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{{f5samples
{{f5samples
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|accession_numbers=CAGE;DRX007858;DRR008730;DRZ000155;DRZ001540;DRZ011505;DRZ012890
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|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=
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|hg19fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.cell_line.hCAGE/chronic%2520myelogenous%2520leukemia%2520cell%2520line%253aK562.CNhs11250.10454-106G4.hg19.nobarcode.rdna.fa.gz
|hg38bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/hg38_v2/basic/human.cell_line.hCAGE/chronic%2520myelogenous%2520leukemia%2520cell%2520line%253aK562.CNhs11250.10454-106G4.hg38.nobarcode.bam
|hg38ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/hg38_v2/basic/human.cell_line.hCAGE/chronic%2520myelogenous%2520leukemia%2520cell%2520line%253aK562.CNhs11250.10454-106G4.hg38.nobarcode.ctss.bed.gz
|id=FF:10454-106G4
|id=FF:10454-106G4
|is_a=EFO:0002091;;FF:0000210;;FF:0100664
|is_a=EFO:0002091;;FF:0000210;;FF:0100664
Line 46: Line 52:
|library_id=CNhs11250
|library_id=CNhs11250
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|library_id_phase_based=2:CNhs11250
|microRNAs=
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|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/human#cage;sample;10454
|name=chronic myelogenous leukemia cell line:K562
|name=chronic myelogenous leukemia cell line:K562
|namespace=FANTOM5
|namespace=FANTOM5
|part_of=
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Line 90: Line 101:
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|top_motifs=GATA6:4.13578433939;POU2F1..3:2.86811599693;ZBTB16:1.98452330772;MYB:1.96490103867;PITX1..3:1.85149327002;POU3F1..4:1.80143736095;E2F1..5:1.70225764206;RXR{A,B,G}_{NR1H2,PPAR}dimers:1.517146375;ELK1,4_GABP{A,B1}:1.4244950614;OCT4_SOX2{dimer}:1.40458503734;YY1:1.35590992116;CDX1,2,4:1.31379977343;POU1F1:1.28342982732;STAT5{A,B}:1.19007983168;HOX{A6,A7,B6,B7}:1.16545871229;NKX6-1,2:1.15918934169;PBX1:1.10430768053;ZNF143:1.09091861449;RORA:1.0762526408;HOXA9_MEIS1:1.06731147063;NR5A1,2:1.03293388257;ADNP_IRX_SIX_ZHX:1.01177256905;TEF:0.946090988139;NR6A1:0.915258547821;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:0.868725906037;NKX2-1,4:0.865009263834;HOX{A5,B5}:0.863503369061;RBPJ:0.838812526801;IKZF2:0.826134377099;NRF1:0.810666730475;NR1H4:0.809240863266;NANOG:0.799174072414;FOXP1:0.79767165923;NFIX:0.795790217201;PAX8:0.785385346489;ALX1:0.737337885862;PRRX1,2:0.734347111946;NFY{A,B,C}:0.667482515434;EVI1:0.660366440898;HES1:0.640511739069;CRX:0.612074236299;CUX2:0.572648386608;FOXD3:0.517369254544;HOX{A4,D4}:0.492022318551;AHR_ARNT_ARNT2:0.469382436283;bHLH_family:0.453114131597;T:0.394372744681;ARID5B:0.380935809076;BREu{core}:0.374853177515;FOXQ1:0.323166654071;NFE2:0.314617402783;TOPORS:0.248231838334;FOXA2:0.242958524744;AIRE:0.240267174182;PAX4:0.232573608216;ZNF384:0.221817971827;FOX{I1,J2}:0.210261748504;VSX1,2:0.178646389194;PDX1:0.156053449384;ESRRA:0.152642996149;PAX3,7:0.120666756104;PAX6:0.11714561212;LEF1_TCF7_TCF7L1,2:0.0893170737461;NKX3-1:0