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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:10443-106F2
|fonse_cell_line=FF:10443-106F2
|fonse_cell_line_closure=FF:10443-106F2
|fonse_cell_line_closure=FF:10443-106F2

Revision as of 16:40, 29 March 2012


Name:epithelioid sarcoma cell line:HS-ES-1
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
sexunknown
ageNA
cell typeunclassifiable
cell lineHS-ES-1
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-penis0.0122
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-lymphoma0.345
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: CNhs11247

Jaspar motifP-value
MA0002.20.0105
MA0003.10.34
MA0004.10.925
MA0006.10.316
MA0007.10.965
MA0009.10.288
MA0014.10.106
MA0017.10.0555
MA0018.21.03352e-4
MA0019.10.57
MA0024.19.83176e-5
MA0025.10.247
MA0027.10.798
MA0028.10.00478
MA0029.10.606
MA0030.10.0121
MA0031.10.589
MA0035.20.268
MA0038.10.02
MA0039.20.00148
MA0040.10.651
MA0041.10.196
MA0042.10.19
MA0043.10.00177
MA0046.10.14
MA0047.20.0819
MA0048.10.0034
MA0050.10.778
MA0051.10.947
MA0052.10.741
MA0055.11.0022e-5
MA0057.10.919
MA0058.10.741
MA0059.10.91
MA0060.13.25124e-24
MA0061.10.161
MA0062.20.318
MA0065.20.802
MA0066.10.701
MA0067.10.528
MA0068.10.339
MA0069.10.785
MA0070.10.0538
MA0071.10.357
MA0072.10.836
MA0073.10.707
MA0074.10.581
MA0076.10.0841
MA0077.10.533
MA0078.10.144
MA0079.20.878
MA0080.21.5785e-10
MA0081.10.0572
MA0083.10.867
MA0084.10.651
MA0087.10.0778
MA0088.10.00426
MA0090.10.274
MA0091.10.356
MA0092.10.734
MA0093.10.879
MA0099.20.919
MA0100.10.0497
MA0101.10.569
MA0102.20.00174
MA0103.10.484
MA0104.20.937
MA0105.10.934
MA0106.10.00808
MA0107.10.144
MA0108.20.0385
MA0111.10.323
MA0112.20.353
MA0113.10.373
MA0114.10.504
MA0115.10.64
MA0116.10.923
MA0117.10.536
MA0119.10.918
MA0122.10.539
MA0124.10.85
MA0125.10.889
MA0131.10.1
MA0135.10.0262
MA0136.13.55967e-9
MA0137.20.182
MA0138.20.0654
MA0139.10.0397
MA0140.10.0291
MA0141.10.016
MA0142.10.322
MA0143.10.207
MA0144.10.612
MA0145.10.804
MA0146.10.141
MA0147.10.756
MA0148.10.056
MA0149.10.499
MA0150.10.171
MA0152.10.467
MA0153.10.331
MA0154.10.13
MA0155.10.541
MA0156.18.48815e-4
MA0157.10.696
MA0159.10.538
MA0160.10.00324
MA0162.10.751
MA0163.10.606
MA0164.10.886
MA0258.10.561
MA0259.10.529



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: CNhs11247

Novel motifP-value
10.192
100.0761
1000.116
1010.728
1020.655
1030.674
1040.757
1050.499
1060.00374
1070.0213
1080.413
1090.251
110.81
1100.037
1110.784
1120.00587
1130.103
1140.668
1150.593
1160.851
1170.0255
1180.543
1190.43
120.286
1200.471
1210.444
1220.795
1230.42
1240.04
1250.663
1260.663
1270.932
1280.0979
1290.891
130.0288
1300.0387
1310.956
1320.46
1330.0301
1340.577
1350.326
1360.146
1370.941
1380.03
1390.288
140.22
1400.125
1410.746
1420.21
1430.454
1440.366
1450.485
1460.183
1470.805
1480.855
1490.0988
150.909
1500.256
1510.413
1520.725
1530.514
1540.85
1550.799
1560.34
1570.391
1580.217
1590.324
160.447
1600.779
1610.422
1620.263
1630.706
1640.0236
1650.949
1660.332
1670.539
1680.217
1690.32
170.939
180.303
190.865
20.145
200.025
210.638
220.69
230.695
240.452
250.397
260.923
270.178
280.792
290.214
30.529
300.942
310.0825
320.319
330.168
340.166
350.0525
360.699
370.21
380.943
390.546
40.0108
400.939
410.177
420.506
430.951
440.75
450.792
460.824
470.9
480.719
490.233
50.708
500.756
510.721
520.105
530.74
540.501
550.256
560.392
570.925
580.1
590.149
60.841
600.0419
610.732
620.355
630.564
640.622
650.411
664.97679e-12
670.394
680.644
690.337
70.663
700.677
710.711
720.704
730.611
740.797
750.029
760.11
770.963
780.3
790.226
80.365
800.41
810.791
820.705
830.428
840.891
850.407
860.45
870.882
880.524
890.379
90.246
900.0832
910.242
920.424
930.898
940.549
950.00987
960.507
970.806
980.507
990.234



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: CNhs11247


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)
14566 (disease of cellular proliferation)
162 (cancer)
3350 (mesenchymal cell neoplasm)
4 (disease)
6193 (epithelioid 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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