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FF:539-13I7

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Name:placenta, adult pregnant day10
Species:Mouse (Mus musculus)
Library ID:CNhs10472
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 stage10 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  SAMD00005919
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs10472 CAGE DRX009074 DRR009948
Accession ID Mm9

Library idBAMCTSS
CNhs10472 DRZ001373 DRZ002756
Accession ID Mm10

Library idBAMCTSS
CNhs10472 DRZ012723 DRZ014106
Download raw sequence, BAM & CTSS
Mm9
FastaBAMCTSS
downloaddownloaddonwload
Mm10
BAMCTSS
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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

CNhs10472

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 --0.0258
1001 0.0641
1002 0.0147
1003 --0.175
1004 0.129
1005 0.094
1006 --0.0595
1007 0.00944
1008 0
1009 0.0343
101 0.092
1010 0
1011 --0.016
1012 0
1013 0.177
1014 0.00644
1015 --0.115
1016 --0.234
1017 0
1018 0.316
1019 0
102 0
1020 0
1021 0
1022 --0.124
1023 0
1024 0.0916
1025 0.0916
1026 0
1027 --0.048
1028 0
1029 0.105
103 0
1030 0
1031 0.0645
1032 --0.213
1033 --0.0665
1034 0
1035 0
1036 --0.0518
1037 0
1038 --0.127
1039 --0.0886
104 0
1040 0.0719
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: CNhs10472

Jaspar motif P-value
MA0002.2 0.0682
MA0003.1 0.08
MA0004.1 0.411
MA0006.1 0.0393
MA0007.1 0.817
MA0009.1 0.5
MA0014.1 0.358
MA0017.1 0.0312
MA0018.2 0.924
MA0019.1 0.321
MA0024.1 0.53
MA0025.1 0.354
MA0027.1 0.00607
MA0028.1 0.352
MA0029.1 8.2156e-6
MA0030.1 0.332
MA0031.1 0.0545
MA0035.2 0.0476
MA0038.1 0.413
MA0039.2 6.56889e-5
MA0040.1 0.779
MA0041.1 0.45
MA0042.1 0.732
MA0043.1 0.425
MA0046.1 0.689
MA0047.2 0.593
MA0048.1 0.2
MA0050.1 0.021
MA0051.1 0.132
MA0052.1 0.00158
MA0055.1 0.0294
MA0057.1 0.152
MA0058.1 0.16
MA0059.1 0.923
MA0060.1 0.171
MA0061.1 0.233
MA0062.2 0.0147
MA0065.2 0.0543
MA0066.1 0.78
MA0067.1 0.632
MA0068.1 0.328
MA0069.1 0.509
MA0070.1 0.385
MA0071.1 0.922
MA0072.1 0.731
MA0073.1 0.378
MA0074.1 0.469
MA0076.1 0.531
MA0077.1 0.0728
MA0078.1 0.235
MA0079.2 0.00481
MA0080.2 3.74983e-4
MA0081.1 0.596
MA0083.1 0.538
MA0084.1 0.126
MA0087.1 0.61
MA0088.1 0.19
MA0090.1 0.0482
MA0091.1 0.0874
MA0092.1 0.626
MA0093.1 0.383
MA0099.2 3.74413e-30
MA0100.1 0.317
MA0101.1 0.052
MA0102.2 0.631
MA0103.1 0.881
MA0104.2 0.551
MA0105.1 0.687
MA0106.1 0.0756
MA0107.1 0.0678
MA0108.2 5.07198e-5
MA0111.1 0.263
MA0112.2 0.0137
MA0113.1 0.854
MA0114.1 0.0202
MA0115.1 0.0282
MA0116.1 0.92
MA0117.1 0.468
MA0119.1 0.0618
MA0122.1 0.611
MA0124.1 0.137
MA0125.1 0.869
MA0131.1 0.933
MA0135.1 0.6
MA0136.1 0.00117
MA0137.2 0.0457
MA0138.2 0.0795
MA0139.1 0.802
MA0140.1 0.926
MA0141.1 0.678
MA0142.1 0.0535
MA0143.1 0.111
MA0144.1 0.00277
MA0145.1 0.0334
MA0146.1 0.0674
MA0147.1 0.638
MA0148.1 0.0791
MA0149.1 0.111
MA0150.1 7.12013e-4
MA0152.1 0.66
MA0153.1 0.297
MA0154.1 0.0696
MA0155.1 0.897
MA0156.1 1.95255e-4
MA0157.1 0.245
MA0159.1 0.0517
MA0160.1 0.335
MA0162.1 0.701
MA0163.1 0.955
MA0164.1 0.0254
MA0258.1 0.182
MA0259.1 0.742



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: CNhs10472

Novel motif P-value
1 0.603
10 0.693
100 0.718
101 0.134
102 0.133
103 0.552
104 0.732
105 0.405
106 0.0529
107 0.0653
108 0.405
109 0.421
11 0.896
110 0.521
111 0.399
112 0.00618
113 0.948
114 0.382
115 0.823
116 0.739
117 0.0766
118 0.756
119 0.101
12 0.877
120 0.964
121 0.192
122 0.631
123 0.0141
124 0.0457
125 0.502
126 0.483
127 0.801
128 0.283
129 0.826
13 0.0028
130 0.0439
131 0.921
132 0.704
133 0.437
134 0.283
135 0.147
136 0.0159
137 0.0961
138 0.326
139 0.184
14 0.787
140 0.674
141 0.394
142 0.455
143 0.235
144 0.45
145 0.821
146 0.834
147 0.0376
148 0.319
149 0.802
15 0.25
150 0.0885
151 0.957
152 0.00983
153 0.473
154 0.646
155 0.622
156 0.111
157 0.151
158 0.00768
159 0.498
160 0.495
161 0.154
162 0.788
163 0.0323
164 0.0201
165 0.838
166 0.735
167 0.0649
168 0.279
169 0.0444
17 0.119
18 0.697
19 0.0222
2 0.183
20 0.277
21 0.489
22 0.035
23 0.407
24 0.103
25 0.848
26 0.594
27 0.44
28 0.504
29 0.053
3 0.78
30 0.334
31 0.309
32 0.686
33 0.629
34 0.729
35 0.0281
36 0.473
37 0.0381
38 0.791
39 0.978
4 0.188
40 0.83
41 0.997
42 0.801
43 0.572
44 0.709
45 0.044
46 0.718
47 0.677
48 0.81
49 0.545
5 0.92
50 0.101
51 0.949
52 0.259
53 0.891
54 0.793
55 0.515
56 0.971
57 0.338
58 0.645
59 0.284
6 0.461
60 0.289
61 0.209
62 0.512
63 0.794
64 0.499
65 0.765
66 0.722
67 0.626
68 0.525
69 0.213
7 0.487
70 0.186
71 0.787
72 0.298
73 0.0054
74 0.837
75 0.281
76 0.887
77 0.392
78 0.00392
79 0.177
8 0.326
80 0.69
81 0.585
82 0.971
83 0.356
84 0.664
85 0.524
86 0.594
87 0.0803
88 0.537
89 0.619
9 0.61
90 0.198
91 0.195
92 0.713
93 0.619
94 0.0258
95 0.225
96 0.979
97 0.72
98 0.69
99 0.493



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: CNhs10472


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)
0000320 (mouse pregnant day 10 sample)
0011381 (mouse placenta- adult pregnant day10 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)