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{{f5samples
{{f5samples
|F5samples=
|ancestors_in_anatomy_facet=UBERON:0000061,UBERON:0000465,UBERON:0000479,UBERON:0001062,UBERON:0002384
|ancestors_in_anatomy_facet=UBERON:0000061,UBERON:0000465,UBERON:0000479,UBERON:0001062,UBERON:0002384
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000004,CL:0000012,CL:0000034,CL:0000048,CL:0000063,CL:0000134,CL:0000144,CL:0000219,CL:0000255,CL:0000548,CL:0000723,CL:0002320,CL:0002371
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000004,CL:0000012,CL:0000034,CL:0000048,CL:0000063,CL:0000134,CL:0000144,CL:0000219,CL:0000255,CL:0000548,CL:0000723,CL:0002320,CL:0002371
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|creation_date=
|creation_date=
|def=
|def=
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|fonse_cell_line=FF:10568-108B1
|fonse_cell_line=FF:10568-108B1
|fonse_cell_line_closure=FF:10568-108B1
|fonse_cell_line_closure=FF:10568-108B1

Revision as of 16:49, 29 March 2012


Name:mesenchymal stem cell line:Hu5/E18
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 stage42 year old adult
sexfemale
age42
cell typemesenchymal stem cell
cell lineHu5/E18
companyRIKEN Bioresource centre
collaborationYukio Nakamura (RIKEN BRC)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberNA
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-miRNeasy_Mini-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-penis0.0738
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-lymphoma0.581
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
C110-leukemia-chronic-Eosinophils-acute-Whole-CD34-Lymphatic0
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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: CNhs11718

Jaspar motifP-value
MA0002.20.571
MA0003.10.853
MA0004.10.31
MA0006.10.13
MA0007.10.185
MA0009.10.699
MA0014.10.514
MA0017.10.901
MA0018.20.00325
MA0019.10.212
MA0024.19.82029e-4
MA0025.10.00806
MA0027.10.325
MA0028.10.668
MA0029.10.712
MA0030.15.63929e-5
MA0031.10.0292
MA0035.20.137
MA0038.10.305
MA0039.20.241
MA0040.10.564
MA0041.10.35
MA0042.10.539
MA0043.13.12939e-9
MA0046.10.00802
MA0047.20.0106
MA0048.10.863
MA0050.10.00358
MA0051.10.0207
MA0052.10.995
MA0055.10.792
MA0057.10.658
MA0058.10.239
MA0059.10.355
MA0060.10.00949
MA0061.10.109
MA0062.20.00134
MA0065.20.364
MA0066.10.059
MA0067.10.0366
MA0068.10.761
MA0069.10.355
MA0070.10.408
MA0071.10.889
MA0072.10.785
MA0073.10.644
MA0074.10.943
MA0076.10.12
MA0077.10.253
MA0078.10.76
MA0079.20.0362
MA0080.23.53657e-8
MA0081.10.0207
MA0083.10.132
MA0084.10.0999
MA0087.10.737
MA0088.10.21
MA0090.10.00527
MA0091.10.0063
MA0092.10.305
MA0093.10.24
MA0099.20.316
MA0100.10.125
MA0101.13.2387e-5
MA0102.21.24785e-5
MA0103.10.0263
MA0104.20.488
MA0105.10.111
MA0106.10.105
MA0107.11.98737e-5
MA0108.20.368
MA0111.10.612
MA0112.20.00364
MA0113.10.312
MA0114.10.597
MA0115.10.416
MA0116.10.0236
MA0117.10.522
MA0119.15.98872e-4
MA0122.10.789
MA0124.10.175
MA0125.10.407
MA0131.10.345
MA0135.10.787
MA0136.11.21472e-9
MA0137.22.18131e-4
MA0138.20.98
MA0139.10.656
MA0140.10.785
MA0141.10.726
MA0142.10.109
MA0143.10.967
MA0144.10.148
MA0145.10.213
MA0146.10.557
MA0147.10.82
MA0148.10.0328
MA0149.10.139
MA0150.10.317
MA0152.10.443
MA0153.10.121
MA0154.10.122
MA0155.10.82
MA0156.11.96132e-7
MA0157.10.214
MA0159.10.675
MA0160.10.127
MA0162.10.00428
MA0163.10.00141
MA0164.10.826
MA0258.10.142
MA0259.10.634



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: CNhs11718

Novel motifP-value
10.0719
100.0667
1000.306
1010.664
1020.707
1030.367
1040.86
1050.0466
1060.485
1070.0318
1080.451
1090.00966
110.353
1100.0454
1110.0528
1120.663
1130.0074
1140.0929
1150.0351
1160.151
1170.114
1180.268
1190.392
120.353
1200.0611
1210.564
1220.0509
1230.166
1240.722
1250.0423
1260.729
1270.67
1280.754
1290.46
130.142
1300.946
1310.629
1320.382
1330.368
1340.787
1350.8
1360.265
1370.362
1380.447
1390.895
140.713
1400.352
1410.81
1420.506
1430.275
1440.83
1450.218
1460.766
1470.417
1480.291
1490.0115
150.335
1500.397
1510.817
1520.81
1530.879
1540.878
1550.354
1560.515
1570.361
1580.327
1590.543
160.0426
1600.167
1610.891
1620.335
1630.129
1640.627
1650.142
1660.646
1670.302
1680.343
1690.0332
170.157
180.408
190.0143
20.923
200.976
210.145
220.445
230.807
240.999
250.478
260.011
270.837
280.749
290.355
30.284
300.318
310.932
327.22934e-4
330.109
340.127
350.945
360.463
370.103
380.924
390.238
40.637
400.0673
410.562
420.929
430.127
440.0759
450.617
460.021
470.315
480.428
490.308
50.612
500.692
510.842
520.947
530.421
540.991
550.439
560.647
570.157
580.527
590.0128
60.284
600.852
610.787
620.798
630.441
640.922
650.916
660.0345
670.831
680.395
690.148
70.734
700.331
710.0352
720.22
730.109
740.65
750.264
760.918
770.0554
780.145
790.0454
80.0695
800.572
810.619
820.657
830.817
840.124
850.602
860.706
870.911
880.68
890.23
90.91
900.217
910.667
920.759
930.826
940.422
950.122
960.361
970.811
980.579
990.00336



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: CNhs11718


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)
0000134 (mesenchymal cell)
0000219 (motile cell)
0000255 (eukaryotic cell)
0000548 (animal cell)
0000723 (somatic stem cell)
0002320 (connective tissue cell)
0002371 (somatic cell)

UBERON: Anatomy
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000479 (tissue)
0001062 (anatomical entity)
0002384 (connective tissue)

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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