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{{f5samples
{{f5samples
|F5samples=
|ancestors_in_anatomy_facet=UBERON:0000014,UBERON:0000061,UBERON:0000062,UBERON:0000064,UBERON:0000465,UBERON:0000467,UBERON:0000468,UBERON:0000475,UBERON:0000479,UBERON:0000480,UBERON:0001062,UBERON:0002097,UBERON:0002199,UBERON:0002384,UBERON:0002416,UBERON:0003102
|ancestors_in_anatomy_facet=UBERON:0000014,UBERON:0000061,UBERON:0000062,UBERON:0000064,UBERON:0000465,UBERON:0000467,UBERON:0000468,UBERON:0000475,UBERON:0000479,UBERON:0000480,UBERON:0001062,UBERON:0002097,UBERON:0002199,UBERON:0002384,UBERON:0002416,UBERON:0003102
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000004,CL:0000012,CL:0000034,CL:0000048,CL:0000055,CL:0000057,CL:0000063,CL:0000134,CL:0000144,CL:0000219,CL:0000255,CL:0000548,CL:0000723,CL:0002320,CL:0002371
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000004,CL:0000012,CL:0000034,CL:0000048,CL:0000055,CL:0000057,CL:0000063,CL:0000134,CL:0000144,CL:0000219,CL:0000255,CL:0000548,CL:0000723,CL:0002320,CL:0002371
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|creation_date=
|creation_date=
|def=
|def=
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|fonse_cell_line=FF:0100400,FF:0100453
|fonse_cell_line=FF:0100400,FF:0100453
|fonse_cell_line_closure=FF:0100400,FF:0100453
|fonse_cell_line_closure=FF:0100400,FF:0100453

Revision as of 16:55, 29 March 2012


Name:myxofibrosarcoma cell line:NMFH-1
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueunclassifiable
dev stageNA
sexmale
age89
cell typefibroblast
cell lineNMFH-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
Download raw sequence, BAM & CTSS
Hg19
BAMCTSS
[{{{hg19bam}}} download][{{{hg19ctss}}} donwload]
Hg38
BAMCTSS
[{{{hg38bam}}} download][{{{hg38ctss}}} donwload]


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-penis0.053
C106-Hep2-epitheloid-placenta-cervical-rectal-anaplastic-glassy0
C107-Neutrophils-CD14-Eosinophils-Monocytederived-Whole-Peripheral-blood0
C108-breast-hepatoblastoma-MCF7-parotid-salivary-submaxillary-prostate0
C109-Reticulocytes-non-acute-Hodgkin-Burkitt-retinoblastoma-lymphoma0.443
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
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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 no result for this sample


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: CNhs11821

Jaspar motifP-value
MA0002.20.0357
MA0003.10.058
MA0004.10.056
MA0006.10.433
MA0007.10.608
MA0009.10.386
MA0014.10.345
MA0017.10.0294
MA0018.20.441
MA0019.10.991
MA0024.13.8554e-5
MA0025.10.247
MA0027.10.35
MA0028.13.72638e-4
MA0029.10.84
MA0030.10.891
MA0031.10.667
MA0035.20.219
MA0038.10.00224
MA0039.20.224
MA0040.10.999
MA0041.10.204
MA0042.10.525
MA0043.10.27
MA0046.10.524
MA0047.20.638
MA0048.10.298
MA0050.10.394
MA0051.10.628
MA0052.10.354
MA0055.10.311
MA0057.10.678
MA0058.10.00166
MA0059.10.194
MA0060.11.77933e-8
MA0061.10.0031
MA0062.24.45845e-4
MA0065.21.90797e-4
MA0066.10.357
MA0067.10.033
MA0068.10.148
MA0069.10.682
MA0070.10.202
MA0071.10.45
MA0072.10.94
MA0073.10.253
MA0074.10.565
MA0076.14.85791e-5
MA0077.10.228
MA0078.10.111
MA0079.20.876
MA0080.21.61679e-9
MA0081.10.207
MA0083.10.673
MA0084.10.993
MA0087.10.325
MA0088.10.163
MA0090.10.737
MA0091.10.184
MA0092.10.562
MA0093.10.0214
MA0099.23.83199e-10
MA0100.10.0652
MA0101.10.642
MA0102.20.676
MA0103.16.23554e-6
MA0104.20.0796
MA0105.10.00257
MA0106.10.917
MA0107.10.138
MA0108.20.452
MA0111.10.387
MA0112.20.00183
MA0113.10.184
MA0114.10.123
MA0115.10.9
MA0116.10.0113
MA0117.10.961
MA0119.10.859
MA0122.10.325
MA0124.10.342
MA0125.10.971
MA0131.10.388
MA0135.10.47
MA0136.10.00254
MA0137.20.597
MA0138.20.034
MA0139.10.963
MA0140.10.449
MA0141.10.295
MA0142.10.0772
MA0143.10.132
MA0144.10.626
MA0145.10.233
MA0146.10.795
MA0147.10.332
MA0148.10.821
MA0149.10.382
MA0150.10.282
MA0152.10.18
MA0153.10.179
MA0154.15.96461e-4
MA0155.10.0997
MA0156.10.715
MA0157.10.5
MA0159.10.0294
MA0160.10.531
MA0162.10.41
MA0163.10.188
MA0164.10.75
MA0258.10.00352
MA0259.10.717



