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FF:11830-124G3

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Name:Mouse hepatic Sinusoidal Endothelial Cells, donor1
Species:Mouse (Mus musculus)
Library ID:CNhs13209
Sample type:primary cells
Genomic View: UCSC
MicroRNAs:Including candidate novel miRNAs(CAGE samples)
Excluding candidate novel miRNAs(CAGE samples)
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

Accession numbers
MethodSample accession id
CAGE  SAMD00004813
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs13209 CAGE DRX008855 DRR009727
Accession ID Mm9

Library idBAMCTSS
CNhs13209 DRZ001152 DRZ002537
Download raw sequence, BAM & CTSS
Mm9
FastaBAMCTSS
downloaddownloaddonwload
Mm10
BAMCTSS
downloaddonwload


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.
Analyst:NA

link to dataset.
data

CNhs13209

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 0
1001 --0.0275
1002 --0.0941
1003 --0.121
1004 0
1005 0
1006 0
1007 --0.175
1008 0
1009 0.605
101 --0.0411
1010 0
1011 0.00303
1012 0
1013 --0.0181
1014 0
1015 --0.242
1016 --0.183
1017 0
1018 0
1019 0
102 0.078
1020 0.199
1021 0.199
1022 0.219
1023 0.521
1024 1.071
1025 0.221
1026 0
1027 0
1028 0
1029 --0.0206
103 --0.0788
1030 0
1031 0.42
1032 --0.142
1033 0.434
1034 0.334
1035 0
1036 0.386
1037 0
1038 0.253
1039 --0.027
104 0
1040 0.425
1041 0



Repeat families with enriched expression in this sampleSummary:Ranked list of repeat family expression in this sample relative to the median expression in the FANTOM5 collection is shown. Value is log10 transformed.
Analyst:NA

link to dataset.
data



TFBS(DNA)motifs over-represented in proximal region of promoters active in this sample


JASPAR motifsSummary:Association of JASPAR motif to the promoter expression in this sample. Pearson's correlation between the number of TFBSs estimated by using the position-weight matrix for each promoter and its expression is expressed as Z-score by taking the ones based on random position-weight matrix, and the tail probability of the normal distribution corresponding to the Z-score is taken as the resulting P-value. Lower P-value indicates more (non-random) association of the motif to promoter expression
Analyst: Michiel de Hoon


link to dataset.
data

library id: CNhs13209

Jaspar motif P-value
MA0002.2 0.263
MA0003.1 0.342
MA0004.1 0.938
MA0006.1 0.295
MA0007.1 0.61
MA0009.1 0.707
MA0014.1 0.352
MA0017.1 0.466
MA0018.2 3.84935e-5
MA0019.1 0.193
MA0024.1 0.777
MA0025.1 4.29731e-6
MA0027.1 0.322
MA0028.1 0.0821
MA0029.1 0.486
MA0030.1 0.0604
MA0031.1 0.0157
MA0035.2 0.564
MA0038.1 0.167
MA0039.2 0.00124
MA0040.1 0.288
MA0041.1 0.535
MA0042.1 0.853
MA0043.1 6.36573e-6
MA0046.1 3.66825e-7
MA0047.2 0.1
MA0048.1 0.392
MA0050.1 1.68011e-9
MA0051.1 6.37324e-12
MA0052.1 2.50566e-4
MA0055.1 0.00178
MA0057.1 0.882
MA0058.1 0.644
MA0059.1 0.00923
MA0060.1 0.766
MA0061.1 8.89864e-6
MA0062.2 3.01688e-4
MA0065.2 0.548
MA0066.1 0.0172
MA0067.1 0.00184
MA0068.1 2.84187e-5
MA0069.1 0.778
MA0070.1 0.432
MA0071.1 0.719
MA0072.1 0.977
MA0073.1 0.82
MA0074.1 0.368
MA0076.1 0.0733
MA0077.1 0.509
MA0078.1 0.137
MA0079.2 0.0629
MA0080.2 6.3141e-6
MA0081.1 0.0466
MA0083.1 2.01785e-5
MA0084.1 0.73
MA0087.1 0.138
MA0088.1 0.384
MA0090.1 0.0745
MA0091.1 0.0146
MA0092.1 0.481
MA0093.1 0.79
MA0099.2 6.36128e-4
MA0100.1 0.221
MA0101.1 2.39453e-10
MA0102.2 0.0772
MA0103.1 0.0116
MA0104.2 0.0491
MA0105.1 0.795
MA0106.1 0.726
MA0107.1 1.17997e-11
MA0108.2 2.84228e-6
MA0111.1 0.142
MA0112.2 0.0442
MA0113.1 0.937
MA0114.1 0.0828
MA0115.1 0.253
MA0116.1 0.00194
MA0117.1 0.322
MA0119.1 0.572
MA0122.1 0.886
MA0124.1 0.513
MA0125.1 0.0951
MA0131.1 0.866
MA0135.1 0.0927
MA0136.1 8.43568e-7
MA0137.2 2.67507e-13
MA0138.2 0.0276
MA0139.1 0.419
MA0140.1 0.599
MA0141.1 0.0329
MA0142.1 0.0249
MA0143.1 0.014
MA0144.1 1.03229e-8
MA0145.1 0.0262
MA0146.1 0.951
MA0147.1 0.0061
MA0148.1 0.291
MA0149.1 0.302
MA0150.1 0.468
MA0152.1 0.0125
MA0153.1 1.37063e-5
MA0154.1 0.436
MA0155.1 0.622
MA0156.1 8.10408e-10
MA0157.1 0.0403
MA0159.1 0.833
MA0160.1 0.278
MA0162.1 0.909
MA0163.1 0.0951
MA0164.1 0.795
MA0258.1 0.0155
MA0259.1 0.77



