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FF:588-5H2

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Name:mammary gland, adult pregnant day19
Species:Mouse (Mus musculus)
Library ID:CNhs10476
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
tissuemammary gland
dev stage19 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  SAMD00004714
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs10476 CAGE DRX009045 DRR009919
Accession ID Mm9

Library idBAMCTSS
CNhs10476 DRZ001344 DRZ002727
Accession ID Mm10

Library idBAMCTSS
CNhs10476 DRZ012694 DRZ014077
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

CNhs10476

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 0.0687
1001 0.0331
1002 --0.0941
1003 0.166
1004 0
1005 0.106
1006 0
1007 --0.031
1008 0
1009 0.121
101 0.0476
1010 0
1011 0
1012 0
1013 0.25
1014 --0.0874
1015 --0.121
1016 --0.0888
1017 0
1018 0.106
1019 0.898
102 0
1020 0
1021 0.106
1022 0.326
1023 0
1024 0.122
1025 --0.0549
1026 0
1027 --0.048
1028 0
1029 --0.0418
103 0.0507
1030 0
1031 --0.154
1032 --0.119
1033 0
1034 0
1035 0
1036 0.0507
1037 0
1038 --0.075
1039 0.121
104 0
1040 0.0463
1041 1.028



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: CNhs10476

Jaspar motif P-value
MA0002.2 0.0053
MA0003.1 0.29
MA0004.1 0.398
MA0006.1 0.0943
MA0007.1 0.199
MA0009.1 0.259
MA0014.1 0.427
MA0017.1 0.659
MA0018.2 0.0146
MA0019.1 0.915
MA0024.1 4.20843e-4
MA0025.1 0.0425
MA0027.1 0.979
MA0028.1 0.829
MA0029.1 0.0475
MA0030.1 0.16
MA0031.1 0.659
MA0035.2 0.00102
MA0038.1 0.797
MA0039.2 0.00515
MA0040.1 0.0151
MA0041.1 0.682
MA0042.1 0.36
MA0043.1 0.117
MA0046.1 6.064e-15
MA0047.2 0.184
MA0048.1 0.897
MA0050.1 8.08014e-8
MA0051.1 2.88699e-5
MA0052.1 0.922
MA0055.1 0.459
MA0057.1 0.244
MA0058.1 0.429
MA0059.1 0.349
MA0060.1 1.75822e-4
MA0061.1 0.155
MA0062.2 0.238
MA0065.2 0.00439
MA0066.1 0.973
MA0067.1 0.367
MA0068.1 0.132
MA0069.1 0.597
MA0070.1 0.794
MA0071.1 0.938
MA0072.1 0.819
MA0073.1 0.859
MA0074.1 0.793
MA0076.1 0.975
MA0077.1 0.326
MA0078.1 0.343
MA0079.2 0.192
MA0080.2 3.2988e-5
MA0081.1 0.0345
MA0083.1 0.892
MA0084.1 0.765
MA0087.1 0.345
MA0088.1 0.689
MA0090.1 0.576
MA0091.1 0.774
MA0092.1 0.353
MA0093.1 0.391
MA0099.2 0.649
MA0100.1 0.0674
MA0101.1 0.00964
MA0102.2 0.11
MA0103.1 0.00113
MA0104.2 0.97
MA0105.1 0.851
MA0106.1 0.505
MA0107.1 0.0157
MA0108.2 0.0108
MA0111.1 0.501
MA0112.2 1.16983e-4
MA0113.1 0.033
MA0114.1 0.332
MA0115.1 0.392
MA0116.1 0.124
MA0117.1 0.478
MA0119.1 0.324
MA0122.1 0.955
MA0124.1 0.257
MA0125.1 0.0237
MA0131.1 0.323
MA0135.1 0.623
MA0136.1 9.88118e-4
MA0137.2 5.08831e-5
MA0138.2 0.294
MA0139.1 0.452
MA0140.1 0.00299
MA0141.1 0.792
MA0142.1 0.487
MA0143.1 0.217
MA0144.1 1.81966e-5
MA0145.1 0.0426
MA0146.1 0.0128
MA0147.1 0.759
MA0148.1 0.298
MA0149.1 0.514
MA0150.1 0.356
MA0152.1 0.672
MA0153.1 3.94373e-11
MA0154.1 0.0763
MA0155.1 0.532
MA0156.1 3.36526e-5
MA0157.1 0.00542
MA0159.1 0.221
MA0160.1 0.832
MA0162.1 0.329
MA0163.1 0.141
MA0164.1 0.28
MA0258.1 0.0209
MA0259.1 0.662



