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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 16:49, 29 March 2012


Name:myxofibrosarcoma cell line:MFH-ino
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueANATOMICAL SYSTEM
dev stageNA
sexfemale
ageunknown
cell typefibroblast
cell lineMFH-ino
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-penis-0.0439
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-lymphoma0.46
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: CNhs11729

Jaspar motifP-value
MA0002.20.546
MA0003.10.0778
MA0004.10.505
MA0006.10.857
MA0007.10.914
MA0009.10.0355
MA0014.10.881
MA0017.10.305
MA0018.20.181
MA0019.10.132
MA0024.11.25114e-6
MA0025.10.16
MA0027.10.732
MA0028.10.763
MA0029.10.0948
MA0030.10.958
MA0031.10.597
MA0035.20.894
MA0038.10.00926
MA0039.20.911
MA0040.10.968
MA0041.10.31
MA0042.10.192
MA0043.10.0107
MA0046.10.986
MA0047.20.691
MA0048.10.0187
MA0050.10.755
MA0051.10.431
MA0052.10.0807
MA0055.10.227
MA0057.10.524
MA0058.10.0873
MA0059.10.506
MA0060.11.22086e-9
MA0061.18.85966e-4
MA0062.20.0408
MA0065.20.09
MA0066.10.856
MA0067.10.447
MA0068.10.0287
MA0069.10.647
MA0070.10.0495
MA0071.10.587
MA0072.10.656
MA0073.10.323
MA0074.10.262
MA0076.10.686
MA0077.10.266
MA0078.10.82
MA0079.20.622
MA0080.21.67718e-9
MA0081.10.00424
MA0083.10.109
MA0084.10.836
MA0087.10.712
MA0088.10.0156
MA0090.17.72903e-6
MA0091.10.667
MA0092.10.975
MA0093.10.499
MA0099.27.275e-8
MA0100.10.588
MA0101.10.143
MA0102.20.00251
MA0103.10.00293
MA0104.20.492
MA0105.15.99065e-4
MA0106.10.669
MA0107.10.0292
MA0108.20.11
MA0111.10.923
MA0112.20.0698
MA0113.10.979
MA0114.10.589
MA0115.10.727
MA0116.10.0474
MA0117.10.823
MA0119.10.446
MA0122.10.917
MA0124.10.632
MA0125.10.0989
MA0131.10.29
MA0135.10.694
MA0136.16.99984e-10
MA0137.20.135
MA0138.20.0414
MA0139.10.522
MA0140.10.275
MA0141.10.0414
MA0142.10.105
MA0143.10.904
MA0144.10.956
MA0145.10.265
MA0146.10.778
MA0147.10.811
MA0148.10.596
MA0149.10.509
MA0150.10.889
MA0152.10.479
MA0153.10.913
MA0154.10.00863
MA0155.10.105
MA0156.10.00194
MA0157.10.682
MA0159.10.00388
MA0160.10.79
MA0162.10.943
MA0163.10.0023
MA0164.10.629
MA0258.10.023
MA0259.10.491



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: CNhs11729

Novel motifP-value
10.883
100.296
1000.96
1010.362
1020.317
1030.458
1040.967
1050.51
1060.0567
1070.318
1080.371
1090.184
110.176
1100.386
1110.945
1120.218
1130.324
1140.395
1150.436
1160.871
1170.235
1180.574
1190.442
120.0439
1200.104
1210.939
1220.582
1230.243
1240.687
1250.244
1260.154
1270.425
1280.277
1290.71
130.212
1300.084
1310.523
1320.487
1330.841
1340.95
1350.0203
1360.837
1370.147
1380.797
1390.0132
140.323
1400.211
1410.344
1420.302
1430.463
1440.316
1450.804
1460.314
1470.4
1480.00808
1490.0252
150.983
1500.559
1510.353
1520.408
1530.159
1540.494
1550.0854
1560.687
1570.677
1580.0832
1590.618
160.653
1600.947
1610.206
1620.598
1630.556
1640.47
1650.845
1660.713
1670.884
1680.377
1690.318
170.579
180.742
190.246
20.207
200.824
210.637
220.741
230.281
240.135
250.975
260.891
270.356
280.972
290.33
30.0877
300.324
310.219
320.328
330.201
340.152
350.173
360.172
370.344
380.481
390.33
40.341
400.262
410.534
420.717
430.235
440.015
450.882
460.908
470.408
480.242
490.862
50.817
500.563
510.947
520.694
530.52
540.376
550.926
560.872
570.242
580.471
590.0811
60.405
600.16
610.523
620.866
630.129
640.556
650.18
660.00111
670.961
680.195
690.98
70.359
700.0203
710.283
720.238
730.394
740.475
750.17
760.377
770.0681
780.598
790.00389
80.944
800.961
810.924
820.0314
830.233
840.0046
850.00386
860.112
870.713
880.357
890.714
90.943
900.87
910.0266
920.236
930.726
940.875
950.333
960.459
970.126
980.046
990.425



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: CNhs11729


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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