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FF:370-44C7

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Name:pituitary gland, embryo E13
Species:Mouse (Mus musculus)
Library ID:CNhs11009
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 stage13 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  SAMD00005549
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11009 CAGE DRX009068 DRR009942
Accession ID Mm9

Library idBAMCTSS
CNhs11009 DRZ001367 DRZ002750
Accession ID Mm10

Library idBAMCTSS
CNhs11009 DRZ012717 DRZ014100
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

CNhs11009

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0.0356
10 0
100 0.0999
1000 0
1001 -0.0395
1002 0.251
1003 -0.0731
1004 0.377
1005 0
1006 -2.404932e-4
1007 0.141
1008 0
1009 -0.0786
101 -0.0813
1010 0
1011 -0.0178
1012 0
1013 -0.138
1014 0.383
1015 0.358
1016 0.247
1017 0
1018 0
1019 0
102 0
1020 0
1021 0.0528
1022 -0.0704
1023 0
1024 0.0101
1025 0
1026 0
1027 0
1028 0
1029 -0.148
103 0.0683
1030 0
1031 0.374
1032 -0.177
1033 0.0859
1034 0
1035 0
1036 0.152
1037 0
1038 -0.0488
1039 -0.0702
104 0
1040 0.0134
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: CNhs11009
Jaspar motif P-value
MA0002.2 0.0106
MA0003.1 0.973
MA0004.1 0.661
MA0006.1 0.339
MA0007.1 0.636
MA0009.1 0.464
MA0014.1 0.36
MA0017.1 8.28548e-6
MA0018.2 0.305
MA0019.1 0.723
MA0024.1 0.017
MA0025.1 0.164
MA0027.1 0.284
MA0028.1 0.115
MA0029.1 0.0915
MA0030.1 0.243
MA0031.1 0.124
MA0035.2 0.0637
MA0038.1 0.254
MA0039.2 0.338
MA0040.1 0.414
MA0041.1 0.36
MA0042.1 0.949
MA0043.1 0.0242
MA0046.1 2.73061e-16
MA0047.2 0.00327
MA0048.1 0.498
MA0050.1 8.36892e-7
MA0051.1 1.12121e-4
MA0052.1 6.99843e-6
MA0055.1 0.0287
MA0057.1 0.129
MA0058.1 0.654
MA0059.1 0.832
MA0060.1 4.49789e-15
MA0061.1 0.0426
MA0062.2 0.631
MA0065.2 0.00315
MA0066.1 0.11
MA0067.1 0.0257
MA0068.1 0.48
MA0069.1 0.622
MA0070.1 0.716
MA0071.1 0.348
MA0072.1 0.0873
MA0073.1 0.964
MA0074.1 0.391
MA0076.1 0.0573
MA0077.1 0.0114
MA0078.1 0.402
MA0079.2 0.333
MA0080.2 4.46986e-9
MA0081.1 0.415
MA0083.1 0.054
MA0084.1 0.174
MA0087.1 0.23
MA0088.1 0.271
MA0090.1 0.2
MA0091.1 0.654
MA0092.1 0.558
MA0093.1 0.68
MA0099.2 8.4466e-4
MA0100.1 0.899
MA0101.1 0.207
MA0102.2 0.381
MA0103.1 0.528
MA0104.2 0.337
MA0105.1 0.522
MA0106.1 0.139
MA0107.1 0.0349
MA0108.2 0.857
MA0111.1 0.954
MA0112.2 3.2139e-5
MA0113.1 0.947
MA0114.1 1.03346e-4
MA0115.1 0.0162
MA0116.1 0.747
MA0117.1 0.101
MA0119.1 0.0108
MA0122.1 0.455
MA0124.1 0.632
MA0125.1 0.00947
MA0131.1 0.643
MA0135.1 0.00366
MA0136.1 1.28535e-4
MA0137.2 0.0831
MA0138.2 0.0195
MA0139.1 0.815
MA0140.1 0.124
MA0141.1 0.0151
MA0142.1 0.798
MA0143.1 0.00446
MA0144.1 0.116
MA0145.1 0.352
MA0146.1 0.406
MA0147.1 0.267
MA0148.1 7.30044e-6
MA0149.1 0.0137
MA0150.1 4.84486e-5
MA0152.1 0.618
MA0153.1 4.24745e-12
MA0154.1 0.0145
MA0155.1 0.328
MA0156.1 0.0214
MA0157.1 0.23
MA0159.1 0.0385
MA0160.1 0.0345
MA0162.1 0.506
MA0163.1 0.956
MA0164.1 0.579
MA0258.1 7.59046e-4
MA0259.1 0.687



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: CNhs11009
Novel motif P-value
1 0.0316
10 0.204
100 0.66
101 0.675
102 0.744
103 0.126
104 0.902
105 0.18
106 0.0118
107 0.0252
108 0.995
109 0.66
11 0.299
110 0.295
111 0.0445
112 0.0849
113 0.401
114 0.168
115 0.838
116 0.894
117 0.536
118 0.979
119 0.28
12 0.98
120 0.931
121 0.887
122 0.491
123 0.151
124 0.867
125 0.343
126 0.877
127 0.133
128 0.0774
129 0.211
13 0.0925
130 0.399
131 0.338
132 0.576
133 0.651
134 0.435
135 0.168
136 0.327
137 0.51
138 0.706
139 0.013
14 0.362
140 0.0145
141 0.0542
142 0.00375
143 0.846
144 0.9
145 0.335
146 0.357
147 0.465
148 0.361
149 0.512
15 0.0909
150 0.525
151 0.0918
152 0.685
153 0.419
154 0.168
155 0.887
156 7.45976e-4
157 0.743
158 0.217
159 0.24
160 0.438
161 0.741
162 0.492
163 0.0981
164 0.0658
165 0.198
166 0.852
167 0.239
168 0.419
169 0.373
17 0.163
18 0.679
19 0.214
2 0.977
20 0.631
21 0.564
22 0.53
23 0.0989
24 0.923
25 0.142
26 0.378
27 0.781
28 0.362
29 0.398
3 0.423
30 0.907
31 0.615
32 0.258
33 0.637
34 0.678
35 0.484
36 0.561
37 0.0682
38 0.329
39 0.874
4 0.741
40 0.956
41 0.645
42 0.967
43 0.142
44 0.537
45 0.621
46 0.2
47 0.209
48 0.192
49 0.101
5 0.0446
50 0.665
51 0.463
52 0.325
53 0.701
54 0.352
55 0.936
56 0.776
57 0.272
58 0.233
59 0.379
6 0.784
60 0.0675
61 0.869
62 0.087
63 0.269
64 0.963
65 0.305
66 0.16
67 0.607
68 0.399
69 0.879
7 0.118
70 0.0089
71 0.239
72 0.735
73 0.584
74 0.274
75 0.69
76 0.746
77 0.449
78 0.0548
79 0.365
8 0.445
80 0.148
81 0.376
82 0.467
83 0.295
84 0.759
85 0.0721
86 0.557
87 0.226
88 0.484
89 0.301
9 0.376
90 0.178
91 0.457
92 0.0672
93 0.215
94 0.302
95 0.983
96 0.272
97 0.686
98 0.792
99 0.669



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: CNhs11009


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)
0000293 (mouse embryonic day 13 sample)
0011325 (mouse pituitary gland- embryo E13 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)