Personal tools

FF:499-43G4

From FANTOM5_SSTAR

Jump to: navigation, search


Name:liver, embryo E18
Species:Mouse (Mus musculus)
Library ID:CNhs10579
Sample type:developmental
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 stage18 days embryo
sexmixture
ageNA
cell typeCELL MIXTURE - tissue sample
cell lineNA
companyNA
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberNA
sample typeNA
extraction protocol (Details)NA

Accession numbers
MethodSample accession id
CAGE  SAMD00005697
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs10579 CAGE DRX009021 DRR009895
Accession ID Mm9

Library idBAMCTSS
CNhs10579 DRZ001320 DRZ002703
Accession ID Mm10

Library idBAMCTSS
CNhs10579 DRZ012670 DRZ014053
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

CNhs10579

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 0
1001 --0.0749
1002 --0.116
1003 --0.123
1004 0
1005 0.345
1006 --0.071
1007 --0.126
1008 0
1009 --0.0572
101 0.0025
1010 0
1011 --0.298
1012 0
1013 0.276
1014 0.11
1015 --0.203
1016 --0.2
1017 0
1018 0
1019 0
102 0
1020 0
1021 0.11
1022 0.128
1023 0
1024 --0.0297
1025 0.436
1026 0
1027 0
1028 0
1029 --0.00495
103 --0.0528
1030 0
1031 --0.139
1032 --0.177
1033 0
1034 0.638
1035 0
1036 0.0866
1037 0
1038 --0.101
1039 0.223
104 0
1040 --0.106
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: CNhs10579

Jaspar motif P-value
MA0002.2 0.00198
MA0003.1 0.216
MA0004.1 0.872
MA0006.1 0.241
MA0007.1 0.481
MA0009.1 0.553
MA0014.1 0.54
MA0017.1 1.58421e-14
MA0018.2 3.86768e-5
MA0019.1 0.286
MA0024.1 0.644
MA0025.1 0.307
MA0027.1 0.339
MA0028.1 0.866
MA0029.1 0.0289
MA0030.1 0.00244
MA0031.1 0.00268
MA0035.2 1.97636e-10
MA0038.1 0.504
MA0039.2 0.0151
MA0040.1 0.0603
MA0041.1 0.538
MA0042.1 0.961
MA0043.1 0.142
MA0046.1 1.07504e-62
MA0047.2 3.25368e-10
MA0048.1 0.278
MA0050.1 0.00234
MA0051.1 0.0127
MA0052.1 9.10054e-4
MA0055.1 0.326
MA0057.1 0.486
MA0058.1 0.755
MA0059.1 0.315
MA0060.1 0.314
MA0061.1 0.147
MA0062.2 0.922
MA0065.2 3.181e-8
MA0066.1 0.0904
MA0067.1 0.223
MA0068.1 0.716
MA0069.1 0.165
MA0070.1 0.374
MA0071.1 0.0202
MA0072.1 0.00583
MA0073.1 0.732
MA0074.1 0.383
MA0076.1 0.454
MA0077.1 0.0577
MA0078.1 0.296
MA0079.2 0.366
MA0080.2 9.238e-6
MA0081.1 0.356
MA0083.1 0.226
MA0084.1 0.136
MA0087.1 0.0728
MA0088.1 0.147
MA0090.1 0.878
MA0091.1 0.93
MA0092.1 0.0985
MA0093.1 0.901
MA0099.2 0.777
MA0100.1 0.781
MA0101.1 0.566
MA0102.2 0.00622
MA0103.1 0.243
MA0104.2 0.885
MA0105.1 0.00349
MA0106.1 0.376
MA0107.1 0.642
MA0108.2 0.261
MA0111.1 0.782
MA0112.2 1.53651e-4
MA0113.1 0.184
MA0114.1 4.65229e-13
MA0115.1 3.93668e-7
MA0116.1 0.00902
MA0117.1 0.996
MA0119.1 0.00301
MA0122.1 0.35
MA0124.1 0.783
MA0125.1 0.499
MA0131.1 0.805
MA0135.1 0.712
MA0136.1 0.00218
MA0137.2 0.159
MA0138.2 0.997
MA0139.1 0.162
MA0140.1 1.13367e-25
MA0141.1 0.0055
MA0142.1 0.288
MA0143.1 0.242
MA0144.1 0.332
MA0145.1 0.194
MA0146.1 0.092
MA0147.1 0.98
MA0148.1 2.91512e-11
MA0149.1 0.0381
MA0150.1 0.00892
MA0152.1 0.735
MA0153.1 2.24986e-47
MA0154.1 0.0171
MA0155.1 0.659
MA0156.1 0.0266
MA0157.1 0.00364
MA0159.1 0.00695
MA0160.1 0.00363
MA0162.1 0.321
MA0163.1 4.21991e-4
MA0164.1 0.611
MA0258.1 0.016
MA0259.1 0.857



