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FF:11459-119B1: 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, donor6
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 number4820
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-0.0708
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-lymphoma0.513
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: CNhs12060

Jaspar motifP-value
MA0002.20.0466
MA0003.10.701
MA0004.10.64
MA0006.10.749
MA0007.10.211
MA0009.10.281
MA0014.10.816
MA0017.10.438
MA0018.20.33
MA0019.10.604
MA0024.11.4083e-9
MA0025.10.0208
MA0027.10.362
MA0028.12.10257e-4
MA0029.10.349
MA0030.10.00156
MA0031.12.46809e-4
MA0035.20.0412
MA0038.10.0188
MA0039.20.394
MA0040.10.0956
MA0041.10.188
MA0042.10.186
MA0043.10.0142
MA0046.10.119
MA0047.20.104
MA0048.10.049
MA0050.19.39505e-8
MA0051.12.21444e-6
MA0052.10.00117
MA0055.10.00119
MA0057.10.954
MA0058.10.962
MA0059.10.0236
MA0060.11.92145e-5
MA0061.10.135
MA0062.20.664
MA0065.20.329
MA0066.10.595
MA0067.10.109
MA0068.10.222
MA0069.10.371
MA0070.10.433
MA0071.10.423
MA0072.10.474
MA0073.10.492
MA0074.10.89
MA0076.10.0104
MA0077.10.891
MA0078.10.88
MA0079.20.177
MA0080.26.68197e-14
MA0081.10.0162
MA0083.17.01009e-5
MA0084.10.0716
MA0087.10.911
MA0088.11.39222e-5
MA0090.10.0026
MA0091.10.0491
MA0092.10.75
MA0093.10.663
MA0099.20.199
MA0100.10.122
MA0101.10.251
MA0102.26.79728e-4
MA0103.11.52867e-4
MA0104.20.00456
MA0105.10.583
MA0106.10.254
MA0107.10.0386
MA0108.21.83446e-5
MA0111.10.865
MA0112.20.42
MA0113.10.189
MA0114.10.516
MA0115.10.912
MA0116.10.356
MA0117.10.384
MA0119.10.159
MA0122.10.928
MA0124.10.844
MA0125.10.76
MA0131.10.766
MA0135.10.899
MA0136.11.64005e-10
MA0137.20.0367
MA0138.20.761
MA0139.10.1
MA0140.10.251
MA0141.10.103
MA0142.10.0795
MA0143.10.216
MA0144.10.058
MA0145.10.953
MA0146.10.656
MA0147.10.00307
MA0148.10.039
MA0149.10.651
MA0150.10.0371
MA0152.10.115
MA0153.10.436
MA0154.10.204
MA0155.10.926
MA0156.18.87055e-6
MA0157.16.88793e-4
MA0159.10.412
MA0160.10.167
MA0162.10.0642
MA0163.10.0666
MA0164.10.772
MA0258.10.671
MA0259.10.0294



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: CNhs12060

Novel motifP-value
10.528
100.0895
1000.097
1010.201
1020.624
1030.183
1040.584
1050.572
1060.00982
1070.345
1080.935
1090.457
110.419
1100.0293
1110.456
1120.0254
1130.42
1140.425
1150.956
1160.139
1170.262
1180.987
1190.941
120.671
1200.102
1210.599
1220.00924
1230.434
1240.187
1250.297
1260.665
1270.56
1280.0733
1290.444
130.0514
1300.0931
1310.613
1320.9
1330.79
1340.474
1350.0417
1360.853
1370.0905
1380.089
1390.00994
140.107
1400.152
1410.856
1420.406
1430.55
1440.762
1450.503
1460.909
1470.337
1480.669
1490.868
150.319
1500.34
1510.699
1520.857
1530.538
1540.702
1550.0143
1560.368
1570.185
1580.0251
1590.237
160.581
1600.215
1610.812
1620.572
1630.948
1640.419
1650.0325
1660.55
1670.841
1680.941
1690.744
170.94
180.875
190.235
20.903
200.823
210.0302
220.954
230.0771
240.699
250.541
260.0933
270.398
280.175
290.656
30.739
300.736
310.507
320.0132
330.278
340.589
350.261
360.774
370.506
380.741
390.3
40.0932
400.555
410.0185
420.974
430.515
440.356
450.0574
460.989
470.549
480.421
490.455
50.197
500.148
510.996
520.151
530.614
540.671
550.558
560.855
570.481
580.0544
590.785
60.672
600.0324
610.688
620.151
630.731
640.559
650.707
660.314
670.847
680.76
690.922
70.644
700.00336
710.379
720.0286
730.248
740.991
750.704
760.565
770.78
780.97
790.318
80.189
800.0444
810.309
820.0103
830.966
840.956
850.0497
860.306
870.15
880.718
890.383
90.926
900.176
910.452
920.491
930.75
940.647
950.0541
960.568
970.808
980.312
999.34638e-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: CNhs12060


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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