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FF:11825-124F7

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Name:Mouse hepatic Stellate Cells (lipocyte), donor1
Species:Mouse (Mus musculus)
Library ID:CNhs13196
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 typeadipocyte, lipocyte of liver
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  SAMD00005887
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs13196 CAGE DRX008856 DRR009728
Accession ID Mm9

Library idBAMCTSS
CNhs13196 DRZ001153 DRZ002538
Accession ID Mm10

Library idBAMCTSS
CNhs13196 DRZ012503 DRZ013888
Download raw sequence, BAM & CTSS
Mm9
FastaBAMCTSS
downloaddownloaddonwload
Mm10
BAMCTSS
downloaddonwload


Relative expression to median (log10)


Transcription factors with enriched expression in this sample
Ranked 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 sample
Ranked 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

CNhs13196

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 -0.0355
1001 -0.0749
1002 -0.0941
1003 -0.123
1004 0
1005 0
1006 0.00388
1007 -0.144
1008 0
1009 0.0795
101 -0.0954
1010 0
1011 -0.298
1012 0
1013 0.425
1014 -0.0874
1015 -0.316
1016 -0.379
1017 0
1018 0
1019 0
102 0
1020 0
1021 0.179
1022 0.485
1023 0
1024 0.13
1025 0.397
1026 0
1027 0
1028 0
1029 -0.176
103 -0.0787
1030 0
1031 0.0899
1032 -0.227
1033 -0.0665
1034 0.539
1035 0
1036 -0.369
1037 0
1038 0.0498
1039 0.773
104 0
1040 -0.0865
1041 0



Repeat families with enriched expression in this sample
Summary: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 motifs
Summary: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: CNhs13196
Jaspar motif P-value
MA0002.2 0.0803
MA0003.1 0.205
MA0004.1 0.865
MA0006.1 0.168
MA0007.1 0.412
MA0009.1 0.873
MA0014.1 0.195
MA0017.1 5.7771e-17
MA0018.2 0.00157
MA0019.1 0.598
MA0024.1 1.25216e-4
MA0025.1 0.09
MA0027.1 0.795
MA0028.1 0.889
MA0029.1 0.59
MA0030.1 0.0436
MA0031.1 0.00479
MA0035.2 0.0353
MA0038.1 0.654
MA0039.2 0.311
MA0040.1 0.196
MA0041.1 0.24
MA0042.1 0.552
MA0043.1 0.26
MA0046.1 3.97466e-67
MA0047.2 4.53176e-6
MA0048.1 0.608
MA0050.1 4.09488e-4
MA0051.1 3.75642e-5
MA0052.1 0.303
MA0055.1 0.465
MA0057.1 0.415
MA0058.1 0.603
MA0059.1 0.226
MA0060.1 1.16885e-4
MA0061.1 0.129
MA0062.2 0.808
MA0065.2 5.33758e-13
MA0066.1 0.157
MA0067.1 0.325
MA0068.1 0.417
MA0069.1 0.465
MA0070.1 0.411
MA0071.1 7.92163e-5
MA0072.1 6.66368e-6
MA0073.1 0.916
MA0074.1 0.325
MA0076.1 0.55
MA0077.1 0.193
MA0078.1 0.999
MA0079.2 0.393
MA0080.2 0.139
MA0081.1 0.605
MA0083.1 0.305
MA0084.1 0.743
MA0087.1 0.792
MA0088.1 0.352
MA0090.1 0.268
MA0091.1 0.862
MA0092.1 0.151
MA0093.1 0.9
MA0099.2 0.579
MA0100.1 0.184
MA0101.1 0.211
MA0102.2 0.177
MA0103.1 0.427
MA0104.2 0.75
MA0105.1 0.0185
MA0106.1 0.274
MA0107.1 0.251
MA0108.2 0.656
MA0111.1 0.615
MA0112.2 1.40006e-4
MA0113.1 0.528
MA0114.1 1.09405e-15
MA0115.1 9.17531e-8
MA0116.1 0.191
MA0117.1 0.648
MA0119.1 0.021
MA0122.1 0.811
MA0124.1 0.725
MA0125.1 0.195
MA0131.1 0.594
MA0135.1 0.276
MA0136.1 0.259
MA0137.2 7.45415e-4
MA0138.2 0.396
MA0139.1 0.175
MA0140.1 0.566
MA0141.1 6.26011e-5
MA0142.1 0.124
MA0143.1 0.437
MA0144.1 0.0138
MA0145.1 0.0346
MA0146.1 0.246
MA0147.1 0.853
MA0148.1 6.03729e-7
MA0149.1 0.0153
MA0150.1 0.00847
MA0152.1 0.355
MA0153.1 1.82777e-52
MA0154.1 0.066
MA0155.1 0.706
MA0156.1 0.431
MA0157.1 0.00106
MA0159.1 0.00109
MA0160.1 3.27555e-4
MA0162.1 0.176
MA0163.1 5.97778e-4
MA0164.1 0.515
MA0258.1 0.0111
MA0259.1 0.534



