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|rna_weight_ug=1.4725
|rna_weight_ug=1.4725
|sample_age=
|sample_age=
|sample_category=primary cells
|sample_cell_catalog=
|sample_cell_catalog=
|sample_cell_line=
|sample_cell_line=

Revision as of 16:25, 26 December 2012


Name:Mouse hepatic Sinusoidal Endothelial Cells, donor1
Species:Mouse (Mus musculus)
Library ID:{{{library_id}}}
Sample type:primary cells
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissueliver
dev stageNA
sexmale
ageNA
cell typehepatic sinusoidal endothelial cell
cell lineNA
companyNA
collaborationSoichi Kojima (RIKEN ASI)
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
Mm9
BAMCTSS
[{{{mm9bam}}} download][{{{mm9ctss}}} donwload]
Mm10
BAMCTSS
[{{{mm10bam}}} download][{{{mm10ctss}}} 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

CNhs13209

00
10
100
1000
10000
1001-0.0275
1002-0.0941
1003-0.121
10040
10050
10060
1007-0.175
10080
10090.605
101-0.0411
10100
10110.00303
10120
1013-0.0181
10140
1015-0.242
1016-0.183
10170
10180
10190
1020.078
10200.199
10210.199
10220.219
10230.521
10241.071
10250.221
10260
10270
10280
1029-0.0206
103-0.0788
10300
10310.42
1032-0.142
10330.434
10340.334
10350
10360.386
10370
10380.253
1039-0.027
1040
10400.425
10410



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: CNhs13209

Jaspar motifP-value
MA0002.20.263
MA0003.10.342
MA0004.10.938
MA0006.10.295
MA0007.10.61
MA0009.10.707
MA0014.10.352
MA0017.10.466
MA0018.23.84935e-5
MA0019.10.193
MA0024.10.777
MA0025.14.29731e-6
MA0027.10.322
MA0028.10.0821
MA0029.10.486
MA0030.10.0604
MA0031.10.0157
MA0035.20.564
MA0038.10.167
MA0039.20.00124
MA0040.10.288
MA0041.10.535
MA0042.10.853
MA0043.16.36573e-6
MA0046.13.66825e-7
MA0047.20.1
MA0048.10.392
MA0050.11.68011e-9
MA0051.16.37324e-12
MA0052.12.50566e-4
MA0055.10.00178
MA0057.10.882
MA0058.10.644
MA0059.10.00923
MA0060.10.766
MA0061.18.89864e-6
MA0062.23.01688e-4
MA0065.20.548
MA0066.10.0172
MA0067.10.00184
MA0068.12.84187e-5
MA0069.10.778
MA0070.10.432
MA0071.10.719
MA0072.10.977
MA0073.10.82
MA0074.10.368
MA0076.10.0733
MA0077.10.509
MA0078.10.137
MA0079.20.0629
MA0080.26.3141e-6
MA0081.10.0466
MA0083.12.01785e-5
MA0084.10.73
MA0087.10.138
MA0088.10.384
MA0090.10.0745
MA0091.10.0146
MA0092.10.481
MA0093.10.79
MA0099.26.36128e-4
MA0100.10.221
MA0101.12.39453e-10
MA0102.20.0772
MA0103.10.0116
MA0104.20.0491
MA0105.10.795
MA0106.10.726
MA0107.11.17997e-11
MA0108.22.84228e-6
MA0111.10.142
MA0112.20.0442
MA0113.10.937
MA0114.10.0828
MA0115.10.253
MA0116.10.00194
MA0117.10.322
MA0119.10.572
MA0122.10.886
MA0124.10.513
MA0125.10.0951
MA0131.10.866
MA0135.10.0927
MA0136.18.43568e-7
MA0137.22.67507e-13
MA0138.20.0276
MA0139.10.419
MA0140.10.599
MA0141.10.0329
MA0142.10.0249
MA0143.10.014
MA0144.11.03229e-8
MA0145.10.0262
MA0146.10.951
MA0147.10.0061
MA0148.10.291
MA0149.10.302
MA0150.10.468
MA0152.10.0125
MA0153.11.37063e-5
MA0154.10.436
MA0155.10.622
MA0156.18.10408e-10
MA0157.10.0403
MA0159.10.833
MA0160.10.278
MA0162.10.909
MA0163.10.0951
MA0164.10.795
MA0258.10.0155
MA0259.10.77