.0803809909613;SOX{8,9,10}:0.068925259062;SNAI1..3:0.0634495154455;HBP1_HMGB_SSRP1_UBTF:0.0595928962816;NKX3-2:0.0580988459766;NANOG{mouse}:0.0415932287155;NKX2-3_NKX2-5:0.0145112482041;FOX{F1,F2,J1}:-0.00139392708075;AR:-0.0102363804609;SPZ1:-0.0303863455446;ZNF148:-0.0363034043188;ELF1,2,4:-0.061741096431;POU6F1:-0.062226132507;TFDP1:-0.0697347829317;NFE2L2:-0.085790621621;POU5F1:-0.095596915209;SMAD1..7,9:-0.139075476249;ZEB1:-0.151245550087;HNF4A_NR2F1,2:-0.169798011844;ONECUT1,2:-0.181402049279;GFI1:-0.185550599727;MEF2{A,B,C,D}:-0.199167019615;CDC5L:-0.207792202501;IKZF1:-0.245155345237;MYBL2:-0.248510394195;STAT1,3:-0.255833093892;HNF1A:-0.264442096108;EN1,2:-0.284620031765;TLX2:-0.304265359335;ATF5_CREB3:-0.316285163579;DBP:-0.325908863193;SPIB:-0.346209691425;RUNX1..3:-0.351118359261;LHX3,4:-0.362156845992;LMO2:-0.372861780598;HAND1,2:-0.37411538648;CREB1:-0.382532944102;BACH2:-0.38729220069;RXRA_VDR{dimer}:-0.394566906183;FOXP3:-0.405614393365;HLF:-0.409422658132;PAX2:-0.425312421348;SOX5:-0.428504636966;GATA4:-0.438900021105;TGIF1:-0.442100507975;RFX1:-0.44779843233;MYOD1:-0.448580683879;FOSL2:-0.457617663395;NFKB1_REL_RELA:-0.480100577424;NKX2-2,8:-0.480287340372;ATF4:-0.49153817824;UFEwm:-0.496103818043;FOS_FOS{B,L1}_JUN{B,D}:-0.507056277535;FOXN1:-0.512019248007;PPARG:-0.513018451753;CEBPA,B_DDIT3:-0.519635304704;STAT2,4,6:-0.528538981991;SPI1:-0.557461804359;SOX2:-0.577293056758;XBP1:-0.577664908273;RFX2..5_RFXANK_RFXAP:-0.580786453468;HSF1,2:-0.608495773365;MAFB:-0.616781607228;NFE2L1:-0.633144578948;REST:-0.641619097076;KLF4:-0.650062758326;SOX17:-0.651994131529;ATF2:-0.664171713367;NFIL3:-0.674165745799;PAX1,9:-0.676133091525;BPTF:-0.677120174913;ZNF238:-0.708421772207;ETS1,2:-0.717396043888;TBP:-0.739571920657;DMAP1_NCOR{1,2}_SMARC:-0.757774390413;FOX{D1,D2}:-0.774161378695;TP53:-0.784627587236;NHLH1,2:-0.801301368729;ZFP161:-0.820021282512;ZBTB6:-0.878703141028;NFATC1..3:-0.878895693034;TEAD1:-0.931962421633;RXR{A,B,G}:-0.966087101245;ZIC1..3:-0.985578435193;SRF:-1.01639515517;GTF2A1,2:-1.04856091136;IRF7:-1.0495050002;GTF2I:-1.05721828069;MED-1{core}:-1.06463649;ZNF423:-1.07733456439;RREB1:-1.15095810994;JUN:-1.16329834785;IRF1,2:-1.16377220814;FOXL1:-1.17157307274;MYFfamily:-1.1925347013;ALX4:-1.20423368473;TAL1_TCF{3,4,12}:-1.22283875272;SREBF1,2:-1.22849518445;GCM1,2:-1.2316077313;HMX1:-1.2496928181;FOXM1:-1.26581724126;EGR1..3:-1.26779556341;MZF1:-1.27325150132;GFI1B:-1.27353385051;EP300:-1.28646657906;HMGA1,2:-1.31394841899;HIC1:-1.33353413386;NR3C1:-1.34997598281;TFAP4:-1.35676257749;HIF1A:-1.36916744698;GZF1:-1.37448433429;SP1:-1.3992137535;ATF6:-1.4289685405;PRDM1:-1.4302425512;FOXO1,3,4:-1.44339597679;PATZ1:-1.46680389057;ESR1:-1.49243139976;TBX4,5:-1.51070638635;TLX1..3_NFIC{dimer}:-1.56362223761;GLI1..3:-1.61199138628;EBF1:-1.64597189243;MAZ:-1.64915378836;MTE{core}:-1.68071203442;XCPE1{core}:-1.7324836724;TFAP2{A,C}:-1.73671070969;MTF1:-1.74626530715;PAX5:-1.79010600677;TFAP2B:-1.91486743546;TFCP2:-2.39796210592
|xref=
|xref=
|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_human;search_select_hide=table111:FF:10454-106G4;search_select_hide=table117:FF:10454-106G4
}}
}}

