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FF:11451-119A2: 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, donor4
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 number487
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-0.0729
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-lymphoma0.419
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: CNhs12053

Jaspar motifP-value
MA0002.20.018
MA0003.10.846
MA0004.10.793
MA0006.10.956
MA0007.10.0294
MA0009.10.125
MA0014.10.695
MA0017.10.699
MA0018.20.0155
MA0019.10.599
MA0024.11.22997e-7
MA0025.10.00563
MA0027.10.816
MA0028.11.01647e-5
MA0029.10.831
MA0030.11.08862e-4
MA0031.16.52007e-5
MA0035.20.0293
MA0038.10.1
MA0039.20.553
MA0040.10.122
MA0041.10.134
MA0042.10.138
MA0043.10.0253
MA0046.10.0271
MA0047.20.0199
MA0048.10.00109
MA0050.14.80982e-4
MA0051.10.00206
MA0052.10.227
MA0055.15.73443e-4
MA0057.10.906
MA0058.10.949
MA0059.10.213
MA0060.11.47631e-4
MA0061.10.0153
MA0062.20.141
MA0065.20.783
MA0066.10.371
MA0067.10.00467
MA0068.10.126
MA0069.10.851
MA0070.10.403
MA0071.10.422
MA0072.10.613
MA0073.10.704
MA0074.10.805
MA0076.15.93171e-5
MA0077.10.151
MA0078.10.35
MA0079.20.164
MA0080.28.38177e-14
MA0081.10.0364
MA0083.11.27739e-4
MA0084.10.648
MA0087.10.737
MA0088.11.06372e-5
MA0090.10.295
MA0091.10.167
MA0092.10.441
MA0093.10.783
MA0099.20.00382
MA0100.10.343
MA0101.10.0167
MA0102.20.0223
MA0103.15.7113e-5
MA0104.20.021
MA0105.10.566
MA0106.10.406
MA0107.17.13636e-4
MA0108.20.031
MA0111.10.702
MA0112.20.45
MA0113.10.36
MA0114.10.975
MA0115.10.782
MA0116.10.682
MA0117.10.372
MA0119.10.243
MA0122.10.546
MA0124.10.656
MA0125.10.226
MA0131.10.119
MA0135.10.282
MA0136.14.18338e-10
MA0137.20.746
MA0138.20.616
MA0139.10.888
MA0140.10.315
MA0141.10.202
MA0142.10.0698
MA0143.10.775
MA0144.10.532
MA0145.10.583
MA0146.10.283
MA0147.10.0116
MA0148.10.0298
MA0149.10.657
MA0150.10.0302
MA0152.10.0252
MA0153.10.977
MA0154.10.398
MA0155.10.637
MA0156.18.61899e-6
MA0157.10.0027
MA0159.10.42
MA0160.10.13
MA0162.10.517
MA0163.10.00135
MA0164.10.62
MA0258.10.438
MA0259.10.0274



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: CNhs12053

Novel motifP-value
10.478
100.0686
1000.551
1010.204
1020.503
1030.92
1040.916
1050.735
1064.39056e-5
1070.932
1080.771
1090.603
110.339
1100.00706
1110.928
1120.101
1130.0578
1140.227
1150.757
1160.143
1170.275
1180.628
1190.391
120.347
1200.12
1210.71
1220.0115
1230.062
1240.366
1250.894
1260.905
1270.0713
1280.139
1290.155
130.103
1300.175
1310.522
1320.759
1330.605
1340.397
1350.0622
1360.057
1370.0696
1380.0443
1390.139
140.223
1400.138
1410.435
1420.74
1430.255
1440.869
1450.747
1460.874
1470.565
1480.533
1490.461
150.226
1500.807
1510.55
1520.273
1530.501
1540.639
1550.06
1560.214
1570.456
1580.0116
1590.071
160.606
1600.377
1610.948
1620.397
1630.722
1640.275
1650.32
1660.168
1670.335
1680.33
1690.569
170.761
180.617
190.205
20.924
200.714
210.0268
220.831
230.027
240.704
250.641
260.199
270.648
280.0963
290.124
30.942
300.933
310.406
320.01
330.402
340.697
350.344
360.521
370.871
380.404
390.516
40.0308
400.296
410.0061
420.727
430.534
440.421
450.114
460.77
470.738
480.4
490.18
50.327
500.393
510.651
520.156
530.3
540.418
550.572
560.901
570.985
580.191
590.986
60.417
600.0523
610.498
620.198
630.97
640.896
650.309
660.332
670.604
680.298
690.586
70.714
700.0448
710.251
720.232
730.577
740.739
750.405
760.713
770.973
780.905
790.131
80.271
800.0966
810.699
820.0427
830.961
840.717
850.0129
860.547
870.0463
880.917
890.89
90.897
900.64
910.239
920.584
930.769
940.849
950.196
960.295
970.854
980.281
990.00256



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: CNhs12053


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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