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FF:1388-42B2

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Name:diencephalon, neonate N30
Species:Mouse (Mus musculus)
Library ID:CNhs11201
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
tissuediencephalon
dev stage30 days 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  SAMD00005403
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11201 CAGE DRX008950 DRR009824
Accession ID Mm9

Library idBAMCTSS
CNhs11201 DRZ001249 DRZ002632
Accession ID Mm10

Library idBAMCTSS
CNhs11201 DRZ012599 DRZ013982
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

CNhs11201

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0.756
10 0
100 0.0653
1000 --0.0106
1001 0.0303
1002 --0.083
1003 --0.0221
1004 0
1005 0.115
1006 0.585
1007 0.0346
1008 0
1009 --0.19
101 --0.0595
1010 0
1011 0.66
1012 0.361
1013 0.174
1014 --0.0874
1015 --0.0603
1016 --0.0945
1017 0
1018 0
1019 0
102 0
1020 0
1021 0
1022 0
1023 0
1024 0.118
1025 0
1026 0
1027 0.508
1028 0
1029 0.143
103 --0.0829
1030 0
1031 --0.356
1032 0.402
1033 0
1034 0
1035 0.0532
1036 --0.244
1037 0
1038 0.0308
1039 0.136
104 0
1040 --0.31
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: CNhs11201

Jaspar motif P-value
MA0002.2 0.00125
MA0003.1 0.296
MA0004.1 0.485
MA0006.1 0.181
MA0007.1 0.389
MA0009.1 0.741
MA0014.1 0.641
MA0017.1 1.38324e-6
MA0018.2 0.0132
MA0019.1 0.346
MA0024.1 0.0582
MA0025.1 0.00457
MA0027.1 0.0591
MA0028.1 0.0706
MA0029.1 0.437
MA0030.1 0.798
MA0031.1 0.214
MA0035.2 0.0133
MA0038.1 0.285
MA0039.2 0.0383
MA0040.1 0.325
MA0041.1 0.115
MA0042.1 0.221
MA0043.1 0.0562
MA0046.1 1.0205e-11
MA0047.2 8.53604e-5
MA0048.1 0.0428
MA0050.1 1.9755e-5
MA0051.1 0.00199
MA0052.1 0.846
MA0055.1 0.012
MA0057.1 0.357
MA0058.1 0.43
MA0059.1 0.132
MA0060.1 0.716
MA0061.1 0.033
MA0062.2 0.00135
MA0065.2 1.30554e-6
MA0066.1 0.03
MA0067.1 0.562
MA0068.1 0.4
MA0069.1 0.0643
MA0070.1 0.83
MA0071.1 0.0561
MA0072.1 0.428
MA0073.1 0.774
MA0074.1 0.116
MA0076.1 0.168
MA0077.1 0.401
MA0078.1 0.793
MA0079.2 0.341
MA0080.2 3.04834e-10
MA0081.1 0.237
MA0083.1 0.00941
MA0084.1 0.903
MA0087.1 0.248
MA0088.1 0.243
MA0090.1 0.125
MA0091.1 0.214
MA0092.1 0.203
MA0093.1 0.534
MA0099.2 0.00278
MA0100.1 0.276
MA0101.1 0.0169
MA0102.2 0.481
MA0103.1 0.197
MA0104.2 0.83
MA0105.1 0.00699
MA0106.1 0.0527
MA0107.1 0.0423
MA0108.2 0.00286
MA0111.1 0.977
MA0112.2 7.19482e-4
MA0113.1 0.358
MA0114.1 5.98976e-6
MA0115.1 5.89665e-6
MA0116.1 0.0631
MA0117.1 0.955
MA0119.1 0.115
MA0122.1 0.959
MA0124.1 0.447
MA0125.1 0.0186
MA0131.1 0.713
MA0135.1 0.581
MA0136.1 1.41749e-12
MA0137.2 0.0611
MA0138.2 1.73492e-4
MA0139.1 0.493
MA0140.1 1.97393e-4
MA0141.1 0.00287
MA0142.1 0.236
MA0143.1 0.955
MA0144.1 0.0446
MA0145.1 0.145
MA0146.1 0.0247
MA0147.1 0.666
MA0148.1 3.75712e-4
MA0149.1 0.105
MA0150.1 0.159
MA0152.1 0.216
MA0153.1 4.05514e-11
MA0154.1 0.045
MA0155.1 0.406
MA0156.1 2.8707e-8
MA0157.1 0.105
MA0159.1 0.0014
MA0160.1 0.00444
MA0162.1 0.148
MA0163.1 7.54726e-4
MA0164.1 0.82
MA0258.1 0.0178
MA0259.1 0.838



