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FF:427-16B9

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Name:pituitary gland, embryo E15
Species:Mouse (Mus musculus)
Library ID:CNhs10592
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
tissuepituitary gland
dev stage15 days embryo
sexmixture
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  SAMD00005651
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs10592 CAGE DRX009070 DRR009944
Accession ID Mm9

Library idBAMCTSS
CNhs10592 DRZ001369 DRZ002752
Accession ID Mm10

Library idBAMCTSS
CNhs10592 DRZ012719 DRZ014102
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

CNhs10592

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0.105
10 0
100 0.0359
1000 0
1001 0.176
1002 0.0541
1003 --0.0308
1004 0.308
1005 0
1006 0.0674
1007 0.0911
1008 0
1009 --0.0709
101 --0.00159
1010 0
1011 0.0709
1012 0
1013 --0.013
1014 0.258
1015 0.177
1016 0.192
1017 0
1018 0
1019 0
102 0
1020 0
1021 0
1022 0.00785
1023 0
1024 0.0954
1025 0
1026 0
1027 0.0709
1028 0
1029 --0.0158
103 0.117
1030 0
1031 0.41
1032 --0.0935
1033 0.0516
1034 0
1035 0
1036 --0.028
1037 0
1038 0.0257
1039 --0.0457
104 0
1040 0.173
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: CNhs10592

Jaspar motif P-value
MA0002.2 3.00584e-5
MA0003.1 0.234
MA0004.1 0.65
MA0006.1 0.477
MA0007.1 0.66
MA0009.1 0.761
MA0014.1 0.432
MA0017.1 3.1722e-7
MA0018.2 0.0168
MA0019.1 0.605
MA0024.1 0.132
MA0025.1 0.903
MA0027.1 0.758
MA0028.1 0.269
MA0029.1 0.385
MA0030.1 0.554
MA0031.1 0.843
MA0035.2 0.0205
MA0038.1 0.032
MA0039.2 0.526
MA0040.1 0.815
MA0041.1 0.139
MA0042.1 0.734
MA0043.1 0.00202
MA0046.1 8.99287e-20
MA0047.2 0.0316
MA0048.1 0.255
MA0050.1 0.0184
MA0051.1 0.28
MA0052.1 1.01935e-4
MA0055.1 0.721
MA0057.1 0.124
MA0058.1 0.599
MA0059.1 0.115
MA0060.1 1.41195e-9
MA0061.1 0.0408
MA0062.2 0.358
MA0065.2 5.73721e-5
MA0066.1 0.00489
MA0067.1 0.709
MA0068.1 0.412
MA0069.1 0.257
MA0070.1 0.394
MA0071.1 0.0796
MA0072.1 0.141
MA0073.1 0.769
MA0074.1 0.293
MA0076.1 0.0636
MA0077.1 0.195
MA0078.1 0.571
MA0079.2 0.158
MA0080.2 4.05386e-7
MA0081.1 0.571
MA0083.1 0.106
MA0084.1 0.0698
MA0087.1 0.128
MA0088.1 0.665
MA0090.1 0.341
MA0091.1 0.716
MA0092.1 0.415
MA0093.1 0.722
MA0099.2 6.95472e-4
MA0100.1 0.989
MA0101.1 0.233
MA0102.2 0.98
MA0103.1 0.507
MA0104.2 0.676
MA0105.1 1.80099e-4
MA0106.1 0.0694
MA0107.1 0.119
MA0108.2 0.426
MA0111.1 0.736
MA0112.2 5.30851e-8
MA0113.1 0.726
MA0114.1 1.41116e-5
MA0115.1 5.88474e-6
MA0116.1 0.00324
MA0117.1 0.659
MA0119.1 0.0527
MA0122.1 0.724
MA0124.1 0.724
MA0125.1 0.0123
MA0131.1 0.438
MA0135.1 0.0426
MA0136.1 0.00455
MA0137.2 0.579
MA0138.2 0.244
MA0139.1 0.192
MA0140.1 0.013
MA0141.1 0.00119
MA0142.1 0.757
MA0143.1 0.333
MA0144.1 0.252
MA0145.1 0.181
MA0146.1 0.226
MA0147.1 0.502
MA0148.1 0.00532
MA0149.1 0.00476
MA0150.1 0.00263
MA0152.1 0.503
MA0153.1 1.2216e-14
MA0154.1 0.00308
MA0155.1 0.56
MA0156.1 0.537
MA0157.1 0.939
MA0159.1 0.0064
MA0160.1 0.0129
MA0162.1 0.259
MA0163.1 2.51373e-4
MA0164.1 0.59
MA0258.1 2.00199e-5
MA0259.1 0.842



