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|creation_date=2011-03-06T03:58:36Z
|creation_date=2011-03-06T03:58:36Z
|def="Skeletal muscle cells derived from myotubules." [GOC:tfm]
|def="Skeletal muscle cells derived from myotubules." [GOC:tfm]
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|fonse_cell_line=
|fonse_cell_line=
|fonse_cell_line_closure=
|fonse_cell_line_closure=

Revision as of 16:39, 29 March 2012


Name:Skeletal muscle cells differentiated into Myotubes - multinucleated, donor1
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 stage22 weeks old fetus
sexunknown
ageembryo 22week
cell typeskeletal muscle cell
cell lineNA
companyCell Applications
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot number1424
catalog numberCA150D-R10f
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-TRIzol-isopropanol-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-penis-0.053
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-lymphoma0.0155
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
C110-leukemia-chronic-Eosinophils-acute-Whole-CD34-Lymphatic0
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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: CNhs11084

Jaspar motifP-value
MA0002.20.124
MA0003.10.172
MA0004.10.191
MA0006.10.451
MA0007.10.0467
MA0009.10.0196
MA0014.10.633
MA0017.10.109
MA0018.20.0383
MA0019.10.0849
MA0024.10.651
MA0025.10.111
MA0027.10.378
MA0028.10.0315
MA0029.10.413
MA0030.10.137
MA0031.10.018
MA0035.20.0398
MA0038.10.288
MA0039.20.0762
MA0040.10.667
MA0041.10.534
MA0042.10.587
MA0043.10.0114
MA0046.10.288
MA0047.20.00638
MA0048.10.00815
MA0050.10.00113
MA0051.10.0184
MA0052.13.93849e-10
MA0055.15.03024e-4
MA0057.10.922
MA0058.10.0942
MA0059.10.576
MA0060.10.854
MA0061.14.76641e-4
MA0062.26.44404e-8
MA0065.20.317
MA0066.10.489
MA0067.10.012
MA0068.10.0579
MA0069.10.0587
MA0070.10.0906
MA0071.10.778
MA0072.10.634
MA0073.10.639
MA0074.10.447
MA0076.10.0372
MA0077.10.378
MA0078.10.701
MA0079.20.925
MA0080.27.13863e-13
MA0081.10.00357
MA0083.11.58161e-5
MA0084.10.116
MA0087.10.286
MA0088.10.833
MA0090.10.00193
MA0091.11.85543e-11
MA0092.10.706
MA0093.10.235
MA0099.21.88129e-4
MA0100.10.578
MA0101.17.2659e-5
MA0102.20.00971
MA0103.10.0118
MA0104.20.165
MA0105.10.00238
MA0106.10.408
MA0107.12.16562e-4
MA0108.22.46192e-13
MA0111.10.362
MA0112.20.0329
MA0113.10.224
MA0114.10.26
MA0115.10.302
MA0116.10.00789
MA0117.10.399
MA0119.10.475
MA0122.10.506
MA0124.10.697
MA0125.10.401
MA0131.10.237
MA0135.10.124
MA0136.11.2546e-15
MA0137.20.194
MA0138.20.872
MA0139.10.397
MA0140.10.0629
MA0141.10.626
MA0142.10.138
MA0143.10.618
MA0144.10.11
MA0145.10.0127
MA0146.10.312
MA0147.10.302
MA0148.10.00483
MA0149.10.0739
MA0150.11.58935e-4
MA0152.10.00585
MA0153.10.531
MA0154.10.389
MA0155.10.0281
MA0156.11.69171e-14
MA0157.10.0271
MA0159.10.672
MA0160.10.0353
MA0162.10.183
MA0163.10.825
MA0164.10.605
MA0258.10.834
MA0259.10.642



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: CNhs11084

Novel motifP-value
10.397
100.0288
1000.946
1010.651
1020.616
1030.195
1040.374
1050.819
1060.232
1070.252
1080.437
1090.32
110.794
1100.705
1110.669
1120.225
1136.19584e-5
1140.576
1150.982
1160.234
1170.154
1180.0795
1190.863
120.645
1200.358
1210.62
1220.0483
1231.31115e-4
1240.108
1250.321
1260.558
1270.422
1280.496
1290.691
130.93
1300.327
1310.0849
1320.501
1330.653
1340.0643
1350.963
1360.0589
1370.266
1380.217
1390.784
140.772
1400.161
1410.0951
1420.987
1430.194
1440.427
1450.57
1460.867
1470.0947
1480.304
1490.0417
150.11
1500.902
1510.837
1520.218
1530.365
1540.484
1550.00555
1560.321
1570.58
1580.0777
1590.876
160.316
1600.735
1610.779
1620.0635
1630.65
1640.159
1650.71
1660.426
1670.025
1680.693
1690.0248
170.971
180.932
190.0355
20.152
200.0831
210.341
220.204
230.892
240.571
250.532
260.297
270.567
280.27
290.157
30.355
300.248
310.888
321.08339e-9
330.259
340.58
350.478
360.151
370.932
380.447
390.227
40.72
400.0791
410.0729
420.401
430.558
440.818
450.577
460.991
470.546
480.746
490.393
50.832
500.439
510.829
520.881
530.656
540.801
550.857
560.876
570.605
580.168
590.597
60.833
600.513
610.47
620.555
630.9
640.508
650.818
660.585
670.823
680.799
690.904
70.742
700.351
710.118
720.197
730.594
740.417
750.251
760.0354
770.632
780.458
790.0113
80.937
800.647
810.379
820.875
830.272
840.592
850.947
860.697
870.222
880.713
890.194
90.198
900.323
910.895
920.891
930.659
940.522
950.0859
960.822
970.775
980.119
990.00294



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: CNhs11084


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

CL: Cell type
0000000 (cell), 0000000 (cell)
0000003 (native cell)
0000034 (stem cell)
0000048 (multi fate stem cell)
0000055 (non-terminally differentiated cell)
0000056 (myoblast)
0000183 (contractile cell)
0000187 (muscle cell)
0000188 (cell of skeletal muscle)
0000211 (electrically active cell)
0000222 (mesodermal cell)
0000255 (eukaryotic cell)
0000355 (multi-potent skeletal muscle stem cell)
0000393 (electrically responsive cell)
0000548 (animal cell)
0000680 (muscle precursor cell)
0000723 (somatic stem cell)
0002321 (embryonic cell)
0002371 (somatic cell)

UBERON: Anatomy
0000061 (anatomical structure)
0000119 (cell layer)
0000383 (musculature of body)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000475 (organism subdivision)
0000479 (tissue)
0000480 (anatomical group)
0000481 (multi-tissue structure)
0000483 (epithelium)
0000486 (multilaminar epithelium)
0000490 (unilaminar epithelium)
0000922 (embryo)
0000923 (germ layer)
0000926 (mesoderm)
0001015 (musculature)
0001062 (anatomical entity)
0001134 (skeletal muscle tissue)
0002036 (striated muscle tissue)
0002050 (embryonic structure)
0002204 (musculoskeletal system)
0002329 (somite)
0002385 (muscle tissue)
0002532 (epiblast (generic))
0003059 (presomitic mesoderm)
0003077 (paraxial mesoderm)
0003082 (myotome)
0003104 (mesenchyme)
0004120 (mesoderm-derived structure)
0004290 (dermomyotome)
0005291 (embryonic tissue)
0005423 (developing anatomical structure)
0009142 (entire embryonic mesenchyme)

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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