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{{f5samples
{{f5samples
|DRA_sample_Accession=CAGE@SAMD00004812
|DRA_sample_Accession=CAGE@SAMD00004812
|accession_numbers=CAGE;DRX007819;DRR008691;DRZ000116;DRZ001501
|accession_numbers=CAGE;DRX007819;DRR008691;DRZ000116;DRZ001501;DRZ011466;DRZ012851
|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%2520M6%2529%2520cell%2520line%253aF-36P.CNhs13505.10837-111D9.hg19.nobarcode.bam
|hg19ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.cell_line.hCAGE/acute%2520myeloid%2520leukemia%2520%2528FAB%2520M6%2529%2520cell%2520line%253aF-36P.CNhs13505.10837-111D9.hg19.ctss.bed.gz
|hg19fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.cell_line.hCAGE/acute%2520myeloid%2520leukemia%2520%2528FAB%2520M6%2529%2520cell%2520line%253aF-36P.CNhs13505.10837-111D9.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%2520M6%2529%2520cell%2520line%253aF-36P.CNhs13505.10837-111D9.hg38.nobarcode.bam
|hg38ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/hg38_v2/basic/human.cell_line.hCAGE/acute%2520myeloid%2520leukemia%2520%2528FAB%2520M6%2529%2520cell%2520line%253aF-36P.CNhs13505.10837-111D9.hg38.nobarcode.ctss.bed.gz
|id=FF:10837-111D9
|id=FF:10837-111D9
|is_a=EFO:0002091;;FF:0000210;;FF:0101883
|is_a=EFO:0002091;;FF:0000210;;FF:0101883
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|library_id=CNhs13505
|library_id=CNhs13505
|library_id_phase_based=2:CNhs13505
|library_id_phase_based=2:CNhs13505
|microRNAs=
|microRNAs_nn=
|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/human#cage;sample;10837
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/human#cage;sample;10837
|name=acute myeloid leukemia (FAB M6) cell line:F-36P
|name=acute myeloid leukemia (FAB M6) cell line:F-36P
|namespace=FANTOM5
|namespace=FANTOM5
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|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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|top_motifs=GATA6:3.41116887503;ALX1:2.24219614767;MYB:1.51538073445;E2F1..5:1.26693290325;NFY{A,B,C}:1.2301010305;HOXA9_MEIS1:1.21238255465;ZNF143:1.19629519989;NR6A1:1.13884650161;PBX1:1.12348095401;PITX1..3:1.10576598723;PAX4:1.10395864647;STAT1,3:1.09849025438;HES1:1.06749643251;STAT5{A,B}:1.02485548172;POU1F1:1.01167225671;PPARG:1.00344039959;AIRE:1.00161776714;PAX8:0.965830298484;ELK1,4_GABP{A,B1}:0.955713721634;POU2F1..3:0.909808490731;HOX{A6,A7,B6,B7}:0.907277544746;NR5A1,2:0.869661870247;ELF1,2,4:0.80470354992;YY1:0.791612974957;FOXD3:0.755066335225;ZBTB16:0.733737586947;POU6F1:0.710998373731;bHLH_family:0.687054977455;SPIB:0.647328214291;CRX:0.623478310272;RBPJ:0.623070590583;FOX{I1,J2}:0.548891209264;IKZF2:0.54665203149;SOX{8,9,10}:0.533622143296;NRF1:0.472994215117;EN1,2:0.467689929698;LHX3,4:0.459236276701;AR:0.442749952401;SPI1:0.415095513202;RXR{A,B,G}_{NR1H2,PPAR}dimers:0.401358774626;ZNF148:0.332975288289;HOX{A4,D4}:0.316569704038;CDX1,2,4:0.315626890807;OCT4_SOX2{dimer}:0.310215190949;BREu{core}:0.303985269424;RXR{A,B,G}:0.303874071122;ETS1,2:0.29150338242;RORA:0.287297167682;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:0.270597292557;PAX6:0.260128014702;NANOG:0.244571600127;ARID5B:0.202399052252;ONECUT1,2:0.198517546198;FOXP1:0.174585999338;ADNP_IRX_SIX_ZHX:0.172148699486;FOXP3:0.150667074329;NFE2L1:0.143962243538;NKX2-1,4:0.128046408505;NKX2-2,8:0.125715347686;RUNX1..3:0.100427557735;HNF4A_NR2F1,2:0.0865565007629;POU3F1..4:0.0501254727467;PRRX1,2:0.0466133709163;HOX{A5,B5}:0.0349958077156;MYBL2:0.024106044341;CUX2:0.0111296242352;SOX17:-0.0311753996708;REST:-0.0425492583324;FOXQ1:-0.0567925473994;TGIF1:-0.0708856527024;NFIX:-0.0917684382906;EVI1:-0.0977792399066;DMAP1_NCOR{1,2}_SMARC:-0.102823185021;SNAI1..3:-0.106931008561;VSX1,2:-0.11580876225;NKX3-2:-0.128021780499;TFAP4:-0.148378805433;FOXN1:-0.164879591143;TOPORS:-0.179215803201;NFE2:-0.198802893671;HAND1,2:-0.221842217083;KLF4:-0.237058683234;TFDP1:-0.237219630111;ATF5_CREB3:-0.238836239092;GCM1,2:-0.252846733585;POU5F1:-0.277941560282;SMAD1..7,9:-0.280123424688;RFX2..5_RFXANK_RFXAP:-0.286015575284;NKX3-1:-0.288884933468;FOXA2:-0.304760037846;HNF1A:-0.316010217169;IRF7:-0.323109704875;HSF1,2:-0.32586766368;NANOG{mouse}:-0.333309542582;ZNF238:-0.335744658213;TLX2:-0.33854432903;UFEwm:-0.360211729533;GFI1:-0.364075284719;LEF1_TCF7_TCF7L1,2:-0.379140365695;NFKB1_REL_RELA:-0.383430782754;T:-0.387683761594;ZFP161:-0.394831779334;SOX5:-0.396205189345;PAX1,9:-0.399772203804;PAX5:-0.424916890839;ZNF423:-0.426297753786;NHLH1,2:-0.46150508786;AHR_ARNT_ARNT2:-0.463980084778;MEF2{A,B,C,D}:-0.464675390212;NFIL3:-0.465414483465;XBP1:-0.483224398666;ZNF384:-0.49484235839;ESRRA:-0.502450200427;TEF:-0.507195234103;GATA4:-0.508873434079;ZEB1:-0.529627949908;MZF1:-0.559355655561;MYOD1:-0.559644492378;PAX2:-0.567211220259;ZBTB6:-0.568012671624;IRF1,2:-0.574602925589;RREB1:-0.608400537266;RXRA_VDR{dimer}:-0.626116606318;NKX2-3_NKX2-5:-0.628146367669;HIF1A:-0.630099066779;GTF2I:-0.632470535707;HMGA1,2:-0.633951635359;FOSL2:-0.638035988083;NFE2L2:-0.652176986912;BACH2:-0.660258490506;FOS_FOS{B,L1}_JUN{B,D}:-0.670666580378;FOXM1:-0.67923015191;ZIC1..3:-0.711900348126;DBP:-0.720528153714;GTF2A1,2:-0.72307104315;CEBPA,B_DDIT3:-0.726919744858;HLF:-0.740762934747;NKX6-1,2:-0.753781797922;SRF:-0.764433165776;TLX1..3_NFIC{dimer}:-0.790794690485;NFATC1..3:-0.79590433227;MYFfamily:-0.803166999845;IKZF1:-0.810230174623;PAX3,7:-0.812877805555;MAFB:-0.821900657599;RFX1:-0.823543444321;FOX{F1,F2,J1}:-0.826217249086;HBP1_HMGB_SSRP1_UBTF:-0.84472383105;ATF4:-0.851131804337;SOX2:-0.864139012652;SREBF1,2:-0.873298890853;TFAP2{A,C}:-0.878089783391;TEAD1:-0.883069829849;EBF1:-0.914103478832;CREB1:-0.916065395441;XCPE1{core}:-0.919144269566;GZF1:-0.951875184224;PRDM1:-0.953216865181;BPTF:-0.955525847636;HMX1:-0.990261742982;EP300:-0.996399947723;EGR1..3:-1.00850507953;NR1H4:-1.02900595616;STAT2,4,6:-1.04036089629;MAZ:-1.05679004205;HIC1:-1.07467898941;ATF6:-1.11136291329;PATZ1:-1.12729798577;TAL1_TCF{3,4,12}:-1.1444354146;ATF2:-1.21832685421;FOXO1,3,4:-1.23343102156;SP1:-1.25255145939;GLI1..3:-1.25866011827;JUN:-1.26373831575;FOXL1:-1.28333622949;TP53:-1.2920354539;MTF1:-1.30697054642;SPZ1:-1.36866370261;TBP:-1.37605583132;MTE{core}:-1.38246148588;CDC5L:-1.3936227006;MED-1{core}:-1.39478266226;GFI1B:-1.43466443389;FOX{D1,D2}:-1.44215619461;TFAP2B:-1.47231785815;PDX1:-1.50645517464;NR3C1:-1.52841585872;LMO2:-1.65513331396;TBX4,5:-1.71323403554;ALX4:-1.78891411277;ESR1:-1.79170649973;TFCP2:-2.49784825387
|xref=
|xref=
|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_human;search_select_hide=table111:FF:10837-111D9;search_select_hide=table117:FF:10837-111D9
}}
}}

