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FF:11281-116I3: 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 16:39, 29 March 2012


Name:Skeletal Muscle Cells, 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 numberCA150-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-0.11
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-lymphoma-0.196
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: CNhs11083

Jaspar motifP-value
MA0002.20.0974
MA0003.10.156
MA0004.10.487
MA0006.10.441
MA0007.10.17
MA0009.10.0642
MA0014.10.537
MA0017.10.0958
MA0018.20.0553
MA0019.10.45
MA0024.10.255
MA0025.10.758
MA0027.10.217
MA0028.10.469
MA0029.10.467
MA0030.10.513
MA0031.10.0703
MA0035.20.167
MA0038.10.449
MA0039.20.127
MA0040.10.686
MA0041.10.777
MA0042.10.898
MA0043.10.208
MA0046.10.482
MA0047.20.0671
MA0048.10.932
MA0050.10.00358
MA0051.10.0665
MA0052.10.246
MA0055.10.134
MA0057.10.949
MA0058.10.653
MA0059.10.206
MA0060.17.20639e-4
MA0061.10.259
MA0062.20.00276
MA0065.20.234
MA0066.10.93
MA0067.10.00911
MA0068.10.0408
MA0069.10.276
MA0070.10.026
MA0071.10.965
MA0072.10.351
MA0073.10.861
MA0074.10.3
MA0076.10.598
MA0077.10.301
MA0078.10.765
MA0079.20.987
MA0080.21.64858e-11
MA0081.10.0167
MA0083.10.0277
MA0084.10.0657
MA0087.10.578
MA0088.10.0977
MA0090.10.0242
MA0091.11.88517e-4
MA0092.10.509
MA0093.10.511
MA0099.20.158
MA0100.10.659
MA0101.10.0161
MA0102.20.214
MA0103.10.0964
MA0104.20.651
MA0105.10.564
MA0106.10.153
MA0107.10.0589
MA0108.22.31564e-5
MA0111.10.205
MA0112.20.353
MA0113.10.576
MA0114.10.0342
MA0115.10.04
MA0116.10.281
MA0117.10.039
MA0119.10.677
MA0122.10.42
MA0124.10.377
MA0125.10.737
MA0131.10.394
MA0135.10.247
MA0136.11.14546e-9
MA0137.20.509
MA0138.20.932
MA0139.10.93
MA0140.10.00709
MA0141.10.863
MA0142.10.00376
MA0143.10.981
MA0144.10.191
MA0145.10.304
MA0146.10.191
MA0147.10.47
MA0148.10.0204
MA0149.10.123
MA0150.10.00259
MA0152.10.0185
MA0153.10.493
MA0154.10.465
MA0155.10.0339
MA0156.11.22632e-8
MA0157.10.0658
MA0159.10.866
MA0160.10.0105
MA0162.10.122
MA0163.10.245
MA0164.10.379
MA0258.10.476
MA0259.10.916



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: CNhs11083

Novel motifP-value
10.286
100.0288
1000.917
1010.389
1020.789
1030.693
1040.168
1050.762
1060.261
1070.154
1080.735
1090.641
110.996
1100.263
1110.192
1120.273
1130.669
1140.205
1150.806
1160.112
1170.867
1180.163
1190.842
120.497
1200.29
1210.737
1220.0247
1230.00166
1240.247
1250.869
1260.441
1270.432
1280.579
1290.482
130.96
1300.0847
1310.883
1320.268
1330.522
1340.067
1350.648
1360.138
1370.044
1380.153
1390.86
140.508
1400.03
1410.0276
1420.78
1430.136
1440.66
1450.49
1460.481
1470.638
1480.313
1490.0493
150.131
1500.893
1510.784
1520.0501
1530.372
1540.18
1550.0481
1560.217
1570.98
1580.0128
1590.616
160.596
1600.765
1610.672
1620.0315
1630.176
1640.935
1650.526
1660.998
1670.0654
1680.836
1690.117
170.675
180.39
190.0807
20.159
200.383
210.337
220.335
230.565
240.363
250.193
260.611
270.553
280.0766
290.939
30.579
300.216
310.774
320.00808
330.829
340.541
350.519
360.163
370.31
380.269
390.111
40.595
400.343
410.011
420.518
430.512
440.745
450.793
460.823
470.659
480.761
490.314
50.231
500.375
510.708
520.667
530.364
540.91
550.225
560.717
570.404
580.132
590.249
60.812
600.332
610.811
620.233
630.946
640.914
650.696
660.554
670.835
680.428
690.903
70.348
700.92
710.141
720.555
730.0963
740.55
750.968
760.339
770.373
780.0338
790.00471
80.994
800.667
810.351
820.892
830.143
840.702
850.696
860.789
870.744
880.586
890.301
90.387
900.185
910.666
920.845
930.57
940.432
950.948
960.884
970.718
980.0937
990.00177



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: CNhs11083


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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