Latest revision as of 14:03, 3 June 2020

Name:chronic myelogenous leukemia cell line:K562
Species:Human (Homo sapiens)
Library ID:CNhs11250
Sample type:cell lines
Genomic View: UCSC
RefEX:Specific genes
CAGEd-oPOSSUM:link
ZENBU report :link
Additional information
Sample information
strainNA
tissueblood
dev stageNA
sexfemale
age53
cell typegranulocyte
cell lineK562
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  SAMD00004875
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11250 CAGE DRX007858 DRR008730
Accession ID Hg19

Library idBAMCTSS
CNhs11250 DRZ000155 DRZ001540
Accession ID Hg38

Library idBAMCTSS
CNhs11250 DRZ011505 DRZ012890
Download raw sequence, BAM & CTSS
Hg19
FastaBAMCTSS
downloaddownloaddonwload
Hg38
BAMCTSS
downloaddonwload
HumanCAGEScan Download raw sequence, BAM & CTSS

Library id3prime-FASTQ5prime-FASTQBAMCTSS
NCig10060downloaddownloaddownloaddownload


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-penis0.0646
C106-Hep2-epitheloid-placenta-cervical-rectal-anaplastic-glassy0
C107-Neutrophils-CD14-Eosinophils-Monocytederived-Whole-Peripheral-blood0
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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-papillotubular0.714
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: CNhs11250

