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FF:595-22B6

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Name:mammary gland, adult lactating day02
Species:Mouse (Mus musculus)
Library ID:CNhs10480
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 stage2 days lactation 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  SAMD00005704
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs10480 CAGE DRX009044 DRR009918
Accession ID Mm9

Library idBAMCTSS
CNhs10480 DRZ001343 DRZ002726
Accession ID Mm10

Library idBAMCTSS
CNhs10480 DRZ012693 DRZ014076
Download raw sequence, BAM & CTSS
Mm9
FastaBAMCTSS
downloaddownloaddonwload
Mm10
BAMCTSS
downloaddonwload


Relative expression to median (log10)


Transcription factors with enriched expression in this sample
Ranked 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 sample
Ranked 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

CNhs10480

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 0.2
1001 0.0326
1002 -0.0577
1003 0.16
1004 0
1005 0
1006 0
1007 -0.00387
1008 0
1009 0.0377
101 1.64964e-4
1010 0
1011 -3.231029e-4
1012 0
1013 0.555
1014 -0.0874
1015 -0.221
1016 -0.206
1017 0
1018 0.181
1019 1.954
102 0
1020 0
1021 0.0648
1022 0.394
1023 0
1024 0.0865
1025 0
1026 0
1027 0
1028 0
1029 -0.0455
103 0
1030 0
1031 -0.424
1032 0.0723
1033 0
1034 0
1035 0
1036 -0.0646
1037 0
1038 -0.14
1039 0.122
104 0
1040 -0.121
1041 1.015



Repeat families with enriched expression in this sample
Summary: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 motifs
Summary: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: CNhs10480
Jaspar motif P-value
MA0002.2 0.00288
MA0003.1 0.293
MA0004.1 0.751
MA0006.1 0.127
MA0007.1 0.274
MA0009.1 0.433
MA0014.1 0.393
MA0017.1 0.219
MA0018.2 0.0268
MA0019.1 0.822
MA0024.1 0.0162
MA0025.1 0.3
MA0027.1 0.406
MA0028.1 0.758
MA0029.1 0.243
MA0030.1 0.0433
MA0031.1 0.711
MA0035.2 0.0137
MA0038.1 0.58
MA0039.2 0.00679
MA0040.1 0.0183
MA0041.1 0.225
MA0042.1 0.132
MA0043.1 0.0897
MA0046.1 1.22044e-12
MA0047.2 0.807
MA0048.1 0.952
MA0050.1 6.18869e-4
MA0051.1 3.86315e-4
MA0052.1 0.634
MA0055.1 0.505
MA0057.1 0.158
MA0058.1 0.591
MA0059.1 0.23
MA0060.1 0.204
MA0061.1 0.264
MA0062.2 0.488
MA0065.2 0.00183
MA0066.1 0.588
MA0067.1 0.654
MA0068.1 0.705
MA0069.1 0.379
MA0070.1 0.465
MA0071.1 0.961
MA0072.1 0.667
MA0073.1 0.79
MA0074.1 0.646
MA0076.1 0.741
MA0077.1 0.241
MA0078.1 0.489
MA0079.2 0.972
MA0080.2 9.24739e-4
MA0081.1 0.123
MA0083.1 0.814
MA0084.1 0.71
MA0087.1 0.399
MA0088.1 0.396
MA0090.1 0.985
MA0091.1 0.382
MA0092.1 0.261
MA0093.1 0.659
MA0099.2 0.319
MA0100.1 0.215
MA0101.1 0.205
MA0102.2 0.321
MA0103.1 1.51835e-4
MA0104.2 0.951
MA0105.1 0.376
MA0106.1 0.296
MA0107.1 0.119
MA0108.2 0.0942
MA0111.1 0.614
MA0112.2 1.14672e-4
MA0113.1 0.0406
MA0114.1 0.104
MA0115.1 0.548
MA0116.1 0.0993
MA0117.1 0.341
MA0119.1 0.143
MA0122.1 0.9
MA0124.1 0.226
MA0125.1 0.0989
MA0131.1 0.459
MA0135.1 0.833
MA0136.1 0.0145
MA0137.2 8.6792e-5
MA0138.2 0.578
MA0139.1 0.372
MA0140.1 0.0349
MA0141.1 0.521
MA0142.1 0.487
MA0143.1 0.212
MA0144.1 1.20247e-4
MA0145.1 0.0563
MA0146.1 0.0101
MA0147.1 0.692
MA0148.1 0.691
MA0149.1 0.186
MA0150.1 0.0863
MA0152.1 0.218
MA0153.1 6.99199e-7
MA0154.1 0.0509
MA0155.1 0.596
MA0156.1 0.0184
MA0157.1 0.152
MA0159.1 0.0385
MA0160.1 0.538
MA0162.1 0.248
MA0163.1 0.0489
MA0164.1 0.273
MA0258.1 0.0149
MA0259.1 0.688