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: CNhs10476

Novel motif P-value
1 0.259
10 0.284
100 0.731
101 0.782
102 0.635
103 0.173
104 0.413
105 0.318
106 0.00183
107 0.119
108 0.495
109 0.0297
11 0.0956
110 0.149
111 0.0619
112 0.288
113 0.815
114 0.2
115 0.286
116 0.311
117 0.3
118 0.811
119 0.139
12 0.513
120 0.814
121 0.908
122 0.101
123 0.629
124 0.529
125 0.047
126 0.715
127 0.221
128 0.00364
129 0.067
13 4.88599e-6
130 0.321
131 0.138
132 0.632
133 0.227
134 0.602
135 0.106
136 0.178
137 0.0132
138 0.341
139 0.148
14 0.402
140 0.864
141 0.371
142 0.643
143 0.388
144 0.0778
145 0.0392
146 0.47
147 0.166
148 0.705
149 0.201
15 0.224
150 0.155
151 0.074
152 0.0202
153 0.425
154 0.817
155 0.382
156 0.691
157 0.305
158 0.564
159 0.778
160 0.255
161 0.14
162 0.293
163 0.99
164 0.0109
165 0.339
166 0.765
167 0.103
168 0.788
169 0.0025
17 0.0412
18 0.699
19 0.103
2 0.299
20 0.348
21 0.642
22 0.0977
23 0.483
24 9.01137e-4
25 0.963
26 0.0127
27 0.498
28 0.418
29 0.403
3 0.244
30 0.775
31 0.965
32 0.818
33 0.614
34 0.795
35 0.233
36 0.724
37 0.0363
38 0.146
39 0.194
4 0.548
40 0.446
41 0.936
42 0.194
43 0.0783
44 0.476
45 0.65
46 0.105
47 0.291
48 0.0984
49 0.349
5 0.168
50 0.426
51 0.864
52 0.0641
53 0.601
54 0.853
55 0.679
56 0.403
57 0.958
58 0.4
59 0.405
6 0.184
60 0.0253
61 0.129
62 0.326
63 0.0187
64 0.802
65 0.219
66 0.776
67 0.966
68 0.0999
69 0.459
7 0.0594
70 0.00139
71 0.128
72 0.373
73 0.0169
74 0.712
75 0.312
76 0.707
77 0.554
78 0.00541
79 0.838
8 0.67
80 0.792
81 0.591
82 0.332
83 0.806
84 0.906
85 0.115
86 0.189
87 0.0632
88 0.364
89 0.514
9 0.451
90 0.639
91 0.829
92 0.21
93 0.693
94 0.945
95 0.371
96 0.484
97 0.768
98 0.242
99 0.324



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: CNhs10476


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)
0001911 (mammary gland)
0000479 (tissue)
0004121 (ectoderm-derived structure)
0000062 (organ)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0002365 (exocrine gland)
0002530 (gland)
0010317 (germ layer / neural crest derived structure)
0003100 (female organism)
0002330 (exocrine 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)
0000323 (mouse pregnant day 18)
0011387 (mouse mammary gland- adult pregnant day19 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:0006601 (presumptive ectoderm)
UBERON:0008425 (mammary ridge)
UBERON:0010316 (germ layer / neural crest)