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{{f5samples
{{f5samples
|DRA_sample_Accession=CAGE@SAMD00005310
|DRA_sample_Accession=CAGE@SAMD00005310
|accession_numbers=CAGE;DRX007856;DRR008728;DRZ000153;DRZ001538
|accession_numbers=CAGE;DRX007856;DRR008728;DRZ000153;DRZ001538;DRZ011503;DRZ012888
|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/chronic%2520myelogenous%2520leukemia%2520cell%2520line%253aK562%2520ENCODE%252c%2520biol_rep2.CNhs12335.10825-111C6.hg19.nobarcode.bam
|hg19ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.cell_line.hCAGE/chronic%2520myelogenous%2520leukemia%2520cell%2520line%253aK562%2520ENCODE%252c%2520biol_rep2.CNhs12335.10825-111C6.hg19.ctss.bed.gz
|hg19fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.cell_line.hCAGE/chronic%2520myelogenous%2520leukemia%2520cell%2520line%253aK562%2520ENCODE%252c%2520biol_rep2.CNhs12335.10825-111C6.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%2520ENCODE%252c%2520biol_rep2.CNhs12335.10825-111C6.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%2520ENCODE%252c%2520biol_rep2.CNhs12335.10825-111C6.hg38.nobarcode.ctss.bed.gz
|id=FF:10825-111C6
|id=FF:10825-111C6
|is_a=EFO:0002091;;FF:0000210;;FF:0100664
|is_a=EFO:0002091;;FF:0000210;;FF:0100664
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|library_id=CNhs12335
|library_id=CNhs12335
|library_id_phase_based=2:CNhs12335
|library_id_phase_based=2:CNhs12335
|microRNAs=
|microRNAs_nn=
|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/human#cage;sample;10825
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/human#cage;sample;10825
|name=chronic myelogenous leukemia cell line:K562 ENCODE, biol_rep2
|name=chronic myelogenous leukemia cell line:K562 ENCODE, biol_rep2
|namespace=FANTOM5
|namespace=FANTOM5
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|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:
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|xref=
|xref=
|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_human;search_select_hide=table111:FF:10825-111C6;search_select_hide=table117:FF:10825-111C6
}}
}}

Latest revision as of 15:07, 3 June 2020

Name:chronic myelogenous leukemia cell line:K562 ENCODE, biol_rep2
Species:Human (Homo sapiens)
Library ID:CNhs12335
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
companyNA
collaborationCarrie Davis (Cold spring Harbor Laboratories)
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  SAMD00005310
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs12335 CAGE DRX007856 DRR008728
Accession ID Hg19

Library idBAMCTSS
CNhs12335 DRZ000153 DRZ001538
Accession ID Hg38

Library idBAMCTSS
CNhs12335 DRZ011503 DRZ012888
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-penis0.0259
C106-Hep2-epitheloid-placenta-cervical-rectal-anaplastic-glassy0
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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-papillotubular0.932
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: CNhs12335

