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{{f5samples
 
{{f5samples
 
|DRA_sample_Accession=CAGE@SAMD00005998
 
|DRA_sample_Accession=CAGE@SAMD00005998
|accession_numbers=CAGE;DRX008858;DRR009730;DRZ001155;DRZ002540
+
|accession_numbers=CAGE;DRX008858;DRR009730;DRZ001155;DRZ002540;DRZ012505;DRZ013890
 
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0002107,UBERON:0002100,UBERON:0001007,UBERON:0004119,UBERON:0000062,UBERON:0000475,UBERON:0000061,UBERON:0000465,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0009569,UBERON:0002368,UBERON:0005177,UBERON:0002365,UBERON:0005172,UBERON:0006925,UBERON:0002530,UBERON:0010317,UBERON:0005173,UBERON:0002417,UBERON:0000949,UBERON:0002330,UBERON:0000916,UBERON:0002423
 
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0002107,UBERON:0002100,UBERON:0001007,UBERON:0004119,UBERON:0000062,UBERON:0000475,UBERON:0000061,UBERON:0000465,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0009569,UBERON:0002368,UBERON:0005177,UBERON:0002365,UBERON:0005172,UBERON:0006925,UBERON:0002530,UBERON:0010317,UBERON:0005173,UBERON:0002417,UBERON:0000949,UBERON:0002330,UBERON:0000916,UBERON:0002423
 
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000548,CL:0000066,CL:0002371,CL:0000181,CL:0000417,CL:0000668,CL:0000412,CL:0000255,CL:0000182
 
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000548,CL:0000066,CL:0002371,CL:0000181,CL:0000417,CL:0000668,CL:0000412,CL:0000255,CL:0000182

Latest revision as of 11:57, 10 August 2017


Name:Mouse hepatocyte, donor3
Species:Mouse (Mus musculus)
Library ID:CNhs12615
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
strainCD-1
tissueliver
dev stageNA
sexmale
ageNA
cell typehepatocyte
cell lineNA
companyxenotech
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberM1000.H15
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-TRIzol-ethanol-v1.0

Accession numbers
MethodSample accession id
CAGE  SAMD00005998
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs12615 CAGE DRX008858 DRR009730
Accession ID Mm9

Library idBAMCTSS
CNhs12615 DRZ001155 DRZ002540
Accession ID Mm10

Library idBAMCTSS
CNhs12615 DRZ012505 DRZ013890
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

CNhs12615

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 0.115
1001 0.217
1002 --0.116
1003 0.151
1004 0
1005 0
1006 --0.132
1007 --0.282
1008 0
1009 --0.00265
101 --0.116
1010 0
1011 --0.275
1012 0
1013 0.633
1014 --0.0874
1015 --0.342
1016 --0.261
1017 0
1018 0
1019 0
102 0
1020 0.679
1021 0
1022 0.503
1023 0
1024 --0.0899
1025 0
1026 0
1027 0
1028 0
1029 --0.0318
103 --0.0887
1030 0
1031 --0.875
1032 --0.522
1033 --0.0752
1034 0.787
1035 0
1036 --0.603
1037 0
1038 --0.298
1039 0.756
104 0
1040 --0.256
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: CNhs12615

