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{{f5samples
{{f5samples
|F5samples=
|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:0002204,UBERON:0002384,UBERON:0002418,UBERON:0002532,UBERON:0004120,UBERON:0004755,UBERON:0004765,UBERON:0005423
|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:0002204,UBERON:0002384,UBERON:0002418,UBERON:0002532,UBERON:0004120,UBERON:0004755,UBERON:0004765,UBERON:0005423
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000004,CL:0000012,CL:0000034,CL:0000048,CL:0000055,CL:0000058,CL:0000063,CL:0000134,CL:0000138,CL:0000144,CL:0000151,CL:0000153,CL:0000219,CL:0000255,CL:0000327,CL:0000447,CL:0000499,CL:0000548,CL:0000667,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:0000058,CL:0000063,CL:0000134,CL:0000138,CL:0000144,CL:0000151,CL:0000153,CL:0000219,CL:0000255,CL:0000327,CL:0000447,CL:0000499,CL:0000548,CL:0000667,CL:0000723,CL:0002320,CL:0002371
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|creation_date=
|creation_date=
|def=
|def=
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|fonse_cell_line=FF:0100385
|fonse_cell_line=FF:0100385
|fonse_cell_line_closure=FF:0100385
|fonse_cell_line_closure=FF:0100385

Revision as of 16:30, 29 March 2012


Name:extraskeletal myxoid chondrosarcoma cell line:H-EMC-SS
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 stage77 year old adult
sexfemale
age77
cell typechondroblast
cell lineH-EMC-SS
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-0.109
C106-Hep2-epitheloid-placenta-cervical-rectal-anaplastic-glassy0
C107-Neutrophils-CD14-Eosinophils-Monocytederived-Whole-Peripheral-blood0
C108-breast-hepatoblastoma-MCF7-parotid-salivary-submaxillary-prostate0
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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 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: CNhs10728

Jaspar motifP-value
MA0002.20.00377
MA0003.10.0637
MA0004.10.0501
MA0006.10.239
MA0007.10.192
MA0009.10.0275
MA0014.10.458
MA0017.10.00498
MA0018.20.0079
MA0019.10.241
MA0024.10.101
MA0025.10.096
MA0027.10.294
MA0028.10.00758
MA0029.10.464
MA0030.10.562
MA0031.10.482
MA0035.20.859
MA0038.10.324
MA0039.20.396
MA0040.10.191
MA0041.10.925
MA0042.10.772
MA0043.13.00391e-7
MA0046.10.143
MA0047.20.154
MA0048.10.0661
MA0050.12.41484e-8
MA0051.13.07598e-6
MA0052.10.341
MA0055.10.0152
MA0057.10.213
MA0058.10.026
MA0059.10.882
MA0060.10.73
MA0061.10.00314
MA0062.20.0619
MA0065.20.0113
MA0066.10.734
MA0067.10.763
MA0068.10.872
MA0069.10.636
MA0070.10.457
MA0071.10.576
MA0072.10.136
MA0073.10.306
MA0074.10.0915
MA0076.10.00329
MA0077.10.563
MA0078.10.497
MA0079.20.187
MA0080.21.3821e-12
MA0081.10.0576
MA0083.10.0121
MA0084.10.449
MA0087.10.472
MA0088.10.623
MA0090.10.64
MA0091.10.318
MA0092.10.0322
MA0093.10.0244
MA0099.21.75606e-7
MA0100.10.265
MA0101.10.108
MA0102.20.0119
MA0103.10.407
MA0104.20.145
MA0105.10.0178
MA0106.10.471
MA0107.10.0294
MA0108.23.54889e-6
MA0111.10.866
MA0112.22.40834e-5
MA0113.10.0719
MA0114.10.191
MA0115.10.067
MA0116.10.161
MA0117.10.789
MA0119.10.169
MA0122.10.957
MA0124.10.238
MA0125.10.831
MA0131.10.0435
MA0135.10.286
MA0136.12.14388e-8
MA0137.20.514
MA0138.20.744
MA0139.10.461
MA0140.10.806
MA0141.10.0532
MA0142.10.498
MA0143.10.864
MA0144.10.0161
MA0145.10.0895
MA0146.10.82
MA0147.10.211
MA0148.10.498
MA0149.10.627
MA0150.10.00495
MA0152.10.597
MA0153.10.505
MA0154.10.00623
MA0155.10.43
MA0156.12.03316e-5
MA0157.10.687
MA0159.10.101
MA0160.10.192
MA0162.10.0136
MA0163.10.0678
MA0164.10.858
MA0258.10.0313
MA0259.10.0963



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: CNhs10728

Novel motifP-value
10.623
100.296
1000.92
1010.593
1020.722
1030.0231
1040.741
1050.864
1060.00123
1070.00518
1080.19
1090.305
110.124
1100.869
1110.41
1120.0583
1130.263
1140.339
1150.522
1160.667
1170.708
1180.348
1190.341
120.323
1200.907
1210.181
1220.222
1230.104
1240.917
1250.341
1260.322
1270.0655
1280.056
1290.828
130.542
1300.373
1310.99
1320.851
1330.961
1340.871
1350.176
1360.785
1370.27
1380.909
1390.997
140.451
1402.76837e-6
1410.968
1420.897
1430.00623
1440.887
1450.196
1460.501
1470.802
1480.00224
1490.265
150.511
1500.354
1510.803
1520.14
1530.648
1540.693
1550.43
1560.534
1570.0555
1580.754
1590.878
160.3
1600.0415
1610.439
1620.484
1630.214
1640.94
1650.246
1660.373
1670.438
1680.0959
1690.0773
170.131
180.212
190.143
20.226
200.491
210.394
220.32
230.00861
240.912
250.331
260.793
270.13
280.796
290.396
30.44
300.414
310.989
320.00411
330.542
340.421
350.644
360.116
370.381
380.378
390.117
40.771
400.0364
410.0174
420.719
430.149
440.02
450.33
460.273
470.698
480.404
490.433
50.538
500.82
510.488
520.17
530.908
540.648
550.689
560.828
570.809
580.0792
590.0168
60.256
600.0333
610.95
620.0388
630.149
640.446
650.107
660.781
670.707
680.428
690.594
70.368
700.369
710.175
720.347
730.0912
740.466
750.822
760.483
770.0893
780.319
790.0173
80.319
800.967
810.309
820.0501
830.105
840.847
850.19
860.886
870.56
880.416
890.186
90.0398
900.938
910.0141
920.375
930.0806
940.301
950.367
960.259
970.981
980.612
990.584



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: CNhs10728


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)
0000058 (chondroblast)
0000134 (mesenchymal cell)
0000138 (chondrocyte)
0000151 (secretory cell)
0000153 (GAG secreting cell)
0000219 (motile cell)
0000255 (eukaryotic cell)
0000327 (extracellular matrix secreting cell)
0000447 (carbohydrate secreting cell)
0000499 (stromal cell)
0000548 (animal cell)
0000667 (collagen secreting 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)
201 (connective tissue cancer)
3371 (chondrosarcoma)
4 (disease)
4549 (extraosseous chondrosarcoma)
5861 (myxoid chondrosarcoma)
6496 (extraskeletal myxoid chondrosarcoma)

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)
0002204 (musculoskeletal system)
0002384 (connective tissue)
0002418 (cartilage tissue)
0002532 (epiblast (generic))
0004120 (mesoderm-derived structure)
0004755 (skeletal tissue)
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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