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|rna_box=117
|rna_box=117

Revision as of 15:40, 21 September 2012


Name:Skeletal Muscle Satellite Cells, 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 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 number514
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
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C85-neuroblastoma-carcinoid-retinoblastoma-small-pineal-rhabdomyosarcoma-medulloblastoma0
C86-colon-carcinoid-small-neuroectodermal-giant-large-neuroepithelioma0
C87-retinoblastoma-left-nonsmall-heart-small-diaphragm-bronchogenic0
C88-Melanocyte-melanoma-Macrophage-Mesenchymal-migratory-Dendritic-Monocytederived0
C89-small-retinoblastoma-medulloblastoma-iPS-acantholytic-eye-bronchogenic0
C9-skeletal-diaphragm-tongue-throat-penis-heart-left0
C90-neuroectodermal-peripheral-neuroepithelioma-neuroblastoma-carcinoid-parietal-putamen0
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



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: CNhs11964

Jaspar motifP-value
MA0002.20.00155
MA0003.10.602
MA0004.10.167
MA0006.10.306
MA0007.10.0954
MA0009.10.147
MA0014.10.38
MA0017.10.26
MA0018.20.018
MA0019.10.497
MA0024.10.1
MA0025.11.277e-4
MA0027.10.83
MA0028.10.559
MA0029.10.77
MA0030.10.0291
MA0031.10.232
MA0035.20.00386
MA0038.10.419
MA0039.20.234
MA0040.10.262
MA0041.10.191
MA0042.10.348
MA0043.10.0554
MA0046.10.0362
MA0047.20.101
MA0048.10.00574
MA0050.10.00236
MA0051.13.69541e-4
MA0052.10.721
MA0055.10.214
MA0057.10.51
MA0058.10.062
MA0059.10.255
MA0060.10.542
MA0061.11.70576e-4
MA0062.21.17e-4
MA0065.20.237
MA0066.10.421
MA0067.15.45128e-4
MA0068.10.173
MA0069.10.0761
MA0070.10.882
MA0071.10.963
MA0072.10.173
MA0073.10.484
MA0074.10.116
MA0076.10.943
MA0077.10.52
MA0078.10.577
MA0079.20.774
MA0080.22.89775e-12
MA0081.10.0056
MA0083.10.543
MA0084.10.0151
MA0087.10.903
MA0088.10.0248
MA0090.10.0284
MA0091.10.14
MA0092.10.289
MA0093.10.166
MA0099.22.7401e-11
MA0100.10.537
MA0101.17.72942e-4
MA0102.20.218
MA0103.13.1222e-4
MA0104.20.14
MA0105.10.0881
MA0106.10.415
MA0107.12.10446e-5
MA0108.20.669
MA0111.10.977
MA0112.20.667
MA0113.10.142
MA0114.10.573
MA0115.10.402
MA0116.10.419
MA0117.10.153
MA0119.10.399
MA0122.10.264
MA0124.10.751
MA0125.10.75
MA0131.10.526
MA0135.10.0894
MA0136.19.21855e-15
MA0137.20.889
MA0138.20.645
MA0139.10.0602
MA0140.10.00657
MA0141.10.888
MA0142.10.114
MA0143.10.811
MA0144.10.69
MA0145.10.82
MA0146.10.00229
MA0147.10.194
MA0148.10.043
MA0149.10.292
MA0150.14.0787e-6
MA0152.10.106
MA0153.10.567
MA0154.10.0459
MA0155.10.748
MA0156.18.54489e-13
MA0157.10.195
MA0159.10.154
MA0160.10.0174
MA0162.10.135
MA0163.10.0219
MA0164.10.98
MA0258.10.639
MA0259.10.465



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: CNhs11964

Novel motifP-value
10.713
100.526
1000.664
1010.654
1020.411
1030.598
1040.883
1050.0522
1060.00525
1070.948
1080.896
1090.383
110.842
1100.096
1110.55
1120.116
1130.136
1140.33
1150.385
1160.211
1170.347
1180.665
1190.487
120.306
1200.252
1210.524
1226.62767e-4
1230.0148
1240.0398
1250.68
1260.748
1270.0663
1280.966
1290.078
130.88
1300.448
1310.806
1320.311
1330.955
1340.464
1350.054
1360.179
1370.0215
1380.0492
1390.218
140.363
1400.219
1410.503
1420.819
1430.0532
1440.273
1450.996
1460.736
1470.285
1480.154
1490.678
150.109
1500.569
1510.867
1520.87
1530.901
1540.818
1550.1
1560.0236
1570.31
1580.0114
1590.462
160.419
1600.788
1610.774
1620.0452
1630.936
1640.256
1650.642
1660.0874
1670.0976
1680.175
1690.312
170.323
180.611
190.0281
20.756
200.939
210.0733
220.631
230.169
240.185
250.171
260.383
270.644
280.196
290.668
31
300.81
310.805
321.47766e-9
330.993
340.845
350.223
360.038
370.473
380.405
390.474
40.216
400.0202
410.00107
420.55
430.439
440.453
450.227
460.825
470.931
480.972
490.18
50.134
500.583
510.945
520.587
530.241
540.792
550.635
560.837
570.57
580.0962
590.853
60.919
600.0688
610.788
620.0983
630.777
640.602
650.563
660.673
670.487
680.19
690.675
70.18
700.303
710.944
720.441
730.344
740.243
750.819
760.458
770.949
780.302
790.00944
80.821
800.0147
810.577
820.729
830.0476
840.801
850.0961
860.624
870.336
880.463
890.571
90.987
900.469
910.566
920.649
930.975
940.315
950.852
960.259
970.983
980.2
991.92586e-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: CNhs11964


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)
0000055 (non-terminally differentiated cell)
0000003 (native cell)
0000723 (somatic stem cell)
0000035 (single fate stem cell)
0000548 (animal cell)
0000680 (muscle precursor cell)
0002371 (somatic cell)
0000393 (electrically responsive cell)
0000183 (contractile cell)
0000187 (muscle cell)
0000211 (electrically active cell)
0000255 (eukaryotic cell)
0000188 (cell of skeletal muscle)
0000034 (stem cell)
0000594 (skeletal muscle satellite cell)

UBERON: Anatomy
0000468 (multi-cellular organism)
0001134 (skeletal muscle tissue)
0000479 (tissue)
0004120 (mesoderm-derived structure)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0002036 (striated muscle tissue)
0002385 (muscle tissue)
0010317 (germ layer / neural crest derived structure)
0001015 (musculature)
0002204 (musculoskeletal system)
0000383 (musculature of body)

FF: FANTOM5
0000102 (sample by type)
0000210 (human sample)
0000002 (in vivo cell sample)
0000101 (sample by species)
0000001 (sample)
0000165 (human skeletal muscle satellite cell sample)

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
CL:0000355 (multi-potent skeletal muscle stem cell)
CL:0000222 (mesodermal cell)

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