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|is_obsolete=
 
|is_obsolete=
 
|library_id=CNhs11036
 
|library_id=CNhs11036
|library_ids=CNhs11036
 
 
|name=pituitary gland, embryo E16
 
|name=pituitary gland, embryo E16
 
|namespace=FANTOM5
 
|namespace=FANTOM5

Revision as of 03:44, 25 October 2013


Name:pituitary gland, embryo E16
Species:Mouse (Mus musculus)
Library ID:CNhs11036
Sample type:developmental
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissuepituitary gland
dev stage16 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  DRS008934
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11036 CAGE DRX009071 DRR009945
Accession ID Mm9

Library idBAMCTSS
CNhs11036 DRZ001370 DRZ002753
Download raw sequence, BAM & CTSS
Mm9
BAMCTSS
[{{{mm9bam}}} download][{{{mm9ctss}}} donwload]
Mm10
BAMCTSS
[{{{mm10bam}}} download][{{{mm10ctss}}} donwload]


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

CNhs11036

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0.132
10 0
100 0.0713
1000 0
1001 0.111
1002 0.217
1003 0.109
1004 0.374
1005 0
1006 0.11
1007 1.901339e-4
1008 0
1009 0.116
101 --0.064
1010 0
1011 0.0713
1012 0.132
1013 0.0555
1014 0.329
1015 0.172
1016 0.227
1017 0
1018 0
1019 0
102 0
1020 0
1021 0
1022 --0.0383
1023 0
1024 0.132
1025 0.0714
1026 0
1027 0.0431
1028 0
1029 0.133
103 0.514
1030 0
1031 0.552
1032 --0.0126
1033 0.0713
1034 0
1035 0
1036 0.048
1037 0
1038 0.0426
1039 --0.00758
104 0
1040 0.147
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: CNhs11036

Jaspar motif P-value
MA0002.2 7.35335e-7
MA0003.1 0.15
MA0004.1 0.514
MA0006.1 0.517
MA0007.1 0.497
MA0009.1 0.712
MA0014.1 0.353
MA0017.1 1.19637e-9
MA0018.2 0.0609
MA0019.1 0.545
MA0024.1 0.3
MA0025.1 0.0817
MA0027.1 0.991
MA0028.1 0.69
MA0029.1 0.897
MA0030.1 0.498
MA0031.1 0.686
MA0035.2 0.00112
MA0038.1 0.231
MA0039.2 0.258
MA0040.1 0.124
MA0041.1 0.446
MA0042.1 0.753
MA0043.1 0.0716
MA0046.1 3.62383e-25
MA0047.2 8.77191e-4
MA0048.1 0.373
MA0050.1 0.00518
MA0051.1 0.0068
MA0052.1 2.77157e-7
MA0055.1 0.956
MA0057.1 0.113
MA0058.1 0.448
MA0059.1 0.177
MA0060.1 1.59034e-4
MA0061.1 0.0301
MA0062.2 0.105
MA0065.2 2.2187e-6
MA0066.1 0.0133
MA0067.1 0.592
MA0068.1 0.118
MA0069.1 0.14
MA0070.1 0.916
MA0071.1 0.022
MA0072.1 0.0203
MA0073.1 0.686
MA0074.1 0.358
MA0076.1 0.707
MA0077.1 0.412
MA0078.1 0.307
MA0079.2 0.17
MA0080.2 1.88611e-9
MA0081.1 0.184
MA0083.1 0.104
MA0084.1 0.0696
MA0087.1 0.682
MA0088.1 0.312
MA0090.1 0.372
MA0091.1 0.847
MA0092.1 0.527
MA0093.1 0.581
MA0099.2 2.92432e-5
MA0100.1 0.455
MA0101.1 0.0689
MA0102.2 0.981
MA0103.1 0.393
MA0104.2 0.501
MA0105.1 9.55398e-4
MA0106.1 0.16
MA0107.1 0.0431
MA0108.2 0.306
MA0111.1 0.787
MA0112.2 2.59777e-7
MA0113.1 0.876
MA0114.1 1.36454e-7
MA0115.1 5.16575e-7
MA0116.1 0.0123
MA0117.1 0.54
MA0119.1 0.106
MA0122.1 0.669
MA0124.1 0.374
MA0125.1 0.0284
MA0131.1 0.642
MA0135.1 0.42
MA0136.1 8.22581e-8
MA0137.2 0.0349
MA0138.2 0.528
MA0139.1 0.221
MA0140.1 0.00276
MA0141.1 0.00107
MA0142.1 0.863
MA0143.1 0.522
MA0144.1 0.059
MA0145.1 0.24
MA0146.1 0.104
MA0147.1 0.422
MA0148.1 2.23136e-4
MA0149.1 0.00817
MA0150.1 4.10936e-4
MA0152.1 0.529
MA0153.1 5.72728e-20
MA0154.1 0.00975
MA0155.1 0.823
MA0156.1 0.00255
MA0157.1 0.737
MA0159.1 5.66226e-4
MA0160.1 9.52512e-4
MA0162.1 0.377
MA0163.1 8.6483e-4
MA0164.1 0.668
MA0258.1 4.48369e-5
MA0259.1 0.78