Latest revision as of 15:08, 3 June 2020

Name:acute myeloid leukemia (FAB M6) cell line:F-36P
Species:Human (Homo sapiens)
Library ID:CNhs13505
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
age65
cell typeerythroblast
cell lineF-36P
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  SAMD00004812
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs13505 CAGE DRX007819 DRR008691
Accession ID Hg19

Library idBAMCTSS
CNhs13505 DRZ000116 DRZ001501
Accession ID Hg38

Library idBAMCTSS
CNhs13505 DRZ011466 DRZ012851
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-penis0.218
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: CNhs13505

Jaspar motifP-value
MA0002.20.0216
MA0003.10.796
MA0004.10.162
MA0006.10.425
MA0007.10.796
MA0009.10.394
MA0014.10.902
MA0017.10.135
MA0018.23.54138e-4
MA0019.10.329
MA0024.11.48673e-7
MA0025.10.0705
MA0027.10.528
MA0028.14.91433e-7
MA0029.10.165
MA0030.10.0126
MA0031.10.264
MA0035.27.27475e-24
MA0038.10.0126
MA0039.20.681
MA0040.10.0481
MA0041.10.152
MA0042.10.42
MA0043.11.16141e-4
MA0046.10.454
MA0047.20.0961
MA0048.10.317
MA0050.10.0929
MA0051.10.313
MA0052.13.67192e-4
MA0055.10.00828
MA0057.10.286
MA0058.10.111
MA0059.10.00107
MA0060.11.17438e-10
MA0061.10.883
MA0062.28.85822e-10
MA0065.20.0191
MA0066.10.503
MA0067.10.359
MA0068.10.147
MA0069.10.0552
MA0070.10.334
MA0071.10.124
MA0072.10.491
MA0073.10.931
MA0074.10.249
MA0076.11.63238e-7
MA0077.10.318
MA0078.10.36
MA0079.20.641
MA0080.21.01389e-7
MA0081.10.00387
MA0083.10.0106
MA0084.10.607
MA0087.10.0706
MA0088.11.01087e-4
MA0090.10.00412
MA0091.10.657
MA0092.10.447
MA0093.10.126
MA0099.21.34985e-6
MA0100.10.0257
MA0101.10.849
MA0102.20.0177
MA0103.10.905
MA0104.27.51539e-4
MA0105.10.0029
MA0106.10.805
MA0107.10.198
MA0108.21.06016e-13
MA0111.10.0381
MA0112.20.105
MA0113.10.318
MA0114.10.187
MA0115.10.451
MA0116.12.27922e-4
MA0117.10.688
MA0119.10.455
MA0122.10.68
MA0124.10.634
MA0125.10.182
MA0131.10.555
MA0135.10.512
MA0136.14.54081e-9
MA0137.20.197
MA0138.20.658
MA0139.10.309
MA0140.18.72511e-37
MA0141.10.0657
MA0142.10.975
MA0143.10.0463
MA0144.10.153
MA0145.10.331
MA0146.10.124
MA0147.16.09774e-5
MA0148.10.359
MA0149.10.0696
MA0150.10.302
MA0152.10.143
MA0153.10.0264
MA0154.10.0847
MA0155.10.968
MA0156.12.26997e-7
MA0157.10.503
MA0159.10.751
MA0160.10.0525
MA0162.10.483
MA0163.11.29207e-13
MA0164.10.832
MA0258.10.165
MA0259.10.0587



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: CNhs13505

Novel motifP-value
10.0192
100.022
1000.476
1010.235
1020.464
1030.138
1040.771
1050.727
1060.453
1070.397
1080.368
1090.0217
110.0555
1100.411
1110.0204
1120.401
1130.465
1140.0156
1150.225
1160.168
1170.0392
1180.185
1190.385
120.603
1200.911
1210.734
1220.71
1230.28
1240.0356
1250.259
1260.33
1270.136
1280.319
1290.613
130.0067
1300.542
1310.539
1320.367
1330.884
1340.314
1350.681
1360.377
1370.752
1380.721
1390.283
140.323
1400.792
1410.515
1420.664
1430.801
1440.335
1450.21
1460.986
1470.0699
1480.435
1490.2
150.228
1500.66
1510.818
1520.239
1530.184
1540.899
1550.221
1560.25
1570.441
1580.954
1590.37
160.946
1600.0702
1610.0141
1620.815
1630.109
1640.78
1650.8
1660.275
1670.158
1680.719
1690.435
170.641
180.839
190.778
20.439
200.716
210.105
220.736
230.0256
240.0678
250.289
260.0164
270.856
280.813
290.0311
30.147
300.106
310.658
320.0602
330.255
340.773
350.19
360.0557
370.291
380.353
390.219
40.152
400.279
410.858
420.184
430.533
440.937
450.918
460.19
470.0424
480.074
490.173
50.561
500.669
510.533
520.264
530.381
540.414
550.224
560.898
570.0895
580.315
590.691
60.395
600.957
610.472
620.213
630.82
640.231
650.994
660.0015
670.471
680.504
690.869
70.0578
700.92
710.0157
720.962
730.985
740.99
750.0198
760.221
770.47
780.0068
790.121
80.0571
800.0686
810.427
820.792
830.0346
840.886
850.837
860.969
870.192
880.185
890.725
90.999
900.0185
910.642
920.352
930.575
940.556
950.0179
960.996
970.38
980.228
990.825



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: CNhs13505


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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