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{{f5samples
{{f5samples
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|DRA_sample_Accession=CAGE@SAMD00005476
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|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000055,CL:0000003,CL:0000548,CL:0002320,CL:0002371,CL:0000255,CL:0000062
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000055,CL:0000003,CL:0000548,CL:0002320,CL:0002371,CL:0000255,CL:0000062
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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/osteosarcoma%2520cell%2520line%253aHS-Os-1.CNhs11290.10558-107I9.hg19.nobarcode.rdna.fa.gz
|hg38bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/hg38_v2/basic/human.cell_line.hCAGE/osteosarcoma%2520cell%2520line%253aHS-Os-1.CNhs11290.10558-107I9.hg38.nobarcode.bam
|hg38ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/hg38_v2/basic/human.cell_line.hCAGE/osteosarcoma%2520cell%2520line%253aHS-Os-1.CNhs11290.10558-107I9.hg38.nobarcode.ctss.bed.gz
|id=FF:10558-107I9
|id=FF:10558-107I9
|is_a=EFO:0002091;;FF:0000210;;FF:0100407
|is_a=EFO:0002091;;FF:0000210;;FF:0100407
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|library_id=CNhs11290
|library_id=CNhs11290
|library_id_phase_based=2:CNhs11290
|library_id_phase_based=2:CNhs11290
|microRNAs=
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|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/human#cage;sample;10558
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/human#cage;sample;10558
|name=osteosarcoma cell line:HS-Os-1
|name=osteosarcoma cell line:HS-Os-1
|namespace=FANTOM5
|namespace=FANTOM5
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|part_of=
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Line 90: Line 101:
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|xref=
|xref=
|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_human;search_select_hide=table111:FF:10558-107I9;search_select_hide=table117:FF:10558-107I9
}}
}}

Latest revision as of 14:29, 3 June 2020

Name:osteosarcoma cell line:HS-Os-1
Species:Human (Homo sapiens)
Library ID:CNhs11290
Sample type:cell lines
Genomic View: UCSC
RefEX:Specific genes
CAGEd-oPOSSUM:link
ZENBU report :link
Additional information
Sample information
strainNA
tissuebone
dev stageNA
sexfemale
age11
cell typeosteoblast
cell lineHS-Os-1
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  SAMD00005476
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11290 CAGE DRX007978 DRR008850
Accession ID Hg19

Library idBAMCTSS
CNhs11290 DRZ000275 DRZ001660
Accession ID Hg38

Library idBAMCTSS
CNhs11290 DRZ011625 DRZ013010
Download raw sequence, BAM & CTSS
Hg19
FastaBAMCTSS
downloaddownloaddonwload
Hg38
BAMCTSS
downloaddonwload
HumanCAGEScan Download raw sequence, BAM & CTSS

Library id3prime-FASTQ5prime-FASTQBAMCTSS
NCig10064downloaddownloaddownloaddownload
NCig10128downloaddownloaddownloaddownload


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
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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: CNhs11290