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: CNhs11036

Novel motif P-value
1 0.0759
10 0.0668
100 0.992
101 0.524
102 0.835
103 0.134
104 0.586
105 0.608
106 0.013
107 0.0601
108 0.711
109 0.148
11 0.135
110 0.0856
111 0.0329
112 0.0454
113 0.669
114 0.0908
115 0.627
116 0.49
117 0.0275
118 0.703
119 0.0606
12 0.812
120 0.635
121 0.564
122 0.72
123 0.598
124 0.809
125 0.346
126 0.261
127 0.0144
128 0.0743
129 0.33
13 0.00733
130 0.913
131 0.644
132 0.736
133 0.4
134 0.765
135 0.251
136 0.693
137 0.615
138 0.474
139 0.0361
14 0.573
140 0.0528
141 0.618
142 0.181
143 0.97
144 0.671
145 0.157
146 0.463
147 0.655
148 0.41
149 0.366
15 0.0508
150 0.228
151 0.276
152 0.291
153 0.946
154 0.655
155 0.633
156 4.37932e-4
157 0.712
158 0.202
159 0.311
160 0.481
161 0.559
162 0.972
163 0.0696
164 0.0339
165 0.0194
166 0.503
167 0.238
168 0.772
169 2.75037e-4
17 0.126
18 0.461
19 0.203
2 0.976
20 0.774
21 0.901
22 0.28
23 0.321
24 0.353
25 0.276
26 0.0294
27 0.593
28 0.412
29 0.0813
3 0.162
30 0.956
31 0.603
32 0.496
33 0.293
34 0.829
35 0.425
36 0.157
37 0.0489
38 0.295
39 0.662
4 0.412
40 0.249
41 0.0532
42 0.493
43 0.0942
44 0.103
45 0.588
46 0.103
47 0.181
48 0.0821
49 0.0904
5 0.0413
50 0.839
51 0.45
52 0.301
53 0.935
54 0.487
55 0.184
56 0.613
57 0.441
58 0.268
59 0.147
6 0.729
60 0.0384
61 0.15
62 0.0611
63 0.113
64 0.546
65 0.175
66 0.879
67 0.788
68 0.0868
69 0.83
7 0.0695
70 0.0118
71 0.0311
72 0.468
73 0.0996
74 0.39
75 0.0272
76 0.975
77 0.266
78 0.00834
79 0.726
8 0.0432
80 0.253
81 0.443
82 0.121
83 0.292
84 0.236
85 0.0161
86 0.199
87 0.357
88 0.36
89 0.0941
9 0.523
90 0.209
91 0.265
92 0.183
93 0.0675
94 0.37
95 0.174
96 0.274
97 0.756
98 0.259
99 0.84



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: CNhs11036


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)
0000299 (mouse embryonic day 16 sample)
0011353 (mouse pituitary gland- embryo E16 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)