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: CNhs10579

Novel motif P-value
1 0.159
10 0.24
100 0.718
101 0.813
102 0.216
103 0.0152
104 0.646
105 0.442
106 0.0306
107 0.0261
108 0.46
109 0.0241
11 0.105
110 0.0864
111 0.102
112 0.0106
113 0.92
114 0.134
115 0.938
116 0.851
117 0.052
118 0.141
119 0.0934
12 0.592
120 0.621
121 0.735
122 0.583
123 0.179
124 0.299
125 0.592
126 0.306
127 0.328
128 0.0341
129 0.747
13 6.06525e-4
130 0.429
131 0.0678
132 0.895
133 0.785
134 0.842
135 0.981
136 0.211
137 0.316
138 0.446
139 0.987
14 0.695
140 0.154
141 0.839
142 0.237
143 0.204
144 0.93
145 0.0593
146 0.223
147 0.936
148 0.6
149 0.604
15 0.0937
150 0.149
151 0.303
152 0.154
153 0.36
154 0.648
155 0.556
156 0.0431
157 0.86
158 0.811
159 0.287
160 0.0622
161 0.3
162 0.698
163 0.618
164 0.014
165 0.505
166 0.924
167 0.698
168 0.71
169 0.00732
17 0.0815
18 0.819
19 0.0765
2 0.639
20 0.545
21 0.949
22 0.137
23 0.17
24 0.227
25 0.734
26 3.52945e-4
27 0.352
28 0.396
29 0.0784
3 0.025
30 0.686
31 0.47
32 0.348
33 0.182
34 0.745
35 0.804
36 0.0667
37 0.119
38 0.399
39 0.457
4 0.54
40 0.0754
41 1
42 0.107
43 0.0505
44 0.182
45 0.66
46 0.0731
47 0.274
48 0.187
49 0.0627
5 0.0958
50 0.43
51 0.333
52 0.218
53 0.781
54 0.377
55 0.347
56 0.332
57 0.671
58 0.539
59 0.0691
6 0.972
60 0.072
61 0.292
62 0.118
63 0.104
64 0.408
65 0.169
66 0.6
67 0.929
68 0.476
69 0.857
7 0.0795
70 0.403
71 0.0335
72 0.416
73 0.2
74 0.608
75 0.0398
76 0.988
77 0.395
78 0.0133
79 0.812
8 0.0422
80 0.0201
81 0.848
82 0.208
83 0.363
84 0.86
85 0.208
86 0.255
87 0.106
88 0.755
89 0.37
9 0.528
90 0.363
91 0.148
92 0.154
93 0.726
94 0.728
95 0.087
96 0.189
97 0.854
98 0.142
99 0.185



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: CNhs10579


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

UBERON: Anatomy
0000468 (multi-cellular organism)
0000922 (embryo)
0002107 (liver)
0002100 (trunk)
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)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000999 (fetal tissue sample)
0000292 (embryonic day sample - mouse)
0000004 (tissue sample)
0000302 (mouse embryonic day 18 sample)
0011376 (mouse liver- embryo E18 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

UBERON:0001041 (foregut)
UBERON:0002532 (epiblast (generic))
UBERON:0006595 (presumptive endoderm)
UBERON:0003104 (mesenchyme)
UBERON:0004161 (septum transversum)
UBERON:0009497 (epithelium of foregut-midgut junction)
UBERON:0010316 (germ layer / neural crest)
FF:0000294 (mouse embryonic day 11 sample)