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{{f5samples
{{f5samples
|F5samples=
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|ancestors_in_anatomy_facet=UBERON:0000061,UBERON:0000062,UBERON:0000465,UBERON:0000467,UBERON:0000468,UBERON:0000479,UBERON:0000480,UBERON:0000922,UBERON:0000923,UBERON:0000926,UBERON:0001062,UBERON:0001434,UBERON:0001474,UBERON:0002050,UBERON:0002193,UBERON:0002204,UBERON:0002371,UBERON:0002384,UBERON:0002390,UBERON:0002405,UBERON:0002532,UBERON:0004120,UBERON:0004765,UBERON:0005423
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|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000004,CL:0000012,CL:0000034,CL:0000035,CL:0000037,CL:0000040,CL:0000048,CL:0000049,CL:0000054,CL:0000055,CL:0000062,CL:0000063,CL:0000092,CL:0000134,CL:0000137,CL:0000144,CL:0000151,CL:0000219,CL:0000255,CL:0000335,CL:0000375,CL:0000548,CL:0000557,CL:0000559,CL:0000566,CL:0000576,CL:0000723,CL:0000738,CL:0000763,CL:0000766,CL:0000837,CL:0000839,CL:0000988,CL:0001012,CL:0002009,CL:0002031,CL:0002032,CL:0002087,CL:0002092,CL:0002194,CL:0002320,CL:0002371
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|creation_date=
|creation_date=
|def=
|def=
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|fonse_cell_line=FF:0100583
|fonse_cell_line=FF:0100583
|fonse_cell_line_closure=FF:0100583
|fonse_cell_line_closure=FF:0100583

Revision as of 16:55, 29 March 2012


Name:osteoclastoma cell line:Hs 706.T
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuebone
dev stageNA
sexfemale
age16
cell typeosteoclast
cell lineHs 706.T
companyATCC
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
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-0.0386
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-lymphoma0.152
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
C110-leukemia-chronic-Eosinophils-acute-Whole-CD34-Lymphatic0
C111-medulla-lung-trachea-testis-caudate-epididymis-throat0
C112-gastric-pancreas-temporal-duodenum-small-extraskeletal-adrenal0
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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: CNhs11835

Jaspar motifP-value
MA0002.20.672
MA0003.10.473
MA0004.10.143
MA0006.10.0302
MA0007.10.467
MA0009.10.193
MA0014.10.345
MA0017.10.17
MA0018.20.0242
MA0019.10.32
MA0024.10.00871
MA0025.10.353
MA0027.10.737
MA0028.10.0393
MA0029.10.0873
MA0030.10.691
MA0031.10.428
MA0035.20.0355
MA0038.10.123
MA0039.20.0267
MA0040.10.392
MA0041.10.437
MA0042.10.592
MA0043.15.19187e-4
MA0046.10.958
MA0047.20.469
MA0048.10.00373
MA0050.10.0622
MA0051.10.0802
MA0052.10.267
MA0055.10.597
MA0057.10.798
MA0058.10.0312
MA0059.10.806
MA0060.19.69806e-4
MA0061.10.143
MA0062.26.98477e-5
MA0065.20.101
MA0066.10.942
MA0067.10.145
MA0068.10.484
MA0069.10.326
MA0070.10.617
MA0071.10.937
MA0072.10.86
MA0073.10.39
MA0074.10.506
MA0076.10.013
MA0077.10.177
MA0078.10.73
MA0079.20.732
MA0080.21.4565e-8
MA0081.10.00463
MA0083.10.1
MA0084.10.112
MA0087.10.867
MA0088.10.237
MA0090.12.19296e-5
MA0091.10.687
MA0092.10.889
MA0093.10.196
MA0099.20.509
MA0100.10.0673
MA0101.10.00486
MA0102.22.20757e-4
MA0103.18.15945e-5
MA0104.20.0111
MA0105.10.0557
MA0106.10.0227
MA0107.10.0191
MA0108.20.00847
MA0111.10.327
MA0112.20.863
MA0113.10.557
MA0114.10.123
MA0115.10.367
MA0116.10.347
MA0117.10.186
MA0119.10.575
MA0122.10.678
MA0124.10.127
MA0125.10.0643
MA0131.10.252
MA0135.10.0428
MA0136.15.15864e-10
MA0137.20.637
MA0138.20.962
MA0139.10.291
MA0140.10.321
MA0141.10.525
MA0142.10.171
MA0143.10.376
MA0144.10.485
MA0145.10.772
MA0146.10.847
MA0147.10.0691
MA0148.10.807
MA0149.10.32
MA0150.10.633
MA0152.10.0401
MA0153.10.579
MA0154.10.422
MA0155.10.386
MA0156.13.67813e-4
MA0157.10.704
MA0159.10.778
MA0160.10.307
MA0162.10.827
MA0163.10.0863
MA0164.10.798
MA0258.10.87
MA0259.10.196



