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{{f5samples
{{f5samples
|F5samples=
|ancestors_in_anatomy_facet=
|ancestors_in_anatomy_facet=
|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:10737-110B8
|fonse_cell_line=FF:10737-110B8
|fonse_cell_line_closure=FF:10737-110B8
|fonse_cell_line_closure=FF:10737-110B8

Revision as of 16:57, 29 March 2012


Name:spindle cell sarcoma cell line:Hs 132.T
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueconnective tissue
dev stageNA
sexmale
age49
cell typeunclassifiable
cell lineHs 132.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-penis0.0915
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-lymphoma0.129
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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: CNhs11857

Jaspar motifP-value
MA0002.20.114
MA0003.10.71
MA0004.10.0289
MA0006.10.191
MA0007.10.723
MA0009.10.521
MA0014.10.197
MA0017.10.0907
MA0018.20.00254
MA0019.10.98
MA0024.10.732
MA0025.10.0179
MA0027.10.97
MA0028.10.00136
MA0029.10.0798
MA0030.10.193
MA0031.10.033
MA0035.20.0106
MA0038.10.0604
MA0039.20.0305
MA0040.10.57
MA0041.10.507
MA0042.10.712
MA0043.16.1117e-4
MA0046.10.599
MA0047.20.54
MA0048.10.0233
MA0050.10.00919
MA0051.10.0149
MA0052.10.215
MA0055.10.728
MA0057.10.512
MA0058.14.27792e-4
MA0059.10.169
MA0060.11.19335e-6
MA0061.10.00356
MA0062.29.64526e-10
MA0065.20.00585
MA0066.10.843
MA0067.10.00861
MA0068.10.406
MA0069.10.309
MA0070.10.245
MA0071.10.592
MA0072.10.269
MA0073.10.922
MA0074.10.76
MA0076.11.16468e-5
MA0077.10.613
MA0078.10.89
MA0079.20.76
MA0080.24.47245e-8
MA0081.10.00191
MA0083.10.0266
MA0084.10.604
MA0087.10.932
MA0088.10.0821
MA0090.15.75917e-5
MA0091.10.828
MA0092.10.0713
MA0093.10.0235
MA0099.20.0711
MA0100.10.489
MA0101.10.00116
MA0102.20.0142
MA0103.17.57997e-4
MA0104.20.00215
MA0105.14.18663e-4
MA0106.10.452
MA0107.10.00583
MA0108.20.00162
MA0111.10.0894
MA0112.20.477
MA0113.10.924
MA0114.10.00654
MA0115.10.369
MA0116.10.0219
MA0117.10.412
MA0119.10.566
MA0122.10.193
MA0124.10.128
MA0125.10.128
MA0131.10.525
MA0135.10.512
MA0136.13.47696e-13
MA0137.20.11
MA0138.21
MA0139.10.0818
MA0140.10.0969
MA0141.10.324
MA0142.10.133
MA0143.10.797
MA0144.10.752
MA0145.10.779
MA0146.10.12
MA0147.10.0125
MA0148.10.272
MA0149.10.842
MA0150.10.0201
MA0152.10.063
MA0153.10.503
MA0154.10.049
MA0155.10.723
MA0156.13.46451e-8
MA0157.10.105
MA0159.10.291
MA0160.10.0781
MA0162.10.703
MA0163.10.0604
MA0164.10.722
MA0258.10.152
MA0259.10.223



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: CNhs11857

Novel motifP-value
10.349
100.271
1000.166
1010.208
1020.299
1030.765
1040.889
1050.0786
1060.367
1070.0546
1080.29
1090.213
110.5
1100.262
1110.923
1120.84
1130.0173
1140.482
1150.0513
1160.0909
1170.115
1180.119
1190.922
120.334
1200.737
1210.662
1220.411
1230.0045
1240.0871
1250.499
1260.598
1270.746
1280.682
1290.415
130.163
1300.789
1310.93
1320.44
1330.734
1340.321
1350.83
1360.614
1370.347
1380.807
1390.456
140.221
1400.216
1410.112
1420.91
1430.973
1440.721
1450.78
1460.224
1470.00787
1480.298
1490.239
150.295
1500.101
1510.774
1520.0572
1530.561
1540.205
1550.0566
1560.691
1570.147
1580.0168
1590.498
160.152
1600.403
1610.338
1620.936
1630.309
1640.634
1650.165
1660.0769
1670.356
1680.527
1690.918
170.636
180.183
190.405
20.479
200.483
210.365
220.883
230.326
240.0918
250.241
260.843
270.478
280.289
290.307
30.424
300.569
310.868
329.69511e-10
330.163
340.747
350.0576
360.0043
370.584
380.491
390.431
40.648
400.0208
410.38
420.312
430.612
440.779
450.805
460.9
470.145
480.213
490.432
50.744
500.643
510.375
520.728
530.0951
540.994
550.499
560.91
570.865
580.162
590.688
60.739
600.907
610.137
620.372
630.836
640.233
650.848
660.885
670.422
680.324
690.859
70.13
700.839
710.0633
720.31
730.263
740.193
750.183
760.981
770.373
780.268
790.0137
80.833
800.336
810.822
820.25
830.131
840.456
850.746
860.955
870.629
880.929
890.159
90.981
900.749
910.613
920.368
930.974
940.722
950.545
960.92
970.366
980.214
990.0357



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: CNhs11857


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)
4235 (spindle cell sarcoma)

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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