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FF:1308-22E9

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Name:pituitary gland, neonate N00
Species:Mouse (Mus musculus)
Library ID:CNhs11190
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 stage0 day neonate
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  SAMD00004923
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11190 CAGE DRX009073 DRR009947
Accession ID Mm9

Library idBAMCTSS
CNhs11190 DRZ001372 DRZ002755
Accession ID Mm10

Library idBAMCTSS
CNhs11190 DRZ012722 DRZ014105
Download raw sequence, BAM & CTSS
Mm9
FastaBAMCTSS
downloaddownloaddonwload
Mm10
BAMCTSS
downloaddonwload


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

CNhs11190

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0.128
10 0
100 0
1000 0
1001 --0.0749
1002 0
1003 0.203
1004 0.244
1005 --0.0389
1006 0.17
1007 --0.258
1008 0
1009 0.0165
101 --0.15
1010 0
1011 0.115
1012 0
1013 0.157
1014 0.441
1015 0.106
1016 0.24
1017 0
1018 0
1019 0
102 0
1020 0
1021 0.115
1022 0.0573
1023 0
1024 0.192
1025 0
1026 0.086
1027 0
1028 0
1029 --0.0674
103 0.394
1030 0
1031 0.441
1032 0.0282
1033 0.14
1034 0
1035 0
1036 --0.0932
1037 0
1038 0.0276
1039 0.0487
104 0
1040 0.174
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: CNhs11190

Jaspar motif P-value
MA0002.2 0.0222
MA0003.1 0.646
MA0004.1 0.517
MA0006.1 0.704
MA0007.1 0.0132
MA0009.1 0.495
MA0014.1 0.399
MA0017.1 2.51495e-9
MA0018.2 2.65857e-4
MA0019.1 0.816
MA0024.1 0.641
MA0025.1 0.406
MA0027.1 0.891
MA0028.1 0.192
MA0029.1 0.73
MA0030.1 0.141
MA0031.1 0.127
MA0035.2 0.0622
MA0038.1 0.345
MA0039.2 0.841
MA0040.1 0.313
MA0041.1 0.103
MA0042.1 0.364
MA0043.1 6.99592e-4
MA0046.1 1.86597e-12
MA0047.2 0.0354
MA0048.1 0.0315
MA0050.1 0.201
MA0051.1 0.67
MA0052.1 0.134
MA0055.1 0.661
MA0057.1 0.519
MA0058.1 0.521
MA0059.1 0.0814
MA0060.1 0.0025
MA0061.1 0.0815
MA0062.2 0.0306
MA0065.2 0.00129
MA0066.1 0.00447
MA0067.1 0.859
MA0068.1 0.346
MA0069.1 0.166
MA0070.1 0.338
MA0071.1 0.136
MA0072.1 0.0638
MA0073.1 0.968
MA0074.1 0.762
MA0076.1 0.922
MA0077.1 0.177
MA0078.1 0.201
MA0079.2 0.0316
MA0080.2 2.58426e-6
MA0081.1 0.313
MA0083.1 0.747
MA0084.1 0.443
MA0087.1 0.967
MA0088.1 0.0449
MA0090.1 0.534
MA0091.1 0.624
MA0092.1 0.692
MA0093.1 0.592
MA0099.2 0.171
MA0100.1 0.192
MA0101.1 0.0824
MA0102.2 0.872
MA0103.1 0.639
MA0104.2 0.361
MA0105.1 0.0209
MA0106.1 0.0213
MA0107.1 0.0684
MA0108.2 0.00229
MA0111.1 0.816
MA0112.2 8.09445e-5
MA0113.1 0.504
MA0114.1 5.85671e-9
MA0115.1 1.93184e-6
MA0116.1 0.0776
MA0117.1 0.892
MA0119.1 0.127
MA0122.1 0.582
MA0124.1 0.875
MA0125.1 0.096
MA0131.1 0.525
MA0135.1 3.05436e-4
MA0136.1 1.01554e-5
MA0137.2 0.246
MA0138.2 0.157
MA0139.1 0.445
MA0140.1 4.99261e-4
MA0141.1 0.0101
MA0142.1 0.735
MA0143.1 0.656
MA0144.1 0.671
MA0145.1 0.75
MA0146.1 0.916
MA0147.1 0.354
MA0148.1 0.00607
MA0149.1 0.0437
MA0150.1 0.00231
MA0152.1 0.482
MA0153.1 1.38151e-10
MA0154.1 0.126
MA0155.1 0.22
MA0156.1 0.00333
MA0157.1 0.265
MA0159.1 0.00475
MA0160.1 0.0187
MA0162.1 0.298
MA0163.1 0.11
MA0164.1 0.87
MA0258.1 0.00445
MA0259.1 0.486



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: CNhs11190

Novel motif P-value
1 0.027
10 0.0143
100 0.925
101 0.572
102 0.69
103 0.0551
104 0.691
105 0.873
106 0.186
107 0.18
108 0.537
109 0.645
11 0.282
110 0.0324
111 0.0367
112 0.0737
113 0.837
114 0.38
115 0.589
116 0.807
117 0.00596
118 0.245
119 0.171
12 0.847
120 0.864
121 0.732
122 0.182
123 0.803
124 0.744
125 0.333
126 0.171
127 0.14
128 0.314
129 0.315
13 0.00542
130 0.716
131 0.274
132 0.803
133 0.427
134 0.822
135 0.22
136 0.0729
137 0.688
138 0.333
139 0.0394
14 0.928
140 0.0112
141 0.857
142 0.0824
143 0.719
144 0.627
145 0.0916
146 0.965
147 0.748
148 0.406
149 0.805
15 0.0609
150 0.418
151 0.734
152 0.263
153 0.481
154 0.198
155 0.873
156 0.00472
157 0.383
158 0.151
159 0.158
160 0.194
161 0.68
162 0.681
163 0.172
164 0.0356
165 0.262
166 0.89
167 0.038
168 0.535
169 0.146
17 0.456
18 0.744
19 0.156
2 0.419
20 0.464
21 0.73
22 0.628
23 0.571
24 0.576
25 0.307
26 0.00411
27 0.924
28 0.319
29 0.0427
3 0.157
30 0.427
31 0.884
32 0.941
33 0.788
34 0.562
35 0.281
36 0.545
37 0.123
38 0.617
39 0.602
4 0.606
40 0.823
41 0.418
42 0.422
43 0.0636
44 0.444
45 0.966
46 0.0279
47 0.29
48 0.229
49 0.0562
5 0.0325
50 0.77
51 0.46
52 0.727
53 0.828
54 0.506
55 0.329
56 0.868
57 0.223
58 0.169
59 0.853
6 0.622
60 0.142
61 0.0882
62 0.0692
63 0.277
64 0.815
65 0.633
66 0.298
67 0.747
68 0.28
69 0.904
7 0.0401
70 0.163
71 0.0142
72 0.605
73 0.737
74 0.109
75 0.0738
76 0.292
77 0.645
78 0.0022
79 0.767
8 0.0533
80 0.307
81 0.525
82 0.454
83 0.342
84 0.559
85 0.0895
86 0.325
87 0.0433
88 0.179
89 0.231
9 0.754
90 0.066
91 0.294
92 0.217
93 0.0135
94 0.0398
95 0.798
96 0.135
97 0.7
98 0.828
99 0.784



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: CNhs11190


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)
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)
0000004 (tissue sample)
0000303 (neonate sample - mouse)
0000304 (mouse neonate N0 sample)
0011507 (mouse pituitary gland- neonate N00 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)