FANTOM5 phase1 novel unique motifsSummary: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 in 169 novel and unique motifs. Their association to the promoter expression is evaluated in the same way to the JASPAR motif above
Analyst: Michiel de Hoon


link to dataset.
data

library id: CNhs13209

Novel motif P-value
1 0.118
10 0.257
100 0.884
101 0.368
102 0.749
103 0.172
104 0.78
105 0.551
106 0.141
107 0.33
108 0.715
109 0.949
11 0.261
110 0.849
111 0.0917
112 0.628
113 0.858
114 0.0392
115 0.376
116 0.325
117 0.51
118 0.304
119 0.414
12 0.802
120 0.96
121 0.065
122 0.752
123 0.156
124 0.173
125 0.233
126 0.617
127 0.477
128 0.108
129 0.418
13 0.0632
130 0.14
131 0.953
132 0.71
133 0.912
134 0.877
135 0.0378
136 0.0207
137 0.574
138 0.126
139 0.0657
14 0.916
140 0.287
141 0.961
142 0.666
143 0.36
144 0.702
145 0.91
146 0.75
147 0.959
148 0.907
149 0.576
15 0.529
150 0.299
151 0.188
152 0.00872
153 0.346
154 0.96
155 0.269
156 2.80876e-40
157 0.236
158 0.976
159 0.0605
160 0.148
161 0.201
162 0.528
163 0.552
164 0.966
165 0.166
166 0.658
167 0.278
168 0.703
169 0.365
17 0.872
18 0.0308
19 0.92
2 0.974
20 0.275
21 0.29
22 0.931
23 0.851
24 0.676
25 0.536
26 0.323
27 0.157
28 0.912
29 0.193
3 0.375
30 0.823
31 0.335
32 0.0309
33 0.362
34 0.731
35 3.04646e-4
36 0.274
37 0.412
38 0.595
39 0.843
4 0.495
40 0.375
41 0.603
42 0.411
43 0.289
44 0.0679
45 0.795
46 0.257
47 0.272
48 0.347
49 0.19
5 0.638
50 0.513
51 0.428
52 0.52
53 0.789
54 0.586
55 0.272
56 0.809
57 0.0833
58 0.492
59 0.445
6 0.28
60 0.568
61 0.983
62 0.137
63 0.772
64 0.129
65 0.547
66 0.755
67 0.441
68 0.658
69 0.141
7 0.818
70 0.297
71 0.194
72 0.685
73 0.0714
74 0.0934
75 0.783
76 0.456
77 0.238
78 0.448
79 0.548
8 0.011
80 0.792
81 0.258
82 0.129
83 0.744
84 0.613
85 0.448
86 0.945
87 0.0186
88 0.758
89 0.554
9 0.901
90 0.131
91 0.279
92 0.417
93 0.538
94 0.00747
95 0.287
96 0.0524
97 0.572
98 0.556
99 0.988



de novo motifs identified by HOMER in promoters active in this sampleSummary:The result of HOMER in this sample is shown.
Analyst:NA
library id: CNhs13209


FANTOM5 (FF) ontology


Direct parent terms


Ancestor terms (non development)Summary:Connected ontology terms with is_a, part_of or located_in relationship
Analyst: Hideya Kawaji

link to source data
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)Summary:Connected ontology terms with develops_from, derives_from or preceded_by relationship
Analyst: Hideya Kawaji

link to source data
data

CL:0000134 (mesenchymal cell)
CL:0000222 (mesodermal cell)
CL:0000223 (endodermal cell)