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FF:346-16E6

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Name:pituitary gland, embryo E12
Species:Mouse (Mus musculus)
Library ID:CNhs11018
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 stage12 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  SAMD00005702
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11018 CAGE DRX009067 DRR009941
Accession ID Mm9

Library idBAMCTSS
CNhs11018 DRZ001366 DRZ002749
Accession ID Mm10

Library idBAMCTSS
CNhs11018 DRZ012716 DRZ014099
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

CNhs11018

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0.0537
10 0
100 0.116
1000 -0.0355
1001 0
1002 0.353
1003 -0.102
1004 0.418
1005 -0.0967
1006 -0.0538
1007 0.17
1008 0
1009 -0.0241
101 0.0875
1010 0
1011 0.0204
1012 0
1013 -0.203
1014 0.318
1015 0.318
1016 0.167
1017 0
1018 0
1019 0
102 0
1020 0
1021 0.0232
1022 0
1023 0
1024 -0.0607
1025 0.134
1026 0
1027 0.229
1028 0
1029 -0.014
103 0
1030 0
1031 0.238
1032 -0.0878
1033 0.024
1034 0
1035 0
1036 0.109
1037 0
1038 -0.0194
1039 -0.123
104 0
1040 0.0199
1041 0



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: CNhs11018
Jaspar motif P-value
MA0002.2 2.48882e-5
MA0003.1 0.12
MA0004.1 0.768
MA0006.1 0.372
MA0007.1 0.364
MA0009.1 0.368
MA0014.1 0.402
MA0017.1 1.3671e-5
MA0018.2 0.187
MA0019.1 0.823
MA0024.1 9.89778e-4
MA0025.1 0.00292
MA0027.1 0.202
MA0028.1 0.239
MA0029.1 0.384
MA0030.1 0.174
MA0031.1 0.00677
MA0035.2 0.00937
MA0038.1 0.00386
MA0039.2 0.0358
MA0040.1 0.0706
MA0041.1 0.24
MA0042.1 0.444
MA0043.1 0.0362
MA0046.1 1.89899e-26
MA0047.2 4.2476e-5
MA0048.1 0.293
MA0050.1 1.64522e-5
MA0051.1 4.90417e-4
MA0052.1 3.67965e-8
MA0055.1 0.145
MA0057.1 0.0276
MA0058.1 0.793
MA0059.1 0.809
MA0060.1 7.18174e-16
MA0061.1 0.0402
MA0062.2 0.546
MA0065.2 2.25613e-5
MA0066.1 0.0518
MA0067.1 0.366
MA0068.1 0.237
MA0069.1 0.327
MA0070.1 0.653
MA0071.1 0.16
MA0072.1 0.0979
MA0073.1 0.667
MA0074.1 0.534
MA0076.1 0.128
MA0077.1 0.0419
MA0078.1 0.41
MA0079.2 0.943
MA0080.2 1.16685e-10
MA0081.1 0.244
MA0083.1 0.0349
MA0084.1 0.704
MA0087.1 0.139
MA0088.1 0.478
MA0090.1 0.233
MA0091.1 0.58
MA0092.1 0.272
MA0093.1 0.819
MA0099.2 1.43858e-6
MA0100.1 0.668
MA0101.1 0.244
MA0102.2 0.609
MA0103.1 0.0351
MA0104.2 0.76
MA0105.1 0.00817
MA0106.1 0.214
MA0107.1 0.114
MA0108.2 0.944
MA0111.1 0.51
MA0112.2 6.38339e-7
MA0113.1 0.43
MA0114.1 1.87445e-4
MA0115.1 0.0199
MA0116.1 0.0119
MA0117.1 0.553
MA0119.1 0.00473
MA0122.1 0.755
MA0124.1 0.4
MA0125.1 0.00315
MA0131.1 0.389
MA0135.1 0.942
MA0136.1 1.95343e-6
MA0137.2 0.294
MA0138.2 0.00196
MA0139.1 0.0526
MA0140.1 0.0507
MA0141.1 0.00389
MA0142.1 0.186
MA0143.1 0.00538
MA0144.1 0.193
MA0145.1 0.0127
MA0146.1 0.233
MA0147.1 0.855
MA0148.1 1.42278e-5
MA0149.1 0.011
MA0150.1 0.00529
MA0152.1 0.1
MA0153.1 9.98276e-18
MA0154.1 9.94653e-4
MA0155.1 0.602
MA0156.1 0.0242
MA0157.1 0.0556
MA0159.1 0.0125
MA0160.1 0.0142
MA0162.1 0.53
MA0163.1 0.0143
MA0164.1 0.669
MA0258.1 1.39695e-4
MA0259.1 0.733



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: CNhs11018
Novel motif P-value
1 0.0845
10 0.266
100 0.76
101 0.653
102 0.859
103 0.0917
104 0.631
105 0.12
106 0.00973
107 0.0922
108 0.717
109 0.134
11 0.0995
110 0.167
111 0.00907
112 0.0234
113 0.45
114 0.0448
115 0.856
116 0.476
117 0.393
118 0.945
119 0.0962
12 0.898
120 0.608
121 0.7
122 0.922
123 0.279
124 0.196
125 0.395
126 0.448
127 0.032
128 0.0412
129 0.188
13 0.0997
130 0.474
131 0.163
132 0.442
133 0.494
134 0.706
135 0.0978
136 0.983
137 0.722
138 0.549
139 0.0162
14 0.337
140 0.00611
141 0.0744
142 0.461
143 0.425
144 0.971
145 0.196
146 0.327
147 0.702
148 0.244
149 0.147
15 0.0983
150 0.535
151 0.135
152 0.0444
153 0.655
154 0.599
155 0.613
156 0.9
157 0.982
158 0.392
159 0.495
160 0.571
161 0.832
162 0.565
163 0.0917
164 0.138
165 0.123
166 0.773
167 0.934
168 0.15
169 0.0011
17 0.0697
18 0.502
19 0.135
2 0.404
20 0.551
21 0.977
22 0.206
23 0.0597
24 0.431
25 0.447
26 0.154
27 0.395
28 0.471
29 0.463
3 0.177
30 0.657
31 0.576
32 0.0868
33 0.611
34 0.661
35 0.503
36 0.357
37 0.0461
38 0.2
39 0.61
4 0.386
40 0.319
41 0.345
42 0.511
43 0.129
44 0.108
45 0.405
46 0.196
47 0.135
48 0.114
49 0.133
5 0.138
50 0.907
51 0.523
52 0.26
53 0.563
54 0.473
55 0.603
56 0.386
57 0.456
58 0.277
59 0.0374
6 0.647
60 0.0663
61 0.865
62 0.0944
63 0.102
64 0.48
65 0.0896
66 0.439
67 0.654
68 0.147
69 0.363
7 0.165
70 9.87886e-4
71 0.128
72 0.329
73 0.0673
74 0.51
75 0.234
76 0.663
77 0.138
78 0.0859
79 0.185
8 0.24
80 0.182
81 0.325
82 0.0566
83 0.505
84 0.5
85 0.0163
86 0.366
87 0.603
88 0.765
89 0.126
9 0.339
90 0.25
91 0.362
92 0.0892
93 0.191
94 0.423
95 0.174
96 0.208
97 0.699
98 0.238
99 0.693



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: CNhs11018


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)
0000295 (mouse embryonic day 12 sample)
0011317 (mouse pituitary gland- embryo E12 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)