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FF:11240-116D7: 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 16:36, 29 March 2012


Name:Skeletal Muscle Satellite 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 stagefetus
sexunknown
agefetal
cell typesatellite cell, skeletal muscle
cell lineNA
companySciencell/3H
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot number2068
catalog numberSC3515
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-0.0781
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-lymphoma0.265
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
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C91-Fibroblast-Smooth-mesenchymal-Mesothelial-Small-Preadipocyte-Hair0
C92-CD14CD16-CD14-Eosinophils-Basophils-Neutrophils-Macrophage-Whole0
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: CNhs10869

Jaspar motifP-value
MA0002.25.57917e-4
MA0003.10.271
MA0004.10.158
MA0006.10.798
MA0007.10.49
MA0009.10.443
MA0014.10.663
MA0017.10.157
MA0018.20.00174
MA0019.10.102
MA0024.10.15
MA0025.18.49128e-5
MA0027.10.878
MA0028.10.00285
MA0029.10.638
MA0030.10.285
MA0031.10.902
MA0035.21.15753e-4
MA0038.10.255
MA0039.20.104
MA0040.10.321
MA0041.10.29
MA0042.10.587
MA0043.10.194
MA0046.10.0704
MA0047.20.41
MA0048.10.0128
MA0050.10.147
MA0051.10.0403
MA0052.10.017
MA0055.10.087
MA0057.10.187
MA0058.10.118
MA0059.10.164
MA0060.10.341
MA0061.16.00074e-4
MA0062.20.334
MA0065.20.0158
MA0066.10.891
MA0067.10.0118
MA0068.10.0724
MA0069.10.0388
MA0070.10.958
MA0071.10.474
MA0072.10.133
MA0073.10.697
MA0074.10.546
MA0076.10.0316
MA0077.10.405
MA0078.10.142
MA0079.20.306
MA0080.21.65371e-11
MA0081.10.0554
MA0083.10.834
MA0084.10.00581
MA0087.10.994
MA0088.15.11704e-4
MA0090.10.0236
MA0091.10.313
MA0092.10.371
MA0093.10.164
MA0099.24.23316e-6
MA0100.10.176
MA0101.10.00616
MA0102.20.617
MA0103.11.33357e-5
MA0104.20.34
MA0105.10.619
MA0106.10.118
MA0107.11.61624e-4
MA0108.20.0272
MA0111.10.388
MA0112.20.503
MA0113.10.224
MA0114.10.417
MA0115.10.154
MA0116.10.725
MA0117.10.305
MA0119.10.425
MA0122.10.3
MA0124.10.0626
MA0125.10.871
MA0131.10.194
MA0135.10.0264
MA0136.13.0788e-10
MA0137.20.00609
MA0138.20.158
MA0139.10.336
MA0140.10.00863
MA0141.10.329
MA0142.10.0615
MA0143.10.531
MA0144.10.425
MA0145.10.844
MA0146.10.278
MA0147.10.396
MA0148.10.175
MA0149.10.273
MA0150.10.00111
MA0152.10.00615
MA0153.10.416
MA0154.10.0804
MA0155.10.226
MA0156.11.68777e-6
MA0157.10.862
MA0159.10.364
MA0160.10.00125
MA0162.10.228
MA0163.10.00988
MA0164.10.677
MA0258.10.117
MA0259.10.756



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: CNhs10869

Novel motifP-value
10.768
100.314
1000.963
1010.834
1020.0758
1030.552
1040.867
1050.604
1061.26717e-4
1070.449
1080.224
1090.254
110.776
1100.137
1110.27
1120.0668
1130.00645
1140.1
1150.125
1160.429
1170.377
1180.583
1190.368
120.282
1200.927
1210.934
1220.00113
1230.135
1240.364
1250.774
1260.893
1270.0365
1280.474
1290.0895
130.817
1300.0849
1310.902
1320.241
1330.922
1340.434
1350.253
1360.539
1370.122
1380.111
1390.0368
140.458
1400.262
1410.343
1420.947
1430.0155
1440.415
1450.965
1460.771
1470.418
1480.3
1490.852
150.116
1500.791
1510.545
1520.0776
1530.565
1540.742
1550.0307
1560.0278
1570.317
1580.0164
1590.531
160.999
1600.876
1610.458
1620.0693
1630.832
1640.407
1650.838
1660.0954
1670.199
1680.222
1690.74
170.277
180.64
190.206
20.789
200.852
210.0159
220.946
230.0745
240.563
250.171
260.726
270.457
280.341
290.417
30.701
300.869
310.681
320.00105
330.849
340.935
350.335
360.0627
370.802
380.357
390.779
40.0256
400.00319
411.3352e-4
420.947
430.336
440.344
450.145
460.552
470.897
480.98
490.172
50.213
500.69
510.858
520.41
530.584
540.487
550.365
560.981
570.803
580.176
590.233
60.487
600.0573
610.88
620.0711
630.461
640.495
650.31
660.984
670.442
680.612
690.597
70.224
700.0438
710.547
720.843
730.757
740.249
750.419
760.628
770.538
780.303
790.0546
80.957
800.155
810.59
820.198
830.81
840.548
850.0176
860.554
870.879
880.411
890.153
90.834
900.803
910.342
920.645
930.68
940.722
950.883
960.523
970.931
980.152
990.0017



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: CNhs10869


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)
0000035 (single fate 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)
0000594 (skeletal muscle satellite 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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