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: CNhs10592

Novel motif P-value
1 0.0528
10 0.0665
100 0.99
101 0.606
102 0.853
103 0.0924
104 0.801
105 0.54
106 0.0066
107 0.0137
108 0.599
109 0.163
11 0.103
110 0.0941
111 0.00772
112 0.0387
113 0.839
114 0.0165
115 0.183
116 0.364
117 0.0629
118 0.653
119 0.0576
12 0.921
120 0.972
121 0.993
122 0.536
123 0.51
124 0.924
125 0.144
126 0.389
127 0.0508
128 0.0184
129 0.182
13 0.0437
130 0.543
131 0.385
132 0.563
133 0.431
134 0.826
135 0.28
136 0.639
137 0.964
138 0.499
139 0.0434
14 0.539
140 0.0192
141 0.591
142 0.0666
143 0.29
144 0.976
145 0.0892
146 0.664
147 0.781
148 0.179
149 0.312
15 0.0926
150 0.198
151 0.271
152 0.267
153 0.904
154 0.41
155 0.335
156 4.9211e-4
157 0.607
158 0.266
159 0.859
160 0.208
161 0.591
162 0.727
163 0.322
164 0.0736
165 0.143
166 0.676
167 0.154
168 0.786
169 1.56263e-4
17 0.0972
18 0.268
19 0.11
2 0.848
20 0.869
21 0.726
22 0.228
23 0.147
24 0.677
25 0.395
26 0.0325
27 0.733
28 0.562
29 0.152
3 0.116
30 0.959
31 0.542
32 0.0893
33 0.286
34 0.703
35 0.377
36 0.134
37 0.0681
38 0.349
39 0.597
4 0.402
40 0.319
41 0.347
42 0.428
43 0.0927
44 0.0854
45 0.679
46 0.0939
47 0.205
48 0.135
49 0.0957
5 0.0427
50 0.714
51 0.476
52 0.21
53 0.772
54 0.411
55 0.224
56 0.526
57 0.227
58 0.346
59 0.0682
6 0.684
60 0.0403
61 0.25
62 0.0865
63 0.103
64 0.451
65 0.165
66 0.455
67 0.69
68 0.0158
69 0.502
7 0.109
70 0.00364
71 0.0383
72 0.595
73 0.136
74 0.267
75 0.0925
76 0.977
77 0.186
78 0.0231
79 0.645
8 0.0516
80 0.445
81 0.346
82 0.125
83 0.139
84 0.82
85 0.0105
86 0.473
87 0.92
88 0.496
89 0.231
9 0.462
90 0.0931
91 0.131
92 0.143
93 0.117
94 0.302
95 0.156
96 0.102
97 0.776
98 0.289
99 0.626



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: CNhs10592


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)
0000922 (embryo)
0000955 (brain)
0000007 (pituitary gland)
0001894 (diencephalon)
0000479 (tissue)
0004121 (ectoderm-derived structure)
0003296 (gland of diencephalon)
0010133 (neuroendocrine gland)
0010314 (structure with developmental contribution from neural crest)
0011216 (organ system subdivision)
0000062 (organ)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000481 (multi-tissue structure)
0000073 (regional part of nervous system)
0000477 (anatomical cluster)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0002368 (endocrine gland)
0002616 (regional part of brain)
0002780 (regional part of forebrain)
0002530 (gland)
0010317 (germ layer / neural crest derived structure)
0001017 (central nervous system)
0001016 (nervous system)
0001890 (forebrain)
0000949 (endocrine system)

FF: FANTOM5
0000102 (sample by type)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000999 (fetal tissue sample)
0000292 (embryonic day sample - mouse)
0000004 (tissue sample)
0000298 (mouse embryonic day 15 sample)
0011345 (mouse pituitary gland- embryo E15 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:0010316 (germ layer / neural crest)
FF:0000294 (mouse embryonic day 11 sample)