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: CNhs11821

Novel motifP-value
10.509
100.22
1000.98
1010.473
1020.892
1030.548
1040.728
1050.308
1060.0387
1070.337
1080.219
1090.695
110.281
1100.42
1110.0617
1120.215
1130.033
1140.0196
1150.86
1160.929
1170.967
1180.411
1190.0503
120.546
1200.717
1210.969
1220.334
1230.095
1240.194
1250.37
1260.623
1270.423
1280.427
1290.0921
130.329
1300.0254
1310.465
1320.465
1330.00672
1340.338
1350.12
1360.534
1370.625
1380.587
1391.05473e-4
140.412
1400.015
1410.345
1420.669
1430.0115
1440.96
1450.258
1460.57
1470.533
1480.808
1490.272
150.249
1500.416
1510.343
1520.084
1530.28
1540.356
1550.357
1560.632
1570.135
1580.284
1590.107
160.485
1600.153
1610.228
1620.71
1630.977
1640.62
1650.965
1660.739
1670.148
1680.33
1690.227
170.125
180.816
190.566
20.938
200.753
210.499
220.46
230.121
240.993
250.726
260.726
270.133
280.505
290.937
30.382
300.677
310.45
320.53
330.854
340.245
350.295
360.922
370.451
380.4
390.637
40.0761
400.219
410.0914
420.54
430.213
440.187
450.258
460.461
470.31
480.35
490.208
50.0684
500.993
510.416
520.141
530.56
540.519
550.731
560.524
570.49
580.227
590.0711
60.391
600.134
610.954
620.217
630.248
640.654
650.435
660.0911
670.613
680.117
690.332
70.262
700.114
710.441
720.708
730.269
740.13
750.859
760.936
770.123
780.0174
790.959
80.445
800.237
810.719
822.17527e-4
830.737
840.534
850.221
860.46
870.235
880.658
890.0562
90.72
900.239
910.328
920.0616
930.774
940.136
950.929
960.174
970.596
980.642
990.984



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: CNhs11821


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)
0000034 (stem cell)
0000048 (multi fate stem cell)
0000055 (non-terminally differentiated cell)
0000057 (fibroblast)
0000134 (mesenchymal cell)
0000219 (motile cell)
0000255 (eukaryotic cell)
0000548 (animal cell)
0000723 (somatic stem cell)
0002320 (connective tissue cell)
0002371 (somatic cell)

DOID: Disease
0050686 (organ system cancer)
0050687 (cell type cancer)
0060100 (musculoskeletal system cancer)
1115 (sarcoma)
14566 (disease of cellular proliferation)
162 (cancer)
1907 (malignant fibroxanthoma)
201 (connective tissue cancer)
4 (disease)
4231 (histiocytoma)

UBERON: Anatomy
0000014 (zone of skin)
0000061 (anatomical structure)
0000062 (organ)
0000064 (organ part)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000475 (organism subdivision)
0000479 (tissue)
0000480 (anatomical group)
0001062 (anatomical entity)
0002097 (skin of body)
0002199 (integument)
0002384 (connective tissue)
0002416 (integumental system)
0003102 (surface structure)

FF: FANTOM5
NA

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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