Jaspar motifP-value
MA0002.20.0959
MA0003.10.125
MA0004.10.197
MA0006.10.285
MA0007.10.201
MA0009.10.56
MA0014.10.991
MA0017.10.00102
MA0018.20.701
MA0019.10.94
MA0024.10.0454
MA0025.10.447
MA0027.10.693
MA0028.10.403
MA0029.10.997
MA0030.10.828
MA0031.10.598
MA0035.20.0252
MA0038.10.0944
MA0039.20.936
MA0040.10.29
MA0041.10.191
MA0042.10.713
MA0043.10.513
MA0046.10.505
MA0047.20.132
MA0048.10.0183
MA0050.19.74736e-5
MA0051.10.0268
MA0052.12.68574e-4
MA0055.10.117
MA0057.10.476
MA0058.10.118
MA0059.10.377
MA0060.12.04507e-5
MA0061.10.00556
MA0062.20.844
MA0065.20.00114
MA0066.10.0584
MA0067.10.945
MA0068.10.00509
MA0069.10.754
MA0070.10.00253
MA0071.10.776
MA0072.10.536
MA0073.10.434
MA0074.10.139
MA0076.10.0815
MA0077.10.622
MA0078.10.537
MA0079.20.739
MA0080.24.43069e-11
MA0081.10.05
MA0083.10.292
MA0084.10.489
MA0087.10.22
MA0088.10.677
MA0090.10.823
MA0091.10.122
MA0092.10.154
MA0093.10.134
MA0099.21.23484e-11
MA0100.10.938
MA0101.10.0548
MA0102.20.117
MA0103.10.00456
MA0104.20.083
MA0105.15.49314e-5
MA0106.10.114
MA0107.10.0147
MA0108.20.00524
MA0111.10.899
MA0112.22.26472e-4
MA0113.10.959
MA0114.10.0255
MA0115.10.0411
MA0116.12.79376e-4
MA0117.10.788
MA0119.10.184
MA0122.10.118
MA0124.10.308
MA0125.10.87
MA0131.10.309
MA0135.10.164
MA0136.11.93411e-7
MA0137.20.268
MA0138.20.0502
MA0139.10.0689
MA0140.10.035
MA0141.10.0449
MA0142.10.0612
MA0143.10.52
MA0144.10.089
MA0145.10.0209
MA0146.10.208
MA0147.10.179
MA0148.10.0814
MA0149.10.182
MA0150.10.00132
MA0152.10.00225
MA0153.10.643
MA0154.10.00256
MA0155.10.455
MA0156.10.00381
MA0157.10.419
MA0159.10.00122
MA0160.10.0831
MA0162.10.0798
MA0163.11.7155e-5
MA0164.10.956
MA0258.10.00366
MA0259.10.413



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: CNhs11290

Novel motifP-value
10.169
100.0854
1000.851
1010.693
1020.789
1030.00889
1040.302
1050.0625
1060.00355
1070.0828
1080.73
1090.11
110.116
1100.178
1110.43
1120.0636
1130.58
1140.0234
1150.452
1160.521
1170.0646
1180.271
1190.192
120.881
1200.611
1210.813
1220.936
1230.32
1240.404
1250.104
1260.22
1270.19
1280.014
1290.261
130.343
1300.0633
1310.0644
1320.773
1330.693
1340.563
1350.0574
1360.896
1370.144
1380.222
1393.01561e-4
140.357
1400.537
1410.362
1420.834
1430.0755
1440.798
1450.0194
1460.703
1470.955
1480.0116
1490.0488
150.168
1500.436
1510.267
1520.265
1530.145
1540.722
1550.0834
1560.195
1570.75
1580.883
1590.135
160.123
1600.0551
1610.274
1620.811
1630.199
1640.726
1650.385
1660.633
1670.854
1680.545
1690.0188
170.3
180.122
190.248
20.181
200.515
210.824
220.296
230.0444
240.979
250.516
260.118
270.0655
280.976
290.42
30.0713
300.919
310.613
320.351
330.234
340.59
350.205
360.13
370.388
380.379
390.814
40.81
400.196
410.0801
420.215
430.135
440.0141
450.416
460.0498
470.246
480.375
490.232
50.209
500.673
510.534
520.229
530.899
540.348
550.0575
560.342
570.524
580.166
590.0238
60.997
600.086
610.381
620.0717
630.274
640.244
650.074
660.421
670.807
680.832
690.904
70.424
700.128
710.0643
720.159
730.206
740.255
750.126
760.662
770.232
780.562
790.778
80.18
800.851
810.577
820.109
830.242
840.978
850.0111
860.478
870.151
880.904
890.187
90.308
900.506
910.182
920.127
930.756
940.0315
950.307
960.213
970.827
980.522
990.291



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: CNhs11290


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)
0000055 (non-terminally differentiated cell)
0000003 (native cell)
0000548 (animal cell)
0002320 (connective tissue cell)
0002371 (somatic cell)
0000255 (eukaryotic cell)
0000062 (osteoblast)

UBERON: Anatomy
0000468 (multi-cellular organism)
0001474 (bone element)
0002384 (connective tissue)
0000479 (tissue)
0000062 (organ)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0004765 (skeletal element)
0002204 (musculoskeletal system)
0001434 (skeletal system)

FF: FANTOM5
0000102 (sample by type)
0000003 (cell line sample)
0000210 (human sample)
0000101 (sample by species)
0000001 (sample)
0100385 (bone cancer cell line sample)
0100407 (osteosarcoma 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:0000134 (mesenchymal cell)
CL:0000335 (mesenchyme condensation cell)

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