FANTOM5 phase1 novel unique motifs
Summary: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: CNhs10480
Novel motif P-value
1 0.202
10 0.0878
100 0.791
101 0.915
102 0.434
103 0.0713
104 0.739
105 0.374
106 0.0163
107 0.199
108 0.385
109 0.0188
11 0.0507
110 0.0978
111 0.0235
112 0.166
113 0.976
114 0.36
115 0.14
116 0.405
117 0.126
118 0.976
119 0.0348
12 0.451
120 0.665
121 0.638
122 0.0874
123 0.441
124 0.666
125 0.0566
126 0.641
127 0.253
128 0.0114
129 0.137
13 2.7623e-5
130 0.839
131 0.142
132 0.752
133 0.362
134 0.38
135 0.119
136 0.685
137 0.0959
138 0.652
139 0.0759
14 0.617
140 0.593
141 0.222
142 0.406
143 0.696
144 0.0532
145 0.0302
146 0.285
147 0.331
148 0.461
149 0.148
15 0.182
150 0.151
151 0.141
152 0.0303
153 0.469
154 0.865
155 0.814
156 0.349
157 0.388
158 0.302
159 0.557
160 0.283
161 0.52
162 0.525
163 0.403
164 0.153
165 0.23
166 0.791
167 0.414
168 0.735
169 0.00115
17 0.0251
18 0.915
19 0.105
2 0.425
20 0.435
21 0.792
22 0.139
23 0.33
24 0.0169
25 0.539
26 0.0321
27 0.597
28 0.477
29 0.221
3 0.17
30 0.871
31 0.736
32 0.714
33 0.366
34 0.93
35 0.815
36 0.303
37 0.041
38 0.15
39 0.178
4 0.955
40 0.466
41 0.954
42 0.184
43 0.183
44 0.228
45 0.759
46 0.126
47 0.0886
48 0.128
49 0.214
5 0.133
50 0.633
51 0.65
52 0.184
53 0.993
54 0.869
55 0.352
56 0.331
57 0.415
58 0.242
59 0.429
6 0.345
60 0.0585
61 0.167
62 0.135
63 0.0252
64 0.612
65 0.189
66 0.927
67 0.933
68 0.025
69 0.626
7 0.0458
70 0.00253
71 0.0487
72 0.304
73 0.0253
74 0.981
75 0.187
76 0.735
77 0.282
78 0.0143
79 0.937
8 0.283
80 0.616
81 0.41
82 0.569
83 0.84
84 0.794
85 0.0616
86 0.205
87 0.153
88 0.219
89 0.15
9 0.846
90 0.904
91 0.317
92 0.198
93 0.835
94 0.958
95 0.272
96 0.827
97 0.915
98 0.145
99 0.351



de novo motifs identified by HOMER in promoters active in this sample
Summary:The result of HOMER in this sample is shown.
Analyst:NA

library id: CNhs10480


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)
0000324 (mouse lactating sample)
0011390 (mouse mammary gland- adult lactating day02 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)