87524e-7
MA0100.10.00308
MA0101.10.31
MA0102.20.486
MA0103.10.178
MA0104.21.65452e-4
MA0105.10.00404
MA0106.10.696
MA0107.10.0713
MA0108.21.86996e-17
MA0111.10.403
MA0112.20.0532
MA0113.10.784
MA0114.10.0549
MA0115.10.0183
MA0116.16.67637e-5
MA0117.10.963
MA0119.10.351
MA0122.10.435
MA0124.10.915
MA0125.10.452
MA0131.10.287
MA0135.10.314
MA0136.18.16196e-11
MA0137.20.417
MA0138.20.871
MA0139.10.182
MA0140.10.0245
MA0141.10.0842
MA0142.10.526
MA0143.10.331
MA0144.10.388
MA0145.10.414
MA0146.10.0731
MA0147.11.87856e-5
MA0148.10.138
MA0149.10.0528
MA0150.10.0998
MA0152.10.202
MA0153.10.00585
MA0154.10.06
MA0155.10.909
MA0156.11.87482e-8
MA0157.10.809
MA0159.10.234
MA0160.10.0681
MA0162.10.563
MA0163.11.25764e-15
MA0164.10.967
MA0258.10.0362
MA0259.10.0386



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: CNhs13053

Novel motifP-value
10.0326
100.0075
1000.452
1010.294
1020.57
1030.365
1040.96
1050.65
1060.712
1070.553
1080.614
1090.153
110.0613
1100.15
1110.0145
1120.311
1130.814
1140.0332
1150.751
1160.411
1170.0147
1180.0318
1190.341
120.942
1200.203
1210.801
1220.604
1230.00603
1240.0966
1250.105
1260.414
1270.198
1280.576
1290.41
130.0122
1300.83
1310.759
1320.894
1330.0894
1340.321
1350.484
1360.44
1370.525
1380.98
1390.199
140.807
1400.0041
1410.0885
1420.475
1430.193
1440.809
1450.583
1460.568
1470.0832
1480.157
1490.708
150.0921
1500.888
1510.963
1520.218
1530.637
1540.856
1550.00698
1560.558
1570.135
1580.355
1590.951
160.712
1600.111
1610.0505
1620.821
1630.355
1640.0847
1650.924
1660.621
1670.043
1680.242
1690.29
170.79
180.59
190.815
20.869
200.626
210.215
220.74
230.225
240.157
250.107
260.0443
270.36
280.876
290.0278
30.0902
300.162
310.501
320.235
330.133
340.869
350.129
360.0428
370.144
380.658
390.578
40.545
400.29
410.712
420.209
430.459
440.0498
450.468
460.0586
470.0317
480.039
490.125
50.815
500.978
510.788
520.195
530.417
540.714
550.625
560.837
570.0702
580.314
590.506
60.572
600.957
610.0705
620.0784
630.373
640.13
650.874
660.185
670.807
680.455
690.84
70.0384
700.285
710.0115
720.708
730.615
740.756
750.0124
760.114
770.965
780.0817
790.557
80.0448
800.135
810.195
820.231
830.464
840.692
850.364
860.855
870.63
880.508
890.542
90.817
900.0121
910.61
920.842
930.444
940.316
950.0485
960.641
970.175
980.19
990.522



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: CNhs13053


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)
0000988 (hematopoietic cell)
0000548 (animal cell)
0000763 (myeloid cell)
0002371 (somatic cell)
0000255 (eukaryotic cell)

DOID: Disease
4 (disease)
0050686 (organ system cancer)
162 (cancer)
2531 (hematologic cancer)
14566 (disease of cellular proliferation)
0060083 (immune system cancer)
1240 (leukemia)
8692 (myeloid leukemia)

FF: FANTOM5
0000102 (sample by type)
0000003 (cell line sample)
0000210 (human sample)
0000101 (sample by species)
0000001 (sample)
0100737 (leukemia cell line sample)
0101035 (hematopoietic cell line sample)
0101883 (acute myeloid leukemia cell line sample)
0100740 (myeloid leukemia 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:0000049 (common myeloid progenitor)
CL:0000134 (mesenchymal cell)

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