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FF:583-22A8

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Name:amnion, adult pregnant day17.5
Species:Mouse (Mus musculus)
Library ID:CNhs10488
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
tissueamnion
dev stage17.5 days pregnant adult
sexfemale
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  SAMD00004853
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs10488 CAGE DRX008934 DRR009808
Accession ID Mm9

Library idBAMCTSS
CNhs10488 DRZ001233 DRZ002616
Accession ID Mm10

Library idBAMCTSS
CNhs10488 DRZ012583 DRZ013966
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

CNhs10488

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 --0.0355
1001 0.0685
1002 0.0481
1003 --0.138
1004 0
1005 0.0879
1006 --0.0215
1007 --0.0277
1008 0
1009 0.0853
101 --0.101
1010 0
1011 --0.263
1012 0
1013 0.0979
1014 0.476
1015 --0.19
1016 --0.138
1017 0
1018 0.445
1019 0
102 0
1020 0
1021 0
1022 --0.315
1023 0
1024 0.0846
1025 0.512
1026 0.0959
1027 --0.048
1028 0
1029 0.202
103 0.179
1030 0
1031 0.0426
1032 --0.0877
1033 0
1034 0.0959
1035 0
1036 --0.25
1037 0
1038 0.102
1039 0.0409
104 0
1040 0.178
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: CNhs10488

Jaspar motif P-value
MA0002.2 0.827
MA0003.1 0.234
MA0004.1 0.884
MA0006.1 0.0452
MA0007.1 0.014
MA0009.1 0.0918
MA0014.1 0.301
MA0017.1 8.48255e-13
MA0018.2 0.0977
MA0019.1 0.396
MA0024.1 2.69002e-7
MA0025.1 0.929
MA0027.1 0.169
MA0028.1 0.413
MA0029.1 1.87786e-4
MA0030.1 1.04612e-4
MA0031.1 8.60996e-7
MA0035.2 0.0467
MA0038.1 0.00717
MA0039.2 1.83139e-4
MA0040.1 0.188
MA0041.1 0.426
MA0042.1 0.553
MA0043.1 0.552
MA0046.1 9.87144e-29
MA0047.2 4.31631e-7
MA0048.1 0.644
MA0050.1 0.945
MA0051.1 0.576
MA0052.1 0.328
MA0055.1 0.315
MA0057.1 0.323
MA0058.1 0.666
MA0059.1 0.221
MA0060.1 9.97623e-12
MA0061.1 0.232
MA0062.2 0.683
MA0065.2 4.73482e-7
MA0066.1 0.787
MA0067.1 0.133
MA0068.1 0.744
MA0069.1 0.186
MA0070.1 0.643
MA0071.1 0.543
MA0072.1 0.906
MA0073.1 0.616
MA0074.1 0.174
MA0076.1 0.349
MA0077.1 0.0116
MA0078.1 0.0653
MA0079.2 0.00792
MA0080.2 0.904
MA0081.1 0.518
MA0083.1 0.172
MA0084.1 0.38
MA0087.1 0.159
MA0088.1 0.617
MA0090.1 1.1507e-6
MA0091.1 0.164
MA0092.1 0.0714
MA0093.1 0.905
MA0099.2 2.42319e-26
MA0100.1 0.234
MA0101.1 0.242
MA0102.2 0.19
MA0103.1 2.35328e-4
MA0104.2 0.0524
MA0105.1 0.923
MA0106.1 0.227
MA0107.1 0.132
MA0108.2 0.492
MA0111.1 0.664
MA0112.2 0.00729
MA0113.1 0.013
MA0114.1 1.3704e-12
MA0115.1 1.97441e-10
MA0116.1 0.754
MA0117.1 0.117
MA0119.1 0.629
MA0122.1 0.624
MA0124.1 0.227
MA0125.1 0.334
MA0131.1 0.983
MA0135.1 0.597
MA0136.1 0.932
MA0137.2 2.90568e-7
MA0138.2 0.716
MA0139.1 0.662
MA0140.1 0.481
MA0141.1 0.347
MA0142.1 0.113
MA0143.1 0.225
MA0144.1 5.24908e-5
MA0145.1 0.0126
MA0146.1 0.021
MA0147.1 0.0365
MA0148.1 1.44936e-7
MA0149.1 0.29
MA0150.1 0.0115
MA0152.1 0.85
MA0153.1 3.75339e-17
MA0154.1 0.0142
MA0155.1 0.63
MA0156.1 0.764
MA0157.1 9.10388e-5
MA0159.1 0.0189
MA0160.1 0.202
MA0162.1 0.507
MA0163.1 0.324
MA0164.1 0.0783
MA0258.1 0.194
MA0259.1 0.567



