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FF:577-18G3

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Name:placenta, adult pregnant day17
Species:Mouse (Mus musculus)
Library ID:CNhs10464
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
tissueplacenta
dev stage17 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  SAMD00005396
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs10464 CAGE DRX009075 DRR009949
Accession ID Mm9

Library idBAMCTSS
CNhs10464 DRZ001374 DRZ002757
Accession ID Mm10

Library idBAMCTSS
CNhs10464 DRZ012724 DRZ014107
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

CNhs10464

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 --0.0355
1001 0.00614
1002 --0.0327
1003 --0.156
1004 0
1005 0
1006 -9.149961e-4
1007 0.0104
1008 0
1009 0.156
101 --0.0736
1010 0
1011 --0.0489
1012 0
1013 0.135
1014 0.308
1015 --0.195
1016 --0.152
1017 0
1018 0.562
1019 0
102 0
1020 0
1021 0
1022 --0.162
1023 0
1024 0.0741
1025 0.356
1026 0
1027 --0.048
1028 0.0834
1029 0.168
103 0
1030 0
1031 --0.0143
1032 0.0829
1033 --0.0665
1034 0
1035 0
1036 --0.266
1037 0
1038 0.162
1039 --0.149
104 0
1040 0.143
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: CNhs10464

Jaspar motif P-value
MA0002.2 0.707
MA0003.1 0.169
MA0004.1 0.786
MA0006.1 0.118
MA0007.1 0.625
MA0009.1 0.0217
MA0014.1 0.119
MA0017.1 0.0189
MA0018.2 0.285
MA0019.1 0.135
MA0024.1 3.609e-4
MA0025.1 0.325
MA0027.1 0.655
MA0028.1 0.0684
MA0029.1 0.00252
MA0030.1 0.0215
MA0031.1 2.82025e-5
MA0035.2 0.0159
MA0038.1 0.623
MA0039.2 9.16484e-5
MA0040.1 0.469
MA0041.1 0.21
MA0042.1 0.726
MA0043.1 0.682
MA0046.1 0.453
MA0047.2 0.144
MA0048.1 0.442
MA0050.1 0.298
MA0051.1 0.0466
MA0052.1 0.0504
MA0055.1 0.0104
MA0057.1 0.282
MA0058.1 0.324
MA0059.1 0.268
MA0060.1 7.30053e-4
MA0061.1 0.941
MA0062.2 0.0109
MA0065.2 0.00531
MA0066.1 0.297
MA0067.1 0.0623
MA0068.1 0.876
MA0069.1 0.93
MA0070.1 0.619
MA0071.1 0.161
MA0072.1 0.731
MA0073.1 0.884
MA0074.1 0.905
MA0076.1 0.132
MA0077.1 0.136
MA0078.1 0.311
MA0079.2 0.00219
MA0080.2 0.968
MA0081.1 0.879
MA0083.1 0.0104
MA0084.1 0.62
MA0087.1 0.889
MA0088.1 0.416
MA0090.1 3.76677e-4
MA0091.1 0.0329
MA0092.1 0.933
MA0093.1 0.664
MA0099.2 1.44241e-23
MA0100.1 0.317
MA0101.1 0.574
MA0102.2 0.808
MA0103.1 0.0822
MA0104.2 0.14
MA0105.1 0.051
MA0106.1 0.383
MA0107.1 0.556
MA0108.2 0.00406
MA0111.1 0.535
MA0112.2 0.14
MA0113.1 0.637
MA0114.1 0.00245
MA0115.1 6.31628e-4
MA0116.1 0.351
MA0117.1 0.0272
MA0119.1 0.00947
MA0122.1 0.424
MA0124.1 0.154
MA0125.1 0.95
MA0131.1 0.773
MA0135.1 0.74
MA0136.1 0.559
MA0137.2 0.00157
MA0138.2 0.388
MA0139.1 0.993
MA0140.1 0.673
MA0141.1 0.478
MA0142.1 0.137
MA0143.1 0.326
MA0144.1 0.0111
MA0145.1 0.0718
MA0146.1 0.0105
MA0147.1 0.101
MA0148.1 0.707
MA0149.1 0.554
MA0150.1 0.00145
MA0152.1 0.207
MA0153.1 0.891
MA0154.1 0.186
MA0155.1 0.704
MA0156.1 0.243
MA0157.1 0.00329
MA0159.1 0.1
MA0160.1 0.182
MA0162.1 0.981
MA0163.1 0.454
MA0164.1 0.0322
MA0258.1 0.352
MA0259.1 0.492



