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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 16:42, 29 March 2012


Name:rhabdomyosarcoma cell line:RMS-YM
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueskeletal muscle
dev stageNA
sexmale
age2
cell typeskeletal muscle cell
cell lineRMS-YM
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-penis0.0629
C106-Hep2-epitheloid-placenta-cervical-rectal-anaplastic-glassy0
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C89-small-retinoblastoma-medulloblastoma-iPS-acantholytic-eye-bronchogenic0
C9-skeletal-diaphragm-tongue-throat-penis-heart-left0
C90-neuroectodermal-peripheral-neuroepithelioma-neuroblastoma-carcinoid-parietal-putamen0
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: CNhs11269

Jaspar motifP-value
MA0002.27.98936e-4
MA0003.10.119
MA0004.10.363
MA0006.10.18
MA0007.10.263
MA0009.10.313
MA0014.10.266
MA0017.10.00402
MA0018.20.776
MA0019.10.252
MA0024.11.50709e-8
MA0025.10.649
MA0027.10.271
MA0028.10.107
MA0029.10.628
MA0030.10.0693
MA0031.10.421
MA0035.20.696
MA0038.12.46507e-5
MA0039.20.0186
MA0040.10.49
MA0041.10.179
MA0042.10.482
MA0043.10.996
MA0046.10.0882
MA0047.20.0639
MA0048.10.5
MA0050.15.32268e-4
MA0051.10.0398
MA0052.10.918
MA0055.10.846
MA0057.10.215
MA0058.10.481
MA0059.10.611
MA0060.12.80125e-13
MA0061.10.0113
MA0062.20.852
MA0065.20.0997
MA0066.10.0583
MA0067.10.15
MA0068.16.39223e-6
MA0069.10.808
MA0070.10.574
MA0071.10.562
MA0072.10.332
MA0073.10.552
MA0074.10.0945
MA0076.10.0621
MA0077.10.663
MA0078.10.989
MA0079.20.128
MA0080.22.70042e-12
MA0081.10.0585
MA0083.10.00222
MA0084.10.602
MA0087.10.937
MA0088.10.525
MA0090.10.399
MA0091.10.476
MA0092.10.154
MA0093.10.349
MA0099.24.12171e-15
MA0100.10.11
MA0101.10.119
MA0102.24.55939e-4
MA0103.10.0274
MA0104.20.0833
MA0105.10.0873
MA0106.10.274
MA0107.10.0249
MA0108.20.101
MA0111.10.826
MA0112.27.59939e-4
MA0113.10.245
MA0114.10.116
MA0115.10.365
MA0116.10.0435
MA0117.10.349
MA0119.10.801
MA0122.10.4
MA0124.10.433
MA0125.10.19
MA0131.10.197
MA0135.10.259
MA0136.13.48335e-9
MA0137.20.161
MA0138.20.126
MA0139.10.189
MA0140.10.861
MA0141.10.12
MA0142.10.945
MA0143.10.963
MA0144.10.0113
MA0145.10.103
MA0146.10.262
MA0147.10.099
MA0148.10.0813
MA0149.10.0973
MA0150.14.53606e-5
MA0152.10.336
MA0153.10.158
MA0154.10.0145
MA0155.10.444
MA0156.17.43962e-5
MA0157.10.984
MA0159.10.0425
MA0160.10.0474
MA0162.10.242
MA0163.10.262
MA0164.10.792
MA0258.10.0179
MA0259.10.145



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: CNhs11269

Novel motifP-value
10.369
100.44
1000.753
1010.969
1020.82
1030.0726
1040.844
1050.935
1060.00439
1070.692
1080.829
1090.0181
110.0628
1100.934
1110.557
1123.74919e-4
1130.00322
1140.0131
1150.276
1160.781
1170.829
1180.253
1190.219
120.297
1200.864
1210.569
1220.171
1230.611
1240.534
1250.317
1260.203
1270.32
1280.139
1290.845
130.776
1300.0248
1310.959
1320.945
1330.611
1340.562
1350.142
1360.262
1370.0571
1380.589
1390.0578
140.163
1400.408
1410.746
1420.233
1430.0456
1440.666
1450.923
1460.707
1470.437
1480.115
1490.0579
150.204
1500.513
1510.528
1520.00863
1530.98
1540.663
1550.806
1560.533
1570.492
1580.852
1590.233
160.105
1600.75
1610.825
1620.571
1630.564
1640.164
1650.323
1660.889
1670.475
1680.632
1690.052
170.503
180.623
190.363
20.186
200.981
210.909
220.167
230.0131
240.512
250.579
260.473
270.0377
280.949
290.455
30.418
300.364
310.55
320.0198
330.705
340.604
350.697
360.542
370.0745
380.275
390.726
40.381
400.14
410.337
420.984
430.249
440.0611
450.291
460.103
470.335
480.34
490.81
50.202
500.887
510.948
520.148
530.622
540.98
550.299
560.97
570.623
580.345
590.0199
60.555
600.0375
611
620.278
630.337
640.247
650.0424
660.0109
670.589
680.702
690.251
70.919
700.0304
710.148
720.038
730.00721
740.0994
750.477
760.998
770.0487
780.393
790.593
80.355
800.191
810.38
820.00253
830.357
840.491
850.00309
860.274
870.0149
880.595
890.0443
90.186
900.406
910.189
920.153
930.577
940.518
950.0218
960.203
970.917
980.303
990.779



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: CNhs11269


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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