Jaspar motif P-value
MA0002.2 0.103
MA0003.1 0.753
MA0004.1 0.361
MA0006.1 0.425
MA0007.1 0.127
MA0009.1 0.947
MA0014.1 0.125
MA0017.1 2.18793e-17
MA0018.2 3.86816e-4
MA0019.1 0.901
MA0024.1 3.47234e-4
MA0025.1 0.436
MA0027.1 0.927
MA0028.1 0.561
MA0029.1 0.563
MA0030.1 0.0245
MA0031.1 0.00697
MA0035.2 0.0793
MA0038.1 0.0755
MA0039.2 0.356
MA0040.1 0.477
MA0041.1 0.331
MA0042.1 0.793
MA0043.1 0.172
MA0046.1 4.24853e-75
MA0047.2 3.20429e-6
MA0048.1 0.276
MA0050.1 0.662
MA0051.1 0.811
MA0052.1 0.00688
MA0055.1 0.428
MA0057.1 0.611
MA0058.1 0.265
MA0059.1 0.0147
MA0060.1 1.95194e-5
MA0061.1 0.664
MA0062.2 0.824
MA0065.2 9.38401e-13
MA0066.1 0.00707
MA0067.1 0.225
MA0068.1 0.427
MA0069.1 0.149
MA0070.1 0.278
MA0071.1 1.58017e-5
MA0072.1 7.403e-5
MA0073.1 0.85
MA0074.1 0.155
MA0076.1 0.984
MA0077.1 0.0265
MA0078.1 0.739
MA0079.2 0.129
MA0080.2 5.6211e-5
MA0081.1 0.133
MA0083.1 0.00448
MA0084.1 0.678
MA0087.1 0.256
MA0088.1 0.2
MA0090.1 0.551
MA0091.1 0.883
MA0092.1 0.306
MA0093.1 0.395
MA0099.2 0.838
MA0100.1 0.681
MA0101.1 0.835
MA0102.2 0.547
MA0103.1 0.0418
MA0104.2 0.301
MA0105.1 0.0137
MA0106.1 0.023
MA0107.1 0.37
MA0108.2 3.83941e-5
MA0111.1 0.861
MA0112.2 6.06022e-6
MA0113.1 0.303
MA0114.1 4.81164e-17
MA0115.1 8.63658e-12
MA0116.1 0.0215
MA0117.1 0.623
MA0119.1 0.0462
MA0122.1 0.177
MA0124.1 0.807
MA0125.1 0.441
MA0131.1 0.86
MA0135.1 0.551
MA0136.1 4.21035e-4
MA0137.2 0.118
MA0138.2 0.533
MA0139.1 0.0811
MA0140.1 0.704
MA0141.1 1.28718e-6
MA0142.1 0.27
MA0143.1 0.164
MA0144.1 0.414
MA0145.1 0.158
MA0146.1 0.0782
MA0147.1 0.21
MA0148.1 4.99283e-9
MA0149.1 0.0041
MA0150.1 0.00385
MA0152.1 0.779
MA0153.1 6.88402e-55
MA0154.1 0.0956
MA0155.1 0.823
MA0156.1 0.0345
MA0157.1 0.00887
MA0159.1 5.56982e-4
MA0160.1 4.14715e-5
MA0162.1 0.414
MA0163.1 3.12745e-4
MA0164.1 0.931
MA0258.1 3.89487e-4
MA0259.1 0.951



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: CNhs12615

Novel motif P-value
1 0.0562
10 0.105
100 0.398
101 0.868
102 0.302
103 0.00282
104 0.7
105 0.796
106 0.105
107 0.185
108 0.973
109 0.0767
11 0.0586
110 0.0549
111 0.00141
112 0.0135
113 0.9
114 0.00123
115 0.492
116 0.989
117 0.0755
118 0.336
119 0.17
12 0.483
120 0.925
121 0.934
122 0.739
123 0.367
124 0.43
125 0.908
126 0.0865
127 0.831
128 0.0669
129 0.875
13 0.00128
130 0.434
131 0.982
132 0.399
133 0.714
134 0.997
135 0.595
136 0.755
137 0.905
138 0.815
139 0.212
14 0.619
140 0.179
141 0.44
142 0.0509
143 0.405
144 0.631
145 0.15
146 0.747
147 0.353
148 0.482
149 0.0671
15 0.186
150 0.261
151 0.474
152 0.32
153 0.435
154 0.939
155 0.391
156 0.723
157 0.804
158 0.937
159 0.804
160 0.283
161 0.666
162 0.304
163 0.592
164 0.131
165 0.753
166 0.532
167 0.112
168 0.99
169 0.00194
17 0.0483
18 0.633
19 0.128
2 0.959
20 0.41
21 0.927
22 0.193
23 0.294
24 0.227
25 0.582
26 0.00914
27 0.75
28 0.437
29 0.147
3 0.0794
30 0.9
31 0.307
32 0.122
33 0.446
34 0.875
35 0.117
36 0.0984
37 0.0593
38 0.407
39 0.247
4 0.541
40 0.275
41 0.961
42 0.37
43 0.0808
44 6.67159e-4
45 0.879
46 0.0891
47 0.334
48 0.151
49 0.0476
5 0.122
50 0.917
51 0.337
52 0.755
53 0.466
54 0.4
55 0.478
56 0.424
57 0.421
58 0.37
59 0.292
6 0.811
60 0.211
61 0.391
62 0.0895
63 0.153
64 0.447
65 0.234
66 0.707
67 0.72
68 0.139
69 0.658
7 0.245
70 0.0104
71 0.0221
72 0.787
73 0.112
74 0.465
75 0.0111
76 0.606
77 0.373
78 0.0629
79 0.622
8 0.0063
80 0.827
81 0.88
82 0.0375
83 0.379
84 0.0813
85 0.0259
86 0.069
87 0.581
88 0.73
89 0.177
9 0.929
90 0.0432
91 0.371
92 0.127
93 0.0991
94 0.718
95 0.254
96 0.204
97 0.871
98 0.394
99 0.255



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: CNhs12615


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)
0000181 (metabolising cell)
0000417 (endopolyploid cell)
0000668 (parenchymal cell)
0000412 (polyploid cell)
0000255 (eukaryotic cell)
0000182 (hepatocyte)

UBERON: Anatomy
0000468 (multi-cellular organism)
0002107 (liver)
0002100 (trunk)
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)
0000109 (mouse hepatocyte 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:0000223 (endodermal cell)