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: CNhs10488

Novel motif P-value
1 0.826
10 0.605
100 0.305
101 0.493
102 0.564
103 0.196
104 0.498
105 0.79
106 0.0384
107 0.0546
108 0.785
109 0.126
11 0.334
110 0.366
111 0.271
112 0.0874
113 0.595
114 0.0725
115 0.484
116 0.563
117 0.185
118 0.216
119 0.006
12 0.784
120 0.543
121 0.38
122 0.493
123 0.483
124 0.184
125 0.07
126 0.392
127 0.682
128 0.0156
129 0.443
13 5.37441e-4
130 0.0337
131 0.504
132 0.732
133 0.528
134 0.806
135 0.0846
136 0.00273
137 0.54
138 0.0441
139 0.0488
14 0.467
140 0.0875
141 0.1
142 0.817
143 0.776
144 0.652
145 0.246
146 0.258
147 0.462
148 0.743
149 0.0185
15 0.179
150 0.0783
151 0.765
152 0.0178
153 0.641
154 0.971
155 0.414
156 0.0684
157 0.587
158 0.195
159 0.115
160 0.345
161 0.0809
162 0.889
163 0.733
164 0.0288
165 0.505
166 0.0288
167 0.243
168 0.29
169 0.0212
17 0.0198
18 0.896
19 0.0135
2 0.132
20 0.506
21 0.221
22 0.0448
23 0.0476
24 0.296
25 0.598
26 0.0947
27 0.709
28 0.307
29 0.453
3 0.18
30 0.386
31 0.766
32 0.0832
33 0.539
34 0.763
35 0.289
36 0.572
37 0.0804
38 0.483
39 0.754
4 0.118
40 0.316
41 0.516
42 0.62
43 0.0702
44 0.482
45 0.098
46 0.51
47 0.564
48 0.411
49 0.123
5 0.851
50 0.374
51 0.687
52 0.19
53 0.884
54 0.333
55 0.468
56 0.415
57 0.394
58 0.705
59 0.124
6 0.856
60 0.0549
61 0.26
62 0.508
63 0.825
64 0.921
65 0.404
66 0.196
67 0.544
68 0.0821
69 0.148
7 0.319
70 0.0163
71 0.502
72 0.583
73 0.0503
74 0.799
75 0.26
76 0.609
77 0.0448
78 6.05475e-4
79 0.532
8 0.442
80 0.821
81 0.339
82 0.139
83 0.661
84 0.443
85 0.159
86 0.464
87 0.15
88 0.601
89 0.649
9 0.704
90 0.435
91 0.414
92 0.0507
93 0.247
94 0.14
95 0.188
96 0.917
97 0.382
98 0.401
99 0.593



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: CNhs10488


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)
0007023 (adult organism)
0000305 (amnion)
0000479 (tissue)
0004121 (ectoderm-derived structure)
0000064 (organ part)
0000062 (organ)
0004120 (mesoderm-derived structure)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0004923 (organ component layer)
0005631 (extraembryonic membrane)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0000478 (extraembryonic structure)
0010317 (germ layer / neural crest derived structure)
0000158 (membranous layer)

FF: FANTOM5
0000102 (sample by type)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000998 (adult tissue sample)
0000004 (tissue sample)
0000317 (mouse pregnant tissue sample)
0000322 (mouse pregnant day 17.5 sample)
0011386 (mouse amnion - adult pregnant day17.5 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:0004871 (somatic layer of lateral plate mesoderm)
UBERON:0002532 (epiblast (generic))
UBERON:0006601 (presumptive ectoderm)
UBERON:0006603 (presumptive mesoderm)
UBERON:0010316 (germ layer / neural crest)