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: CNhs11835

Novel motifP-value
10.504
100.993
1000.781
1010.712
1020.246
1030.223
1040.285
1050.346
1060.65
1070.497
1080.505
1090.581
110.73
1100.632
1110.468
1120.678
1130.0709
1140.693
1150.667
1160.391
1170.885
1180.374
1190.475
120.369
1200.842
1210.696
1220.409
1230.0851
1240.635
1250.618
1260.724
1270.49
1280.565
1290.354
130.025
1300.56
1310.922
1320.761
1330.799
1340.0615
1350.445
1360.473
1370.405
1380.637
1390.615
140.241
1400.419
1410.485
1420.896
1430.209
1440.449
1450.674
1460.529
1470.0911
1480.355
1490.985
150.397
1500.748
1510.818
1520.0668
1530.987
1540.325
1550.104
1560.474
1570.37
1580.138
1590.182
160.0411
1600.26
1610.95
1620.306
1630.434
1640.731
1650.802
1660.179
1670.822
1680.188
1690.763
170.544
180.0166
190.125
20.531
200.866
210.247
220.407
230.0808
240.342
250.366
260.64
270.586
280.911
290.909
30.783
300.757
310.65
325.25649e-19
330.855
340.988
350.94
360.347
370.406
380.264
390.595
40.66
400.262
410.47
420.518
430.5
440.827
450.751
460.339
470.419
480.968
490.884
50.123
500.615
510.397
520.948
530.104
540.56
550.175
560.924
570.481
580.145
590.0277
60.565
600.994
610.203
620.987
630.552
640.889
650.769
660.565
670.0275
680.383
690.492
70.282
700.156
710.606
720.197
730.0468
740.0144
750.798
760.194
770.111
780.239
790.0514
80.207
800.764
810.693
820.684
830.409
840.447
850.375
860.726
870.396
880.822
890.681
90.88
900.24
910.494
920.746
930.445
940.409
950.599
960.839
970.247
980.321
990.521



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: CNhs11835


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)
0000035 (single fate stem cell)
0000037 (hematopoietic stem cell)
0000040 (monoblast)
0000048 (multi fate stem cell)
0000049 (common myeloid progenitor)
0000054 (bone matrix secreting cell)
0000055 (non-terminally differentiated cell)
0000062 (osteoblast)
0000092 (osteoclast)
0000134 (mesenchymal cell)
0000137 (osteocyte)
0000151 (secretory cell)
0000219 (motile cell)
0000255 (eukaryotic cell)
0000335 (mesenchyme condensation cell)
0000375 (osteoprogenitor cell)
0000548 (animal cell)
0000557 (granulocyte monocyte progenitor cell)
0000559 (promonocyte)
0000566 (angioblastic mesenchymal cell)
0000576 (monocyte)
0000723 (somatic stem cell)
0000738 (leukocyte)
0000763 (myeloid cell)
0000766 (myeloid leukocyte)
0000837 (hematopoietic multipotent progenitor cell)
0000839 (myeloid lineage restricted progenitor cell)
0000988 (hematopoietic cell)
0001012 (CD7-negative lymphoid progenitor OR granulocyte monocyte progenitor)
0002009 (macrophage dendritic cell progenitor)
0002031 (hematopoietic lineage restricted progenitor cell)
0002032 (hematopoietic oligopotent progenitor cell)
0002087 (nongranular leukocyte)
0002092 (bone marrow cell)
0002194 (monopoietic cell)
0002320 (connective tissue cell)
0002371 (somatic cell)

DOID: Disease
0050686 (organ system cancer)
0060083 (immune system cancer)
0060100 (musculoskeletal system cancer)
14566 (disease of cellular proliferation)
162 (cancer)
200 (giant cell tumor)
201 (connective tissue cancer)
2531 (hematologic cancer)
4 (disease)
4305 (bone giant cell tumor)
7 (disease of anatomical entity)

UBERON: Anatomy
0000061 (anatomical structure)
0000062 (organ)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000479 (tissue)
0000480 (anatomical group)
0000922 (embryo)
0000923 (germ layer)
0000926 (mesoderm)
0001062 (anatomical entity)
0001434 (skeletal system)
0001474 (bone element)
0002050 (embryonic structure)
0002193 (hemolymphoid system)
0002204 (musculoskeletal system)
0002371 (bone marrow)
0002384 (connective tissue)
0002390 (hematopoietic system)
0002405 (immune system)
0002532 (epiblast (generic))
0004120 (mesoderm-derived structure)
0004765 (skeletal element)
0005423 (developing anatomical 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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