Jaspar motifP-value
MA0002.20.602
MA0003.10.679
MA0004.10.245
MA0006.10.145
MA0007.10.395
MA0009.10.24
MA0014.10.144
MA0017.10.126
MA0018.20.402
MA0019.10.724
MA0024.16.94911e-7
MA0025.10.553
MA0027.10.516
MA0028.19.74778e-9
MA0029.10.00327
MA0030.10.63
MA0031.10.408
MA0035.21.92261e-24
MA0038.10.214
MA0039.20.00797
MA0040.10.0881
MA0041.10.833
MA0042.10.759
MA0043.10.722
MA0046.10.614
MA0047.20.76
MA0048.10.286
MA0050.12.39736e-6
MA0051.14.69248e-6
MA0052.10.025
MA0055.12.43949e-4
MA0057.10.618
MA0058.10.0432
MA0059.10.00225
MA0060.12.57883e-18
MA0061.10.568
MA0062.24.30295e-11
MA0065.20.0315
MA0066.10.728
MA0067.10.954
MA0068.10.02
MA0069.10.747
MA0070.10.124
MA0071.10.208
MA0072.10.168
MA0073.10.849
MA0074.10.156
MA0076.12.34022e-12
MA0077.10.269
MA0078.10.361
MA0079.20.491
MA0080.20.233
MA0081.10.0862
MA0083.10.116
MA0084.10.73
MA0087.10.116
MA0088.19.73526e-4
MA0090.10.00611
MA0091.10.536
MA0092.10.471
MA0093.10.127
MA0099.20.528
MA0100.10.00349
MA0101.10.474
MA0102.20.0032
MA0103.10.385
MA0104.21.23217e-4
MA0105.10.125
MA0106.10.796
MA0107.10.0261
MA0108.20.0201
MA0111.10.426
MA0112.20.204
MA0113.10.545
MA0114.10.00805
MA0115.10.0676
MA0116.10.0115
MA0117.10.523
MA0119.10.523
MA0122.10.819
MA0124.10.837
MA0125.10.854
MA0131.10.406
MA0135.10.225
MA0136.10.257
MA0137.20.177
MA0138.20.974
MA0139.10.0667
MA0140.11.47945e-41
MA0141.10.00202
MA0142.10.188
MA0143.10.142
MA0144.10.92
MA0145.10.815
MA0146.10.0706
MA0147.17.82976e-6
MA0148.10.319
MA0149.10.0138
MA0150.10.15
MA0152.10.378
MA0153.10.0951
MA0154.10.37
MA0155.10.514
MA0156.18.58306e-4
MA0157.10.476
MA0159.10.391
MA0160.10.0386
MA0162.10.411
MA0163.17.31235e-6
MA0164.10.598
MA0258.10.345
MA0259.10.0105



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: CNhs12335

Novel motifP-value
10.03
100.0954
1000.218
1010.658
1020.391
1030.731
1040.65
1050.832
1060.0276
1070.0116
1080.718
1090.0186
110.147
1100.157
1110.523
1120.801
1130.0952
1140.0218
1150.464
1160.7
1170.0102
1180.196
1190.588
120.827
1200.469
1210.961
1220.0427
1230.837
1240.453
1250.456
1260.135
1270.0942
1280.0578
1290.458
130.00155
1300.0495
1310.356
1320.159
1330.0625
1340.958
1350.296
1360.0309
1370.279
1380.558
1390.424
140.491
1400.026
1410.0313
1420.744
1430.576
1440.504
1450.932
1460.887
1470.737
1480.784
1490.215
150.463
1500.555
1510.383
1520.125
1530.707
1540.337
1550.194
1560.482
1570.352
1580.987
1590.159
160.883
1600.944
1610.0323
1620.708
1630.403
1640.459
1650.964
1660.0345
1670.327
1680.749
1690.711
170.799
180.992
190.903
20.22
200.0702
210.444
220.57
230.0224
240.16
250.324
260.177
270.321
280.549
290.028
30.455
300.168
310.562
320.0643
330.0478
340.392
350.356
360.0269
370.235
380.302
390.2
40.0663
400.137
410.962
420.354
430.622
440.516
450.512
460.508
470.0347
480.181
490.188
50.797
500.961
510.955
520.0257
530.888
540.719
550.0214
560.923
570.451
580.47
590.944
60.279
600.343
610.0604
620.367
630.428
640.422
650.579
668.17077e-6
670.616
680.17
690.787
70.0516
700.429
710.041
720.455
730.951
740.699
750.00623
760.692
770.453
780.00151
790.0803
80.559
800.199
810.346
820.984
830.131
840.505
850.198
860.856
870.0558
880.98
890.569
90.56
900.494
910.0613
920.524
930.987
940.754
950.0264
960.651
970.348
980.32
990.5



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: CNhs12335


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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