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: CNhs11201

Novel motif P-value
1 0.202
10 0.0477
100 0.385
101 0.836
102 0.955
103 0.0617
104 0.954
105 0.666
106 0.0609
107 0.179
108 0.709
109 0.00999
11 0.0717
110 0.0419
111 0.118
112 0.00602
113 0.498
114 0.33
115 0.895
116 0.197
117 0.00361
118 0.338
119 0.213
12 0.949
120 0.718
121 0.564
122 0.61
123 8.15991e-4
124 0.0544
125 0.236
126 0.0266
127 0.214
128 0.0573
129 0.371
13 4.20859e-7
130 0.205
131 0.734
132 0.668
133 0.863
134 0.113
135 0.265
136 0.039
137 0.705
138 0.912
139 0.276
14 0.889
140 0.0232
141 0.63
142 0.917
143 0.362
144 0.799
145 2.93122e-4
146 0.331
147 0.359
148 0.722
149 0.9
15 0.214
150 0.0601
151 0.839
152 0.0993
153 0.85
154 0.959
155 0.29
156 0.00655
157 0.213
158 0.317
159 0.612
160 0.178
161 0.0997
162 0.661
163 0.657
164 0.0402
165 0.147
166 0.814
167 0.644
168 0.554
169 0.00337
17 0.0545
18 0.861
19 0.102
2 0.786
20 0.035
21 0.213
22 0.149
23 0.741
24 0.0631
25 0.698
26 9.73217e-8
27 0.566
28 0.774
29 0.0278
3 0.0613
30 0.767
31 0.929
32 0.468
33 0.136
34 0.738
35 0.807
36 0.215
37 0.0261
38 0.547
39 0.342
4 0.257
40 0.0987
41 0.444
42 0.179
43 0.127
44 0.399
45 0.712
46 0.101
47 0.354
48 0.265
49 0.193
5 0.155
50 0.246
51 0.747
52 0.353
53 0.425
54 0.943
55 0.923
56 0.477
57 0.582
58 0.342
59 0.11
6 0.814
60 0.0454
61 0.0463
62 0.223
63 0.174
64 0.642
65 0.407
66 0.699
67 0.63
68 0.798
69 0.493
7 0.0195
70 0.0634
71 0.00389
72 0.459
73 0.0355
74 0.896
75 0.0459
76 0.409
77 0.407
78 0.00187
79 0.416
8 0.0542
80 0.401
81 0.783
82 0.232
83 0.106
84 0.807
85 0.208
86 0.159
87 0.119
88 0.453
89 0.661
9 0.469
90 0.214
91 0.12
92 0.222
93 0.0722
94 0.813
95 0.0346
96 0.313
97 0.977
98 0.523
99 0.43



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: CNhs11201


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)
0001894 (diencephalon)
0000479 (tissue)
0004121 (ectoderm-derived structure)
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)
0002616 (regional part of brain)
0002780 (regional part of forebrain)
0010317 (germ layer / neural crest derived structure)
0001017 (central nervous system)
0001016 (nervous system)
0001890 (forebrain)

FF: FANTOM5
0000102 (sample by type)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000004 (tissue sample)
0000303 (neonate sample - mouse)
0000310 (mouse neonate N30 sample)
0011470 (mouse diencephalon- neonate N30 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:0006222 (future diencephalon)
UBERON:0010316 (germ layer / neural crest)
FF:0000294 (mouse embryonic day 11 sample)