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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 16:58, 29 March 2012


Name:rhabdomyosarcoma cell line:KYM-1
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueneck
dev stageNA
sexfemale
age9 months
cell typeunclassifiable
cell lineKYM-1
companyJAPAN HEALTH SCIENCES FOUNDATION - Health Science Research Resources Bank
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-endometrial0.841
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-penis0.316
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-lymphoma0.579
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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: CNhs11877

Jaspar motifP-value
MA0002.23.66828e-4
MA0003.10.134
MA0004.10.648
MA0006.10.169
MA0007.10.47
MA0009.10.417
MA0014.10.747
MA0017.10.44
MA0018.20.437
MA0019.10.00286
MA0024.12.93344e-5
MA0025.10.0761
MA0027.10.256
MA0028.10.00393
MA0029.10.968
MA0030.10.0929
MA0031.10.136
MA0035.20.23
MA0038.10.0914
MA0039.20.956
MA0040.10.0839
MA0041.10.258
MA0042.10.487
MA0043.10.29
MA0046.10.235
MA0047.20.275
MA0048.10.256
MA0050.10.164
MA0051.10.215
MA0052.18.80084e-4
MA0055.10.0105
MA0057.10.527
MA0058.10.745
MA0059.10.368
MA0060.11.84505e-9
MA0061.10.0579
MA0062.20.0368
MA0065.20.532
MA0066.10.589
MA0067.10.151
MA0068.10.839
MA0069.10.934
MA0070.10.223
MA0071.10.499
MA0072.10.525
MA0073.10.483
MA0074.10.573
MA0076.10.00427
MA0077.10.115
MA0078.10.132
MA0079.20.218
MA0080.23.6022e-11
MA0081.10.0615
MA0083.14.86893e-4
MA0084.10.106
MA0087.10.0964
MA0088.10.00724
MA0090.10.173
MA0091.10.0228
MA0092.10.305
MA0093.10.549
MA0099.28.20581e-12
MA0100.10.0624
MA0101.10.33
MA0102.22.83908e-4
MA0103.10.935
MA0104.20.0514
MA0105.10.584
MA0106.10.819
MA0107.10.0911
MA0108.22.86017e-4
MA0111.10.851
MA0112.20.0364
MA0113.10.0545
MA0114.10.148
MA0115.10.0819
MA0116.10.37
MA0117.10.715
MA0119.10.674
MA0122.10.824
MA0124.10.463
MA0125.10.616
MA0131.10.0557
MA0135.10.0328
MA0136.12.30547e-8
MA0137.20.183
MA0138.20.215
MA0139.10.408
MA0140.10.537
MA0141.10.751
MA0142.10.813
MA0143.10.0269
MA0144.10.0489
MA0145.10.0248
MA0146.10.782
MA0147.10.0127
MA0148.10.455
MA0149.10.45
MA0150.10.00116
MA0152.10.558
MA0153.10.00515
MA0154.10.278
MA0155.10.517
MA0156.11.92145e-4
MA0157.10.0143
MA0159.10.782
MA0160.10.52
MA0162.10.166
MA0163.10.26
MA0164.10.788
MA0258.10.279
MA0259.10.0199



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: CNhs11877

Novel motifP-value
10.665
100.467
1000.261
1010.994
1020.993
1030.168
1040.683
1050.577
1061.03178e-4
1070.0302
1080.262
1090.897
110.768
1100.326
1110.847
1120.164
1130.0774
1140.381
1150.596
1160.442
1170.0612
1180.465
1190.681
120.344
1200.815
1210.215
1220.286
1230.0301
1240.627
1250.488
1260.862
1270.216
1280.122
1290.117
130.398
1300.652
1310.14
1320.479
1330.886
1340.549
1350.0675
1360.731
1370.282
1380.377
1390.252
140.315
1400.336
1410.529
1420.388
1430.0172
1440.873
1450.874
1460.484
1470.377
1480.174
1490.0229
150.424
1500.968
1510.123
1520.00677
1530.822
1540.777
1550.995
1560.708
1570.651
1580.192
1590.223
160.844
1600.975
1610.115
1620.395
1630.919
1640.438
1650.0429
1660.261
1670.57
1680.101
1690.184
170.333
180.166
190.499
20.109
200.278
210.72
220.261
230.00113
240.294
250.711
260.451
270.102
280.831
290.596
30.437
300.0996
310.721
320.105
330.795
340.24
350.589
360.975
370.587
380.625
390.291
40.798
400.857
410.0354
420.137
430.189
440.972
450.103
460.838
470.681
480.938
490.817
50.259
500.53
510.59
520.0375
530.844
540.483
550.625
560.624
570.297
580.273
590.0645
60.397
600.011
610.818
620.205
630.269
640.698
650.379
660.0468
670.988
680.148
690.809
70.802
700.263
710.751
720.576
730.0862
740.47
750.179
760.696
770.344
780.442
790.069
80.807
800.0336
810.767
820.058
830.286
840.479
850.0879
860.996
870.89
880.821
890.445
90.0434
900.395
910.168
920.213
930.217
940.311
950.184
960.671
970.71
980.83
990.665



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: CNhs11877


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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