FANTOM5 phase1 novel unique motifs
Summary: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: CNhs13196
Novel motif P-value
1 0.0986
10 0.202
100 0.762
101 0.664
102 0.215
103 0.00416
104 0.241
105 0.404
106 0.0213
107 0.0296
108 0.886
109 0.0232
11 0.0508
110 0.0792
111 0.0491
112 0.00569
113 0.632
114 0.0492
115 0.345
116 0.698
117 0.126
118 0.702
119 0.115
12 0.383
120 0.98
121 0.188
122 0.621
123 0.418
124 0.561
125 0.529
126 0.453
127 0.623
128 0.00676
129 0.736
13 7.90275e-4
130 0.979
131 0.107
132 0.533
133 0.745
134 0.547
135 0.366
136 0.46
137 0.763
138 0.534
139 0.716
14 0.441
140 0.537
141 0.131
142 0.329
143 0.506
144 0.95
145 0.133
146 0.534
147 0.52
148 0.985
149 0.133
15 0.177
150 0.22
151 0.59
152 0.0379
153 0.297
154 0.597
155 0.956
156 0.00489
157 0.872
158 0.482
159 0.25
160 0.253
161 0.419
162 0.438
163 0.255
164 0.117
165 0.186
166 0.159
167 0.527
168 0.695
169 0.00408
17 0.0162
18 0.828
19 0.0283
2 0.479
20 0.874
21 0.726
22 0.131
23 0.49
24 0.106
25 0.65
26 0.00767
27 0.695
28 0.542
29 0.457
3 0.0574
30 0.522
31 0.272
32 0.0969
33 0.272
34 0.642
35 0.711
36 0.0273
37 0.0302
38 0.409
39 0.304
4 0.934
40 0.0642
41 0.687
42 0.357
43 0.0742
44 0.0259
45 0.626
46 0.122
47 0.428
48 0.182
49 0.0817
5 0.166
50 0.547
51 0.357
52 0.275
53 0.69
54 0.383
55 0.519
56 0.346
57 0.818
58 0.38
59 0.076
6 0.853
60 0.0827
61 0.375
62 0.145
63 0.0969
64 0.518
65 0.159
66 0.794
67 0.879
68 0.0712
69 0.772
7 0.191
70 0.0254
71 0.0568
72 0.58
73 0.029
74 0.183
75 0.0383
76 0.887
77 0.257
78 0.0866
79 0.744
8 0.00802
80 0.49
81 0.608
82 0.0431
83 0.228
84 0.09
85 0.0385
86 0.215
87 0.0913
88 0.79
89 0.0382
9 0.954
90 0.183
91 0.286
92 0.0751
93 0.082
94 0.898
95 0.171
96 0.931
97 0.503
98 0.493
99 0.16



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

library id: CNhs13196


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)
0000003 (native cell)
0000548 (animal cell)
0000151 (secretory cell)
0002320 (connective tissue cell)
0002371 (somatic cell)
0000499 (stromal cell)
0000327 (extracellular matrix secreting cell)
0000255 (eukaryotic cell)
0000057 (fibroblast)
0000632 (hepatic stellate cell)

UBERON: Anatomy
0000468 (multi-cellular organism)
0002107 (liver)
0002100 (trunk)
0002384 (connective tissue)
0000479 (tissue)
0001007 (digestive system)
0004119 (endoderm-derived structure)
0000062 (organ)
0000475 (organism subdivision)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0009569 (subdivision of trunk)
0002368 (endocrine gland)
0005177 (trunk region element)
0002365 (exocrine gland)
0005172 (abdomen element)
0006925 (digestive gland)
0002530 (gland)
0010317 (germ layer / neural crest derived structure)
0005173 (abdominal segment element)
0002417 (abdominal segment of trunk)
0000949 (endocrine system)
0002330 (exocrine system)
0000916 (abdomen)
0002423 (hepatobiliary system)

FF: FANTOM5
0000102 (sample by type)
0000002 (in vivo cell sample)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000077 (hepatic stellate cell sample)
0011461 (Mouse hepatic Stellate Cells (lipocyte) 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)