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FF:11322-117D8: 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 17:03, 29 March 2012


Name:Myoblast, donor2
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 stage21 years old adult
sexmale
age21
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 numberSKM2
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-penis0.0892
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-lymphoma0.0537
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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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: CNhs11965

Jaspar motifP-value
MA0002.20.086
MA0003.10.528
MA0004.10.79
MA0006.10.0309
MA0007.10.0483
MA0009.10.221
MA0014.10.395
MA0017.10.626
MA0018.26.22989e-5
MA0019.10.825
MA0024.10.114
MA0025.17.76347e-6
MA0027.10.924
MA0028.10.755
MA0029.10.523
MA0030.10.00222
MA0031.10.0236
MA0035.25.8786e-4
MA0038.10.0505
MA0039.20.0102
MA0040.10.508
MA0041.10.283
MA0042.10.156
MA0043.11.00173e-6
MA0046.10.283
MA0047.20.133
MA0048.10.0727
MA0050.10.00674
MA0051.10.0247
MA0052.10.0511
MA0055.10.728
MA0057.10.63
MA0058.10.708
MA0059.10.663
MA0060.18.60254e-9
MA0061.10.00363
MA0062.28.39738e-4
MA0065.20.274
MA0066.10.206
MA0067.10.0033
MA0068.10.171
MA0069.10.341
MA0070.10.474
MA0071.10.832
MA0072.10.264
MA0073.10.867
MA0074.10.0881
MA0076.10.687
MA0077.10.646
MA0078.10.456
MA0079.20.775
MA0080.22.77344e-10
MA0081.10.024
MA0083.10.107
MA0084.10.122
MA0087.10.503
MA0088.10.239
MA0090.10.0117
MA0091.10.0971
MA0092.10.898
MA0093.10.833
MA0099.20.0124
MA0100.10.556
MA0101.15.00857e-6
MA0102.20.235
MA0103.10.00166
MA0104.20.251
MA0105.10.318
MA0106.10.414
MA0107.11.15444e-6
MA0108.20.408
MA0111.10.152
MA0112.20.0787
MA0113.10.415
MA0114.10.492
MA0115.10.398
MA0116.10.658
MA0117.10.323
MA0119.10.0124
MA0122.10.427
MA0124.10.294
MA0125.10.501
MA0131.10.403
MA0135.10.79
MA0136.11.56739e-11
MA0137.20.0976
MA0138.20.294
MA0139.10.668
MA0140.10.00449
MA0141.10.173
MA0142.10.00851
MA0143.10.556
MA0144.10.448
MA0145.10.47
MA0146.10.717
MA0147.10.533
MA0148.10.145
MA0149.10.491
MA0150.10.0254
MA0152.10.181
MA0153.10.934
MA0154.10.503
MA0155.10.658
MA0156.12.66152e-8
MA0157.10.323
MA0159.10.586
MA0160.10.189
MA0162.10.375
MA0163.10.0917
MA0164.10.362
MA0258.10.988
MA0259.10.851



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: CNhs11965

Novel motifP-value
10.699
100.0319
1000.914
1010.651
1020.965
1030.514
1040.596
1050.011
1060.219
1070.161
1080.51
1090.788
110.968
1100.304
1110.715
1120.273
1130.919
1140.535
1150.0693
1160.0692
1170.125
1180.459
1190.665
120.616
1200.0785
1210.809
1220.0029
1230.118
1240.0327
1250.97
1260.96
1270.8
1280.956
1290.383
130.834
1300.81
1310.627
1320.532
1330.817
1340.831
1350.613
1360.0851
1370.106
1380.308
1390.673
140.197
1400.146
1410.113
1420.905
1430.707
1440.587
1450.324
1460.368
1470.207
1480.69
1490.243
150.556
1500.842
1510.784
1520.232
1530.573
1540.779
1550.0449
1560.41
1570.289
1580.00345
1590.378
160.0576
1600.683
1610.482
1620.185
1630.962
1640.44
1650.413
1660.193
1670.983
1680.859
1690.17
170.749
180.995
190.024
20.844
200.86
210.0342
220.34
230.847
240.532
250.273
260.7
270.888
280.283
290.51
30.527
300.533
310.753
322.65898e-8
330.96
340.279
350.957
360.0185
370.072
380.557
390.219
40.0427
400.0326
410.157
420.316
430.713
440.205
450.463
460.57
470.491
480.705
490.281
50.496
500.428
510.751
520.324
530.0631
540.984
550.122
560.905
570.929
580.227
590.285
60.265
600.128
610.428
620.687
630.189
640.296
650.961
660.203
670.924
680.307
690.721
70.305
700.518
710.411
720.259
730.00846
740.214
750.504
760.412
770.0835
780.907
790.0733
80.249
800.0145
810.645
820.832
830.585
840.643
850.513
860.243
870.0756
880.961
890.871
90.936
900.482
910.601
920.675
930.671
940.985
950.942
960.447
970.965
980.166
990.00574



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: CNhs11965


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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