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FF:11397-118D2: 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 17:06, 29 March 2012


Name:Skeletal Muscle Satellite Cells, donor3
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 number1142
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-7.601071e-4
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-lymphoma0.471
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
C110-leukemia-chronic-Eosinophils-acute-Whole-CD34-Lymphatic0
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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: CNhs12008

Jaspar motifP-value
MA0002.20.014
MA0003.10.503
MA0004.10.851
MA0006.10.834
MA0007.10.935
MA0009.10.349
MA0014.10.768
MA0017.10.129
MA0018.20.263
MA0019.10.669
MA0024.13.04102e-9
MA0025.10.0318
MA0027.10.748
MA0028.10.153
MA0029.10.409
MA0030.10.00164
MA0031.10.00168
MA0035.20.00356
MA0038.10.0187
MA0039.20.529
MA0040.10.105
MA0041.10.301
MA0042.10.309
MA0043.10.0367
MA0046.10.0821
MA0047.20.0108
MA0048.10.0893
MA0050.11.04555e-5
MA0051.14.94445e-5
MA0052.10.00525
MA0055.10.23
MA0057.10.455
MA0058.10.774
MA0059.10.718
MA0060.13.07841e-6
MA0061.10.00121
MA0062.20.255
MA0065.20.00644
MA0066.10.82
MA0067.10.0276
MA0068.10.0803
MA0069.10.728
MA0070.10.0863
MA0071.10.745
MA0072.10.174
MA0073.10.86
MA0074.10.59
MA0076.10.273
MA0077.10.46
MA0078.10.892
MA0079.20.918
MA0080.22.70394e-11
MA0081.10.052
MA0083.10.0317
MA0084.10.178
MA0087.10.961
MA0088.10.018
MA0090.10.0273
MA0091.10.379
MA0092.10.38
MA0093.10.705
MA0099.20.00465
MA0100.10.099
MA0101.10.0463
MA0102.20.006
MA0103.17.40395e-5
MA0104.20.556
MA0105.15.36169e-6
MA0106.10.919
MA0107.10.00632
MA0108.26.62708e-11
MA0111.10.509
MA0112.20.067
MA0113.10.887
MA0114.10.0708
MA0115.10.566
MA0116.10.00193
MA0117.10.338
MA0119.10.9
MA0122.10.489
MA0124.10.509
MA0125.10.984
MA0131.10.425
MA0135.10.388
MA0136.19.29117e-10
MA0137.20.25
MA0138.20.324
MA0139.10.00333
MA0140.10.058
MA0141.10.684
MA0142.10.176
MA0143.10.876
MA0144.10.0929
MA0145.10.288
MA0146.10.487
MA0147.10.727
MA0148.10.00177
MA0149.10.39
MA0150.10.00846
MA0152.10.0378
MA0153.10.787
MA0154.10.00355
MA0155.10.769
MA0156.15.6275e-5
MA0157.10.00705
MA0159.10.0094
MA0160.10.0493
MA0162.10.719
MA0163.10.031
MA0164.10.972
MA0258.10.0128
MA0259.10.665



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: CNhs12008

Novel motifP-value
10.586
100.62
1000.82
1010.256
1020.515
1030.216
1040.787
1050.0658
1060.00107
1070.52
1080.533
1090.29
110.585
1100.464
1110.438
1120.0436
1130.899
1140.0422
1150.759
1160.468
1170.636
1180.204
1190.319
120.547
1200.151
1210.489
1220.025
1230.00306
1240.0142
1250.519
1260.968
1270.466
1280.0789
1290.0681
130.875
1300.0528
1310.965
1320.915
1330.749
1340.247
1350.264
1360.643
1370.126
1380.0662
1390.0033
140.286
1400.125
1410.292
1420.948
1430.359
1440.834
1450.68
1460.857
1470.34
1480.17
1490.593
150.127
1500.833
1510.316
1520.341
1530.38
1540.875
1550.00638
1560.0819
1570.0943
1580.0275
1590.369
160.872
1600.558
1610.67
1620.351
1630.704
1640.989
1650.373
1660.928
1670.0916
1680.29
1690.0469
170.338
180.53
190.957
20.807
200.778
210.26
220.715
230.0294
240.663
250.444
260.972
270.368
280.306
290.719
30.361
300.851
310.426
320.0663
330.842
340.754
350.136
360.0446
370.524
380.373
390.656
40.237
400.0793
410.00765
420.405
430.3
440.313
450.153
460.251
470.544
480.755
490.117
50.125
500.479
510.447
520.402
530.131
540.493
550.365
560.66
570.326
580.0856
590.338
60.878
600.0371
610.703
620.077
630.518
640.398
650.254
660.413
670.584
680.472
690.519
70.32
700.00112
710.385
720.171
730.794
740.634
750.351
760.618
770.423
780.289
790.149
80.95
800.0991
810.542
820.00968
830.49
840.787
850.00462
860.305
870.352
880.951
890.261
90.881
900.276
910.324
920.113
930.892
940.167
950.879
960.27
970.596
980.0982
990.0077



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: CNhs12008


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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