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FF:11398-118D3: 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 17:00, 29 March 2012


Name:Myoblast, donor3
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 stage59 years old adult
sexfemale
age59
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 numberSKM3
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-0.132
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-lymphoma0.333
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
C110-leukemia-chronic-Eosinophils-acute-Whole-CD34-Lymphatic0
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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: CNhs11908

Jaspar motifP-value
MA0002.20.752
MA0003.10.504
MA0004.10.543
MA0006.10.447
MA0007.10.584
MA0009.10.0773
MA0014.10.198
MA0017.10.029
MA0018.20.374
MA0019.10.195
MA0024.10.148
MA0025.10.0628
MA0027.10.656
MA0028.10.00737
MA0029.10.133
MA0030.10.168
MA0031.10.589
MA0035.20.00817
MA0038.10.0611
MA0039.20.246
MA0040.10.531
MA0041.10.535
MA0042.10.935
MA0043.10.0149
MA0046.10.786
MA0047.20.246
MA0048.10.685
MA0050.18.82146e-6
MA0051.10.0323
MA0052.10.508
MA0055.10.809
MA0057.10.829
MA0058.10.259
MA0059.10.546
MA0060.10.247
MA0061.10.00114
MA0062.20.108
MA0065.20.00238
MA0066.10.388
MA0067.10.381
MA0068.10.137
MA0069.10.365
MA0070.10.33
MA0071.10.234
MA0072.10.296
MA0073.10.809
MA0074.10.215
MA0076.10.00303
MA0077.10.91
MA0078.10.171
MA0079.20.182
MA0080.27.0012e-7
MA0081.10.619
MA0083.10.0308
MA0084.10.0942
MA0087.10.352
MA0088.10.966
MA0090.18.66853e-5
MA0091.10.263
MA0092.10.647
MA0093.10.413
MA0099.20.0621
MA0100.10.273
MA0101.10.0219
MA0102.20.168
MA0103.19.72742e-6
MA0104.20.341
MA0105.17.31771e-6
MA0106.10.675
MA0107.10.0114
MA0108.25.87133e-6
MA0111.10.241
MA0112.20.0265
MA0113.10.848
MA0114.10.109
MA0115.10.0507
MA0116.10.00117
MA0117.10.812
MA0119.10.442
MA0122.10.726
MA0124.10.664
MA0125.10.611
MA0131.10.992
MA0135.10.236
MA0136.17.51352e-4
MA0137.20.688
MA0138.20.235
MA0139.10.0204
MA0140.10.135
MA0141.10.197
MA0142.10.0134
MA0143.10.428
MA0144.10.369
MA0145.10.432
MA0146.10.499
MA0147.10.282
MA0148.10.674
MA0149.10.787
MA0150.10.615
MA0152.10.177
MA0153.10.976
MA0154.10.00232
MA0155.10.247
MA0156.10.34
MA0157.10.361
MA0159.10.0808
MA0160.10.133
MA0162.10.804
MA0163.12.46045e-6
MA0164.10.739
MA0258.10.00108
MA0259.10.652



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: CNhs11908

Novel motifP-value
10.255
100.453
1000.47
1010.204
1020.601
1030.814
1040.927
1050.148
1060.00327
1070.757
1080.306
1090.686
110.122
1100.412
1110.0629
1120.0319
1130.325
1140.265
1150.179
1160.544
1170.434
1180.388
1190.348
120.921
1200.477
1210.463
1220.0701
1231.18242e-4
1240.0146
1250.818
1260.859
1270.829
1280.111
1290.699
130.587
1300.0269
1310.45
1320.753
1330.196
1340.171
1350.423
1360.357
1370.802
1380.0667
1390.0123
140.437
1400.00903
1410.081
1420.967
1430.264
1440.904
1450.442
1460.714
1470.471
1480.146
1490.941
150.658
1500.453
1510.558
1520.671
1530.887
1540.723
1550.00563
1560.538
1570.077
1580.0209
1590.328
160.922
1600.0259
1610.012
1620.969
1630.312
1640.18
1650.132
1660.641
1670.312
1680.863
1690.39
170.433
180.208
190.793
20.436
200.719
210.991
220.853
230.344
240.999
250.701
260.195
270.465
280.595
290.489
30.275
300.927
310.846
320.812
330.692
340.251
350.0296
360.004
370.443
380.331
390.453
40.433
400.134
410.43
420.161
430.398
440.367
450.307
460.222
470.123
480.278
490.0632
50.747
500.639
510.424
520.652
530.173
540.559
550.524
560.741
570.486
580.172
590.0792
60.958
600.0768
610.755
620.0939
630.596
640.0527
650.103
660.568
670.776
680.352
690.817
70.501
700.0434
710.213
720.525
730.549
740.11
750.223
760.392
770.797
780.619
790.968
80.333
800.41
810.144
820.0878
830.46
840.748
850.149
860.999
870.101
880.188
890.526
90.759
900.581
910.0516
920.662
930.907
940.421
950.593
960.881
970.723
980.105
990.47



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: CNhs11908


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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