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{{f5samples
{{f5samples
|F5samples=
|ancestors_in_anatomy_facet=UBERON:0000061,UBERON:0000465,UBERON:0000479,UBERON:0001062,UBERON:0002384
|ancestors_in_anatomy_facet=UBERON:0000061,UBERON:0000465,UBERON:0000479,UBERON:0001062,UBERON:0002384
|ancestors_in_cell_lineage_facet=
|ancestors_in_cell_lineage_facet=
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|creation_date=
|creation_date=
|def=
|def=
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|fonse_cell_line=FF:0100400
|fonse_cell_line=FF:0100400
|fonse_cell_line_closure=FF:0100400
|fonse_cell_line_closure=FF:0100400

Revision as of 16:56, 29 March 2012


Name:liposarcoma cell line:SW 872
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
age36
cell typeadipocyte
cell lineSW 872
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-penis0.0156
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-lymphoma0.431
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: CNhs11851

Jaspar motifP-value
MA0002.20.00859
MA0003.10.265
MA0004.10.964
MA0006.10.866
MA0007.10.983
MA0009.10.25
MA0014.10.284
MA0017.10.0605
MA0018.20.304
MA0019.10.313
MA0024.10.0011
MA0025.10.951
MA0027.10.311
MA0028.10.0817
MA0029.10.196
MA0030.10.15
MA0031.10.522
MA0035.20.686
MA0038.13.5011e-5
MA0039.20.0915
MA0040.10.921
MA0041.10.243
MA0042.10.0945
MA0043.10.748
MA0046.10.303
MA0047.20.884
MA0048.10.198
MA0050.11.64459e-7
MA0051.14.49751e-9
MA0052.10.476
MA0055.10.0593
MA0057.10.769
MA0058.10.853
MA0059.10.362
MA0060.19.58062e-14
MA0061.10.0317
MA0062.20.0331
MA0065.20.0803
MA0066.10.0398
MA0067.10.841
MA0068.10.994
MA0069.10.59
MA0070.10.0327
MA0071.10.549
MA0072.10.45
MA0073.10.954
MA0074.10.993
MA0076.10.0293
MA0077.10.174
MA0078.10.782
MA0079.20.118
MA0080.29.14368e-7
MA0081.10.294
MA0083.10.67
MA0084.10.933
MA0087.10.406
MA0088.10.365
MA0090.10.907
MA0091.10.0547
MA0092.10.165
MA0093.10.923
MA0099.20.00429
MA0100.10.421
MA0101.10.749
MA0102.20.345
MA0103.10.00957
MA0104.20.614
MA0105.16.14327e-8
MA0106.10.172
MA0107.10.363
MA0108.20.0321
MA0111.10.337
MA0112.21.33597e-5
MA0113.10.303
MA0114.10.161
MA0115.10.714
MA0116.11.1951e-5
MA0117.10.259
MA0119.10.468
MA0122.10.632
MA0124.10.587
MA0125.10.74
MA0131.10.28
MA0135.10.334
MA0136.16.16885e-4
MA0137.20.112
MA0138.20.108
MA0139.10.148
MA0140.10.683
MA0141.10.124
MA0142.10.393
MA0143.10.16
MA0144.10.694
MA0145.10.176
MA0146.10.677
MA0147.10.623
MA0148.10.798
MA0149.10.655
MA0150.10.0395
MA0152.10.493
MA0153.10.794
MA0154.17.99882e-4
MA0155.10.776
MA0156.10.901
MA0157.10.902
MA0159.10.109
MA0160.10.311
MA0162.10.303
MA0163.19.68942e-8
MA0164.10.552
MA0258.19.27692e-4
MA0259.10.586



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: CNhs11851

Novel motifP-value
10.0903
100.0697
1000.808
1010.2
1020.444
1030.229
1040.834
1050.212
1060.00792
1070.275
1080.467
1090.628
110.172
1100.329
1110.655
1120.102
1130.689
1140.14
1150.729
1160.586
1170.501
1180.32
1190.066
120.955
1200.972
1210.555
1220.789
1230.154
1240.0601
1250.595
1260.842
1270.763
1280.0266
1290.589
130.369
1300.19
1310.209
1320.9
1330.174
1340.194
1350.0954
1360.218
1370.656
1380.803
1390.00156
140.472
1400.0956
1410.149
1420.455
1430.175
1440.501
1450.284
1460.544
1470.734
1480.00804
1490.206
150.096
1500.848
1510.347
1520.98
1530.0961
1540.19
1550.201
1560.873
1570.965
1580.316
1590.924
160.196
1600.166
1610.275
1620.686
1630.739
1640.418
1650.157
1660.439
1670.0568
1680.238
1690.0439
170.231
180.0823
190.237
20.427
200.567
210.509
220.687
230.029
240.669
250.258
260.084
270.264
280.708
290.636
30.115
300.909
310.354
320.0124
330.502
340.924
350.108
360.0918
370.193
380.365
390.531
40.75
400.62
410.3
420.422
430.1
440.27
450.777
460.0413
470.253
480.407
490.109
50.0858
500.63
510.43
520.116
530.398
540.554
550.406
560.85
570.151
580.11
590.139
60.684
600.0275
610.572
620.0259
630.416
640.259
650.167
660.0752
670.872
680.866
690.9
70.189
700.00457
710.106
720.407
730.781
740.0118
750.119
760.816
770.329
780.173
790.0552
80.497
800.401
810.148
820.00577
830.627
840.692
850.0171
860.345
870.262
880.587
890.0575
90.41
900.0587
910.11
920.0437
930.194
940.00597
950.862
960.0419
970.527
980.23
990.57



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: CNhs11851


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

DOID: Disease
0050687 (cell type cancer)
1115 (sarcoma)
14566 (disease of cellular proliferation)
162 (cancer)
4 (disease)

UBERON: Anatomy
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000479 (tissue)
0001062 (anatomical entity)
0002384 (connective tissue)

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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