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FF:11455-119A6: Difference between revisions

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|creation_date=
|creation_date=
|def=
|def=
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|fonse_cell_line=
|fonse_cell_line=
|fonse_cell_line_closure=
|fonse_cell_line_closure=

Revision as of 17:09, 29 March 2012


Name:Skeletal Muscle Cells, donor5
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 stagefetus
sexunknown
agefetal
cell typeskeletal muscle cell
cell lineNA
companySciencell/3H
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot number482
catalog numberSC3505
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-0.0338
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-lymphoma0.41
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
C110-leukemia-chronic-Eosinophils-acute-Whole-CD34-Lymphatic0
C111-medulla-lung-trachea-testis-caudate-epididymis-throat0
C112-gastric-pancreas-temporal-duodenum-small-extraskeletal-adrenal0
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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: CNhs12056

Jaspar motifP-value
MA0002.20.00737
MA0003.10.652
MA0004.10.933
MA0006.10.81
MA0007.10.0441
MA0009.10.187
MA0014.10.661
MA0017.10.483
MA0018.20.0554
MA0019.10.596
MA0024.12.56475e-7
MA0025.10.00851
MA0027.10.644
MA0028.10.00146
MA0029.10.884
MA0030.10.00543
MA0031.18.93502e-4
MA0035.20.014
MA0038.10.0928
MA0039.20.454
MA0040.10.169
MA0041.10.194
MA0042.10.263
MA0043.10.066
MA0046.10.0141
MA0047.20.0121
MA0048.10.00644
MA0050.18.1045e-6
MA0051.14.8368e-5
MA0052.10.336
MA0055.10.00568
MA0057.10.845
MA0058.10.709
MA0059.10.16
MA0060.15.44547e-4
MA0061.16.10362e-5
MA0062.20.498
MA0065.20.993
MA0066.10.248
MA0067.10.0048
MA0068.10.225
MA0069.10.7
MA0070.10.547
MA0071.10.262
MA0072.10.31
MA0073.10.881
MA0074.10.485
MA0076.10.0337
MA0077.10.59
MA0078.10.619
MA0079.20.331
MA0080.22.24604e-14
MA0081.10.0231
MA0083.10.00119
MA0084.10.417
MA0087.10.97
MA0088.13.18453e-4
MA0090.10.106
MA0091.10.0266
MA0092.10.409
MA0093.10.93
MA0099.22.40367e-7
MA0100.10.202
MA0101.14.93343e-4
MA0102.20.024
MA0103.13.2561e-5
MA0104.20.0463
MA0105.10.105
MA0106.10.491
MA0107.15.336e-6
MA0108.20.00343
MA0111.10.878
MA0112.20.57
MA0113.10.267
MA0114.10.86
MA0115.10.673
MA0116.10.424
MA0117.10.162
MA0119.10.0593
MA0122.10.533
MA0124.10.734
MA0125.10.708
MA0131.10.392
MA0135.10.342
MA0136.13.65711e-13
MA0137.20.94
MA0138.20.866
MA0139.10.477
MA0140.10.126
MA0141.10.153
MA0142.10.0643
MA0143.10.909
MA0144.10.499
MA0145.10.74
MA0146.10.17
MA0147.10.0359
MA0148.10.0349
MA0149.10.962
MA0150.10.00194
MA0152.10.0294
MA0153.10.758
MA0154.10.239
MA0155.10.816
MA0156.11.40788e-10
MA0157.10.00958
MA0159.10.301
MA0160.10.175
MA0162.10.304
MA0163.10.00826
MA0164.10.881
MA0258.10.382
MA0259.10.0638



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: CNhs12056

Novel motifP-value
10.732
100.147
1000.446
1010.365
1020.492
1030.512
1040.808
1050.312
1060.00122
1070.815
1080.833
1090.686
110.4
1100.00462
1110.848
1120.118
1130.38
1140.132
1150.682
1160.143
1170.373
1180.952
1190.325
120.417
1200.0981
1210.807
1226.72538e-4
1230.101
1240.23
1250.653
1260.67
1270.111
1280.4
1290.183
130.185
1300.299
1310.872
1320.49
1330.807
1340.441
1350.159
1360.114
1370.0309
1380.0295
1390.0821
140.241
1400.436
1410.908
1420.964
1430.112
1440.717
1450.939
1460.771
1470.509
1480.322
1490.762
150.245
1500.974
1510.677
1520.388
1530.476
1540.604
1550.0483
1560.163
1570.324
1580.0102
1590.145
160.511
1600.301
1610.896
1620.0913
1630.347
1640.291
1650.288
1660.227
1670.191
1680.217
1690.456
170.735
180.554
190.21
20.823
200.963
210.0519
220.793
230.0312
240.32
250.632
260.116
270.563
280.102
290.225
30.924
300.949
310.505
320.00184
330.366
340.967
350.218
360.214
370.741
380.571
390.501
40.0612
400.193
410.00448
420.532
430.488
440.13
450.108
460.738
470.894
480.599
490.177
50.296
500.386
510.588
520.294
530.331
540.538
550.946
560.941
570.954
580.128
590.967
60.571
600.0856
610.414
620.135
630.815
640.95
650.54
660.572
670.494
680.203
690.576
70.538
700.024
710.489
720.196
730.622
740.744
750.446
760.935
770.982
780.683
790.0287
80.225
800.0341
810.49
820.07
830.889
840.885
850.00575
860.584
870.0979
880.573
890.679
90.864
900.425
910.442
920.687
930.731
940.718
950.224
960.338
970.885
980.422
998.93668e-4



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: CNhs12056


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