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: CNhs13209

Novel motifP-value
10.118
100.257
1000.884
1010.368
1020.749
1030.172
1040.78
1050.551
1060.141
1070.33
1080.715
1090.949
110.261
1100.849
1110.0917
1120.628
1130.858
1140.0392
1150.376
1160.325
1170.51
1180.304
1190.414
120.802
1200.96
1210.065
1220.752
1230.156
1240.173
1250.233
1260.617
1270.477
1280.108
1290.418
130.0632
1300.14
1310.953
1320.71
1330.912
1340.877
1350.0378
1360.0207
1370.574
1380.126
1390.0657
140.916
1400.287
1410.961
1420.666
1430.36
1440.702
1450.91
1460.75
1470.959
1480.907
1490.576
150.529
1500.299
1510.188
1520.00872
1530.346
1540.96
1550.269
1562.80876e-40
1570.236
1580.976
1590.0605
1600.148
1610.201
1620.528
1630.552
1640.966
1650.166
1660.658
1670.278
1680.703
1690.365
170.872
180.0308
190.92
20.974
200.275
210.29
220.931
230.851
240.676
250.536
260.323
270.157
280.912
290.193
30.375
300.823
310.335
320.0309
330.362
340.731
353.04646e-4
360.274
370.412
380.595
390.843
40.495
400.375
410.603
420.411
430.289
440.0679
450.795
460.257
470.272
480.347
490.19
50.638
500.513
510.428
520.52
530.789
540.586
550.272
560.809
570.0833
580.492
590.445
60.28
600.568
610.983
620.137
630.772
640.129
650.547
660.755
670.441
680.658
690.141
70.818
700.297
710.194
720.685
730.0714
740.0934
750.783
760.456
770.238
780.448
790.548
80.011
800.792
810.258
820.129
830.744
840.613
850.448
860.945
870.0186
880.758
890.554
90.901
900.131
910.279
920.417
930.538
940.00747
950.287
960.0524
970.572
980.556
990.988



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: CNhs13209


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)
0000548 (animal cell)
0000066 (epithelial cell)
0002371 (somatic cell)
0000213 (lining cell)
0002078 (meso-epithelial cell)
0000181 (metabolising cell)
0000417 (endopolyploid cell)
0000668 (parenchymal cell)
0000215 (barrier cell)
0000412 (polyploid cell)
0000255 (eukaryotic cell)
0000115 (endothelial cell)
0000182 (hepatocyte)
0002262 (endothelial cell of sinusoid)
1000398 (endothelial cell of hepatic sinusoid)

UBERON: Anatomy
0000468 (multi-cellular organism)
0002107 (liver)
0002100 (trunk)
0000483 (epithelium)
0000479 (tissue)
0001007 (digestive system)
0000055 (vessel)
0001281 (hepatic sinusoid)
0000064 (organ part)
0004119 (endoderm-derived structure)
0000062 (organ)
0004111 (anatomical conduit)
0000475 (organism subdivision)
0004120 (mesoderm-derived structure)
0000077 (mixed endoderm/mesoderm-derived structure)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0003914 (epithelial tube)
0000025 (tube)
0005911 (endo-epithelium)
0000477 (anatomical cluster)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0000119 (cell layer)
0009569 (subdivision of trunk)
0002368 (endocrine gland)
0000353 (parenchyma)
0003497 (abdomen blood vessel)
0003909 (sinusoid)
0005177 (trunk region element)
0002365 (exocrine gland)
0007500 (epithelial tube open at both ends)
0001981 (blood vessel)
0005172 (abdomen element)
0006925 (digestive gland)
0002049 (vasculature)
0002530 (gland)
0003835 (abdominal segment blood vessel)
0003513 (trunk blood vessel)
0010317 (germ layer / neural crest derived structure)
0007798 (vascular system)
0005173 (abdominal segment element)
0004535 (cardiovascular system)
0002417 (abdominal segment of trunk)
0000949 (endocrine system)
0001280 (liver parenchyma)
0004647 (liver lobule)
0002330 (exocrine system)
0004537 (blood vasculature)
0000916 (abdomen)
0002423 (hepatobiliary system)
0001009 (circulatory system)

FF: FANTOM5
0000102 (sample by type)
0000002 (in vivo cell sample)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000076 (hepatic sinusoidal endothelial cell sample)
0011161 (Mouse hepatic Sinusoidal Endothelial Cells 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:0000134 (mesenchymal cell)
CL:0000222 (mesodermal cell)
CL:0000223 (endodermal cell)

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