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FF:11241-116D8: 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 16:36, 29 March 2012


Name:Myoblast, 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 stagefetus
sexfemale
age58
cell typeskeletal muscle myoblast
cell lineNA
companySciencell/3H
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberSKM1
catalog numberSC3525
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-0.00358
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-lymphoma0.0883
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
C110-leukemia-chronic-Eosinophils-acute-Whole-CD34-Lymphatic0
C111-medulla-lung-trachea-testis-caudate-epididymis-throat0
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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: CNhs10870

Jaspar motifP-value
MA0002.20.478
MA0003.10.888
MA0004.10.704
MA0006.10.533
MA0007.10.0991
MA0009.10.0985
MA0014.10.464
MA0017.10.449
MA0018.22.02598e-4
MA0019.10.299
MA0024.10.0379
MA0025.19.4199e-4
MA0027.10.716
MA0028.10.00221
MA0029.10.356
MA0030.10.00793
MA0031.10.0115
MA0035.20.00272
MA0038.10.487
MA0039.20.847
MA0040.10.986
MA0041.10.992
MA0042.10.717
MA0043.12.36602e-5
MA0046.10.0479
MA0047.20.108
MA0048.10.692
MA0050.10.0105
MA0051.10.433
MA0052.10.0831
MA0055.10.89
MA0057.10.38
MA0058.10.801
MA0059.10.355
MA0060.11.02236e-5
MA0061.10.00756
MA0062.20.687
MA0065.20.126
MA0066.10.511
MA0067.10.0218
MA0068.10.841
MA0069.10.145
MA0070.10.708
MA0071.10.514
MA0072.10.437
MA0073.10.934
MA0074.10.775
MA0076.10.0141
MA0077.10.248
MA0078.10.352
MA0079.20.742
MA0080.21.83327e-7
MA0081.10.19
MA0083.10.00179
MA0084.10.119
MA0087.10.73
MA0088.10.062
MA0090.12.12849e-5
MA0091.10.244
MA0092.10.267
MA0093.10.877
MA0099.20.115
MA0100.10.909
MA0101.15.78582e-5
MA0102.20.0303
MA0103.17.98415e-5
MA0104.20.294
MA0105.10.126
MA0106.10.245
MA0107.11.37591e-4
MA0108.20.0167
MA0111.10.189
MA0112.20.0613
MA0113.10.196
MA0114.10.248
MA0115.10.182
MA0116.10.719
MA0117.10.626
MA0119.10.1
MA0122.10.567
MA0124.10.529
MA0125.10.696
MA0131.10.91
MA0135.10.324
MA0136.12.68323e-6
MA0137.20.976
MA0138.20.405
MA0139.10.481
MA0140.10.205
MA0141.10.88
MA0142.10.0435
MA0143.10.507
MA0144.10.587
MA0145.10.132
MA0146.10.59
MA0147.10.725
MA0148.10.34
MA0149.10.823
MA0150.10.736
MA0152.10.281
MA0153.10.356
MA0154.10.761
MA0155.10.497
MA0156.10.0357
MA0157.10.453
MA0159.10.753
MA0160.10.128
MA0162.10.0866
MA0163.10.332
MA0164.10.965
MA0258.10.47
MA0259.10.0993



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: CNhs10870

Novel motifP-value
10.509
100.108
1000.755
1010.237
1020.251
1030.106
1040.831
1050.00303
1060.0498
1070.815
1080.475
1090.109
110.613
1100.479
1110.644
1120.629
1130.678
1140.108
1150.354
1160.16
1170.374
1180.579
1190.814
120.776
1200.23
1210.867
1220.0529
1230.00111
1240.0982
1250.462
1260.867
1270.719
1280.0956
1290.946
130.882
1300.462
1310.427
1320.719
1330.0714
1340.0176
1350.367
1360.278
1370.377
1380.22
1390.987
140.0702
1400.0764
1410.316
1420.8
1430.556
1440.793
1450.702
1460.572
1470.0904
1480.754
1490.414
150.878
1500.894
1510.881
1520.0688
1530.844
1540.766
1558.49239e-4
1560.375
1570.0286
1580.0205
1590.27
160.123
1600.746
1610.616
1620.926
1630.391
1640.98
1650.287
1660.724
1670.86
1680.602
1690.159
170.859
180.317
190.16
20.473
200.941
210.0199
220.672
230.956
240.612
250.858
260.682
270.646
280.266
290.593
30.595
300.646
310.601
323.34379e-4
330.877
340.18
350.06
360.00902
370.102
380.587
390.159
40.174
400.0625
410.259
420.591
430.664
440.251
450.105
460.779
470.634
480.65
490.167
50.974
500.408
510.632
520.453
530.0323
540.609
550.344
560.965
570.923
580.147
590.83
60.308
600.233
610.778
620.502
630.447
640.08
650.42
660.557
670.398
680.851
690.497
70.676
700.899
710.359
720.645
730.0024
740.16
750.319
760.92
770.141
780.892
790.465
80.428
800.0952
810.519
820.663
830.632
840.966
850.989
860.919
870.0165
880.545
890.386
90.97
900.636
910.282
920.763
930.975
940.619
950.129
960.697
970.875
980.0905
990.00546



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: CNhs10870


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)
0000222 (mesodermal cell)
0000255 (eukaryotic cell)
0000355 (multi-potent skeletal muscle stem cell)
0000515 (skeletal muscle myoblast)
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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