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: CNhs10464

Novel motif P-value
1 0.496
10 0.779
100 0.678
101 0.803
102 0.174
103 0.809
104 0.77
105 0.935
106 0.426
107 0.294
108 0.972
109 0.672
11 0.84
110 0.682
111 0.365
112 0.144
113 0.565
114 0.758
115 0.839
116 0.362
117 0.174
118 0.919
119 0.29
12 0.585
120 0.149
121 0.264
122 0.74
123 0.0315
124 0.242
125 0.226
126 0.665
127 0.915
128 0.432
129 0.931
13 0.0147
130 0.0471
131 0.751
132 0.755
133 0.873
134 0.539
135 0.0795
136 9.28448e-4
137 0.416
138 0.017
139 0.153
14 0.943
140 0.132
141 0.864
142 0.63
143 0.979
144 0.626
145 0.889
146 0.614
147 0.286
148 0.507
149 0.878
15 0.8
150 0.103
151 0.321
152 0.0113
153 0.692
154 0.491
155 0.258
156 0.00505
157 0.359
158 0.0596
159 0.825
160 0.464
161 0.00682
162 0.737
163 0.207
164 0.141
165 0.907
166 0.0171
167 0.0888
168 0.215
169 0.079
17 0.108
18 0.969
19 0.0198
2 0.512
20 0.263
21 1
22 0.0365
23 0.0828
24 0.25
25 0.899
26 0.566
27 0.195
28 0.552
29 0.57
3 0.829
30 0.538
31 0.332
32 0.592
33 0.774
34 0.913
35 0.00474
36 0.15
37 0.0986
38 0.618
39 0.517
4 0.0417
40 0.637
41 0.609
42 0.812
43 0.948
44 0.841
45 0.124
46 0.619
47 0.506
48 0.612
49 0.63
5 0.629
50 0.245
51 0.905
52 0.453
53 0.72
54 0.633
55 0.291
56 0.942
57 0.191
58 0.609
59 0.775
6 0.996
60 0.233
61 0.299
62 0.546
63 0.455
64 0.372
65 0.698
66 0.829
67 0.469
68 0.188
69 0.223
7 0.569
70 0.119
71 0.253
72 0.574
73 0.00626
74 0.776
75 0.475
76 0.349
77 0.699
78 0.00868
79 0.291
8 0.0628
80 0.517
81 0.319
82 0.917
83 0.615
84 0.547
85 0.673
86 0.59
87 0.00236
88 0.326
89 0.825
9 0.719
90 0.0909
91 0.615
92 0.383
93 0.132
94 0.0126
95 0.203
96 0.878
97 0.499
98 0.383
99 0.213



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: CNhs10464


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)
0001987 (placenta)
0000479 (tissue)
0005156 (reproductive structure)
0004119 (endoderm-derived structure)
0000062 (organ)
0004120 (mesoderm-derived structure)
0000077 (mixed endoderm/mesoderm-derived structure)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000990 (reproductive system)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0000478 (extraembryonic structure)
0010317 (germ layer / neural crest derived structure)
0003100 (female organism)
0000474 (female reproductive system)

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)
0000321 (mouse pregnant day 17 sample)
0011384 (mouse placenta- adult pregnant day17 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:0002532 (epiblast (generic))
UBERON:0006595 (presumptive endoderm)
UBERON:0006603 (presumptive mesoderm)
UBERON:0005795 (embryonic uterus)
UBERON:0004872 (splanchnic layer of lateral plate mesoderm)
UBERON:0003124 (chorion)
UBERON:0010316 (germ layer / neural crest)