Jaspar motifP-value
MA0002.20.852
MA0003.10.476
MA0004.10.164
MA0006.10.254
MA0007.10.393
MA0009.10.327
MA0014.10.426
MA0017.10.395
MA0018.20.295
MA0019.10.352
MA0024.14.81614e-6
MA0025.10.117
MA0027.10.678
MA0028.11.55444e-4
MA0029.10.0292
MA0030.10.315
MA0031.10.628
MA0035.22.48374e-21
MA0038.10.639
MA0039.20.686
MA0040.10.147
MA0041.10.152
MA0042.10.324
MA0043.10.0934
MA0046.10.142
MA0047.20.863
MA0048.10.209
MA0050.11.85214e-6
MA0051.16.41325e-6
MA0052.10.011
MA0055.10.00407
MA0057.10.752
MA0058.10.0708
MA0059.15.89754e-4
MA0060.11.15019e-4
MA0061.10.642
MA0062.21.67594e-4
MA0065.20.0405
MA0066.10.367
MA0067.10.776
MA0068.10.0812
MA0069.10.508
MA0070.10.981
MA0071.10.149
MA0072.10.0393
MA0073.10.938
MA0074.10.254
MA0076.11.39276e-5
MA0077.10.283
MA0078.10.486
MA0079.20.128
MA0080.25.01724e-4
MA0081.10.863
MA0083.10.149
MA0084.10.37
MA0087.10.0656
MA0088.11.7917e-4
MA0090.10.0155
MA0091.10.812
MA0092.10.728
MA0093.10.141
MA0099.20.464
MA0100.10.0723
MA0101.10.244
MA0102.20.0129
MA0103.10.38
MA0104.21.52177e-4
MA0105.10.0266
MA0106.10.449
MA0107.10.0164
MA0108.26.57215e-5
MA0111.10.106
MA0112.20.0542
MA0113.10.72
MA0114.10.0382
MA0115.10.0676
MA0116.10.00124
MA0117.10.746
MA0119.10.65
MA0122.10.765
MA0124.10.907
MA0125.10.609
MA0131.10.663
MA0135.10.0026
MA0136.10.243
MA0137.20.893
MA0138.20.889
MA0139.10.138
MA0140.12.04296e-31
MA0141.10.0152
MA0142.10.00754
MA0143.10.541
MA0144.10.79
MA0145.10.694
MA0146.10.217
MA0147.11.12605e-5
MA0148.10.643
MA0149.10.00469
MA0150.10.178
MA0152.10.711
MA0153.10.0118
MA0154.10.258
MA0155.10.494
MA0156.10.71
MA0157.10.211
MA0159.10.251
MA0160.10.0715
MA0162.10.921
MA0163.16.73292e-10
MA0164.10.915
MA0258.10.137
MA0259.10.0375



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: CNhs11250

Novel motifP-value
10.00927
100.0163
1000.126
1010.273
1020.686
1030.575
1040.856
1050.958
1060.484
1070.411
1080.904
1090.0364
110.0975
1100.131
1110.135
1120.627
1130.546
1140.0173
1150.219
1160.242
1170.0195
1180.3
1190.28
120.888
1200.76
1210.658
1220.335
1230.0677
1240.171
1250.285
1260.327
1270.971
1280.424
1290.761
130.0077
1300.183
1310.485
1320.331
1330.152
1340.811
1350.281
1360.341
1370.683
1380.648
1390.152
140.76
1400.0338
1410.0157
1420.64
1430.901
1440.574
1450.475
1460.821
1470.36
1480.175
1490.244
150.235
1500.626
1510.782
1520.157
1530.577
1540.956
1550.331
1560.608
1570.393
1580.751
1590.123
160.648
1600.492
1610.174
1620.771
1630.374
1640.494
1650.662
1660.143
1670.0933
1680.619
1690.527
170.536
180.425
190.805
20.207
200.137
210.241
220.812
230.111
240.279
250.34
260.0326
270.481
280.526
290.0275
30.187
300.0726
310.74
320.197
330.0785
340.424
350.166
360.0165
370.218
380.389
390.642
40.166
400.194
410.778
420.201
430.214
440.543
450.601
460.13
470.0201
480.104
490.0176
50.264
500.953
510.861
520.266
530.483
540.91
550.455
560.868
570.0606
580.379
590.796
60.324
600.963
610.143
620.192
630.901
640.228
650.721
661.45779e-4
670.851
680.233
690.71
70.0749
700.51
710.0135
720.478
730.958
740.832
750.00456
760.317
770.681
780.0045
790.0811
80.128
800.147
810.705
820.4
830.653
840.721
850.641
860.682
870.373
880.842
890.816
90.616
900.0199
910.27
920.737
930.645
940.359
950.173
960.213
970.783
980.178
990.583



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: CNhs11250


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)
1036 (chronic 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)
0102580 (chronic myeloid leukemia cell line sample)
0101035 (hematopoietic cell line sample)
0100740 (myeloid leukemia cell line sample)
0100664 (K-562 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
CL:0000049 (common myeloid progenitor)
CL:0000134 (mesenchymal cell)

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