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{{f5samples
{{f5samples
|DRA_sample_Accession=CAGE@SAMD00004747
|DRA_sample_Accession=CAGE@SAMD00004747
|accession_numbers=CAGE;DRX007956;DRR008828;DRZ000253;DRZ001638
|accession_numbers=CAGE;DRX007956;DRR008828;DRZ000253;DRZ001638;DRZ011603;DRZ012988
|ancestors_in_anatomy_facet=
|ancestors_in_anatomy_facet=
|ancestors_in_cell_lineage_facet=
|ancestors_in_cell_lineage_facet=
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|library_id=CNhs11934
|library_id=CNhs11934
|library_id_phase_based=2:CNhs11934
|library_id_phase_based=2:CNhs11934
|microRNAs=
|microRNAs_nn=
|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/human#cage;sample;10772
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/human#cage;sample;10772
|name=myelodysplastic syndrome cell line:SKM-1
|name=myelodysplastic syndrome cell line:SKM-1
|namespace=FANTOM5
|namespace=FANTOM5
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|profile_rnaseq=
|profile_rnaseq=
|profile_srnaseq=,,,
|profile_srnaseq=,,,
|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 95: Line 99:
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|xref=
|xref=
|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_human;search_select_hide=table111:FF:10772-110F7;search_select_hide=table117:FF:10772-110F7
}}
}}

Latest revision as of 15:03, 3 June 2020

Name:myelodysplastic syndrome cell line:SKM-1
Species:Human (Homo sapiens)
Library ID:CNhs11934
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
age76
cell typemyeloid cell
cell lineSKM-1
companyJAPAN HEALTH SCIENCES FOUNDATION - Health Science Research Resources Bank
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
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  SAMD00004747
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11934 CAGE DRX007956 DRR008828
Accession ID Hg19

Library idBAMCTSS
CNhs11934 DRZ000253 DRZ001638
Accession ID Hg38

Library idBAMCTSS
CNhs11934 DRZ011603 DRZ012988
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: CNhs11934

Jaspar motifP-value
MA0002.20.142
MA0003.10.864
MA0004.10.00584
MA0006.10.027
MA0007.10.67
MA0009.10.557
MA0014.10.231
MA0017.10.389
MA0018.20.124
MA0019.10.171
MA0024.13.57696e-11
MA0025.10.00823
MA0027.10.897
MA0028.12.21684e-8
MA0029.10.566
MA0030.10.234
MA0031.10.106
MA0035.20.6
MA0038.10.318
MA0039.20.922
MA0040.10.59
MA0041.10.439
MA0042.10.7
MA0043.10.00664
MA0046.10.586
MA0047.20.984
MA0048.10.0865
MA0050.10.0243
MA0051.10.0636
MA0052.10.256
MA0055.10.00109
MA0057.10.964
MA0058.12.33201e-4
MA0059.15.95893e-7
MA0060.11.64813e-7
MA0061.10.31
MA0062.23.74097e-13
MA0065.20.305
MA0066.10.552
MA0067.10.631
MA0068.10.702
MA0069.10.318
MA0070.10.899
MA0071.10.368
MA0072.10.676
MA0073.10.752
MA0074.10.338
MA0076.11.8558e-7
MA0077.10.818
MA0078.10.249
MA0079.20.261
MA0080.28.77444e-12
MA0081.11.2234e-4
MA0083.11.43128e-5
MA0084.10.938
MA0087.10.213
MA0088.10.00619
MA0090.12.0052e-6
MA0091.10.257
MA0092.10.62
MA0093.10.00182
MA0099.27.54148e-9
MA0100.13.37203e-6
MA0101.10.0709
MA0102.20.00463
MA0103.10.657
MA0104.21.08117e-6
MA0105.10.985
MA0106.10.797
MA0107.10.00856
MA0108.25.01901e-6
MA0111.10.884
MA0112.20.279
MA0113.10.127
MA0114.10.211
MA0115.10.29
MA0116.10.0309
MA0117.10.919
MA0119.10.715
MA0122.10.944
MA0124.10.284
MA0125.10.656
MA0131.10.0019
MA0135.10.349
MA0136.13.0207e-22
MA0137.20.413
MA0138.20.74
MA0139.10.333
MA0140.10.875
MA0141.10.501
MA0142.10.968
MA0143.10.281
MA0144.10.656
MA0145.10.194
MA0146.10.658
MA0147.18.64875e-8
MA0148.10.292
MA0149.10.148
MA0150.10.0143
MA0152.10.462
MA0153.10.229
MA0154.10.909
MA0155.10.0506
MA0156.18.83176e-15
MA0157.10.152
MA0159.10.458
MA0160.10.56
MA0162.10.96
MA0163.11.45378e-5
MA0164.10.755
MA0258.10.536
MA0259.10.00277



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: CNhs11934

Novel motifP-value
10.231
100.0701
1000.0925
1010.43
1020.694
1030.695
1040.9
1050.903
1060.00122
1070.0457
1080.43
1090.628
110.257
1100.881
1110.356
1120.741
1130.215
1140.87
1150.745
1160.722
1170.168
1180.308
1190.186
120.386
1200.622
1210.559
1220.707
1230.191
1240.79
1250.509
1260.577
1270.15
1280.0635
1290.55
130.00224
1300.445
1310.0404
1320.704
1330.963
1340.435
1350.139
1360.117
1370.781
1380.504
1390.31
140.582
1400.305
1410.658
1420.251
1430.0767
1440.541
1450.496
1460.648
1470.0634
1480.251
1490.0303
150.89
1500.513
1510.182
1520.0109
1530.483
1540.734
1550.231
1560.788
1570.0872
1580.326
1590.818
160.433
1600.706
1610.819
1620.909
1630.52
1640.0574
1650.866
1660.774
1670.535
1680.0645
1690.281
170.336
180.212
190.567
20.0778
200.0575
210.814
220.248
230.00391
240.0782
250.474
260.167
270.713
280.848
290.325
30.447
300.0844
310.0954
320.133
330.351
340.712
350.732
360.0409
370.952
380.846
390.362
40.791
400.151
410.413
420.364
430.466
440.705
450.134
460.973
470.179
480.119
490.642
50.361
500.936
510.648
520.0267
530.846
540.424
550.197
560.573
570.657
580.48
590.711
60.508
600.0581
610.331
620.874
630.963
640.457
650.279
660.162
670.942
680.296
690.646
70.303
700.0381
710.207
720.59
730.198
740.173
750.115
760.276
770.216
780.188
790.0671
80.488
800.26
810.688
820.194
830.674
840.757
850.00156
860.686
870.187
880.407
890.216
90.999
900.278
910.0978
920.0358
930.904
940.915
950.407
960.469
970.383
980.878
990.678



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: CNhs11934


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

DOID: Disease
4 (disease)
1287 (cardiovascular system disease)
7 (disease of anatomical entity)
74 (hematopoietic system disease)
225 (syndrome)

FF: FANTOM5
0000102 (sample by type)
0000003 (cell line sample)
0000210 (human sample)
0000101 (sample by species)
0000001 (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
NA

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