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{{f5samples
{{f5samples
|DRA_sample_Accession=CAGE@SAMD00005508
|DRA_sample_Accession=CAGE@SAMD00005508
|accession_numbers=CAGE;DRX007857;DRR008729;DRZ000154;DRZ001539
|accession_numbers=CAGE;DRX007857;DRR008729;DRZ000154;DRZ001539;DRZ011504;DRZ012889
|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_rep3.CNhs12336.10826-111C7.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_rep3.CNhs12336.10826-111C7.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_rep3.CNhs12336.10826-111C7.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_rep3.CNhs12336.10826-111C7.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_rep3.CNhs12336.10826-111C7.hg38.nobarcode.ctss.bed.gz
|id=FF:10826-111C7
|id=FF:10826-111C7
|is_a=EFO:0002091;;FF:0000210;;FF:0100664
|is_a=EFO:0002091;;FF:0000210;;FF:0100664
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|library_id=CNhs12336
|library_id=CNhs12336
|library_id_phase_based=2:CNhs12336
|library_id_phase_based=2:CNhs12336
|microRNAs=
|microRNAs_nn=
|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/human#cage;sample;10826
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/human#cage;sample;10826
|name=chronic myelogenous leukemia cell line:K562 ENCODE, biol_rep3
|name=chronic myelogenous leukemia cell line:K562 ENCODE, biol_rep3
|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:10826-111C7;search_select_hide=table117:FF:10826-111C7
}}
}}

Latest revision as of 15:07, 3 June 2020

Name:chronic myelogenous leukemia cell line:K562 ENCODE, biol_rep3
Species:Human (Homo sapiens)
Library ID:CNhs12336
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  SAMD00005508
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs12336 CAGE DRX007857 DRR008729
Accession ID Hg19

Library idBAMCTSS
CNhs12336 DRZ000154 DRZ001539
Accession ID Hg38

Library idBAMCTSS
CNhs12336 DRZ011504 DRZ012889
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
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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-papillotubular0.975
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: CNhs12336

Jaspar motifP-value
MA0002.20.455
MA0003.10.671
MA0004.10.302
MA0006.10.164
MA0007.10.604
MA0009.10.44
MA0014.10.24
MA0017.10.192
MA0018.20.289
MA0019.10.653
MA0024.11.35942e-6
MA0025.10.952
MA0027.10.538
MA0028.15.5852e-10
MA0029.10.00271
MA0030.10.599
MA0031.10.313
MA0035.22.21009e-22
MA0038.10.303
MA0039.20.0143
MA0040.10.053
MA0041.10.619
MA0042.10.54
MA0043.10.915
MA0046.10.694
MA0047.20.944
MA0048.10.196
MA0050.18.99034e-7
MA0051.11.35591e-6
MA0052.10.0154
MA0055.13.93607e-4
MA0057.10.666
MA0058.10.0564
MA0059.10.00563
MA0060.17.74926e-19
MA0061.10.606
MA0062.23.21693e-13
MA0065.20.0343
MA0066.10.665
MA0067.10.965
MA0068.10.0185
MA0069.10.683
MA0070.10.167
MA0071.10.171
MA0072.10.241
MA0073.10.99
MA0074.10.121
MA0076.13.15045e-14
MA0077.10.333
MA0078.10.248
MA0079.20.54
MA0080.20.573
MA0081.10.0354
MA0083.10.314
MA0084.10.956
MA0087.10.143
MA0088.16.19267e-4
MA0090.10.00336
MA0091.10.869
MA0092.10.407
MA0093.10.164
MA0099.20.795
MA0100.10.00599
MA0101.10.546
MA0102.20.00788
MA0103.10.544
MA0104.22.99063e-4
MA0105.10.0775
MA0106.10.938
MA0107.10.0369
MA0108.20.00842
MA0111.10.423
MA0112.20.182
MA0113.10.455
MA0114.10.0141
MA0115.10.103
MA0116.10.00706
MA0117.10.485
MA0119.10.546
MA0122.10.962
MA0124.10.731
MA0125.10.767
MA0131.10.417
MA0135.10.199
MA0136.10.0928
MA0137.20.122
MA0138.20.955
MA0139.10.0685
MA0140.13.26892e-39
MA0141.10.00318
MA0142.10.194
MA0143.10.134
MA0144.10.781
MA0145.10.727
MA0146.10.0538
MA0147.12.76705e-5
MA0148.10.357
MA0149.10.0171
MA0150.10.114
MA0152.10.402
MA0153.10.135
MA0154.10.385
MA0155.10.414
MA0156.19.02357e-5
MA0157.10.279
MA0159.10.447
MA0160.10.0393
MA0162.10.246
MA0163.11.36231e-6
MA0164.10.638
MA0258.10.338
MA0259.10.0186



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: CNhs12336

Novel motifP-value
10.0307
100.0686
1000.331
1010.568
1020.35
1030.922
1040.643
1050.941
1060.046
1070.017
1080.962
1090.021
110.182
1100.187
1110.383
1120.869
1130.136
1140.0304
1150.572
1160.508
1170.00819
1180.225
1190.686
120.903
1200.531
1210.896
1220.0961
1230.915
1240.495
1250.608
1260.17
1270.119
1280.0732
1290.765
130.00115
1300.034
1310.476
1320.0935
1330.177
1340.893
1350.257
1360.0343
1370.274
1380.583
1390.391
140.538
1400.016
1410.0166
1420.572
1430.682
1440.64
1450.817
1460.881
1470.614
1480.713
1490.159
150.509
1500.432
1510.387
1520.128
1530.858
1540.339
1550.17
1560.61
1570.485
1580.979
1590.142
160.714
1600.979
1610.0366
1620.448
1630.457
1640.512
1650.813
1660.0413
1670.396
1680.572
1690.558
170.771
180.941
190.902
20.23
200.0576
210.305
220.631
230.0166
240.128
250.332
260.138
270.285
280.445
290.0202
30.399
300.162
310.481
320.0525
330.0404
340.4
350.314
360.0346
370.222
380.314
390.24
40.0623
400.217
410.899
420.264
430.735
440.639
450.518
460.435
470.0282
480.198
490.255
50.982
500.959
510.907
520.0299
530.893
540.623
550.0425
560.814
570.544
580.502
590.892
60.289
600.362
610.0773
620.417
630.412
640.555
650.434
664.49955e-6
670.612
680.0829
690.741
70.0577
700.291
710.0438
720.288
730.994
740.445
750.00584
760.738
770.365
785.05109e-4
790.145
80.495
800.191
810.239
820.895
830.0775
840.548
850.161
860.709
870.0664
880.919
890.645
90.524
900.463
910.0127
920.539
930.78
940.782
950.0284
960.697
970.343
980.468
990.462



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: CNhs12336


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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