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FF:627-43G1

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Name:hippocampus, neonate N00
Species:Mouse (Mus musculus)
Library ID:CNhs11228
Sample type:developmental
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissuehippocampus
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  SAMD00005607
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11228 CAGE DRX008987 DRR009861
Accession ID Mm9

Library idBAMCTSS
CNhs11228 DRZ001286 DRZ002669
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

CNhs11228

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0.423
10 0
100 0.369
1000 --0.0142
1001 0.0441
1002 0.139
1003 0.729
1004 0.0425
1005 0
1006 0.267
1007 0.121
1008 0
1009 --0.19
101 0.0323
1010 0
1011 0.335
1012 0.285
1013 --0.031
1014 --0.0133
1015 0.274
1016 0.262
1017 0
1018 0
1019 0
102 0
1020 0
1021 0.04
1022 --0.0704
1023 0
1024 --0.0583
1025 0.0425
1026 0
1027 0.568
1028 0
1029 0.131
103 --0.0754
1030 0
1031 --0.275
1032 --0.0953
1033 0.0425
1034 0
1035 0
1036 --0.106
1037 0
1038 0.0666
1039 --0.127
104 0
1040 --0.134
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: CNhs11228

Jaspar motif P-value
MA0002.2 0.00107
MA0003.1 0.157
MA0004.1 0.665
MA0006.1 0.125
MA0007.1 0.325
MA0009.1 0.582
MA0014.1 0.454
MA0017.1 1.89779e-6
MA0018.2 0.0647
MA0019.1 0.159
MA0024.1 0.631
MA0025.1 0.515
MA0027.1 0.0816
MA0028.1 0.526
MA0029.1 0.259
MA0030.1 0.986
MA0031.1 0.1
MA0035.2 0.0065
MA0038.1 0.0921
MA0039.2 0.0837
MA0040.1 0.55
MA0041.1 0.255
MA0042.1 0.59
MA0043.1 0.091
MA0046.1 2.86319e-14
MA0047.2 2.88853e-5
MA0048.1 0.4
MA0050.1 1.88117e-4
MA0051.1 0.0189
MA0052.1 1.37714e-4
MA0055.1 0.392
MA0057.1 0.134
MA0058.1 0.543
MA0059.1 0.354
MA0060.1 0.0071
MA0061.1 0.0659
MA0062.2 0.132
MA0065.2 1.32893e-6
MA0066.1 0.0732
MA0067.1 0.79
MA0068.1 0.767
MA0069.1 0.0353
MA0070.1 0.44
MA0071.1 0.0475
MA0072.1 0.0382
MA0073.1 0.689
MA0074.1 0.164
MA0076.1 0.951
MA0077.1 0.078
MA0078.1 0.601
MA0079.2 0.576
MA0080.2 3.5459e-10
MA0081.1 0.494
MA0083.1 6.77577e-4
MA0084.1 0.323
MA0087.1 0.73
MA0088.1 0.341
MA0090.1 0.0318
MA0091.1 0.255
MA0092.1 0.23
MA0093.1 0.688
MA0099.2 3.4404e-5
MA0100.1 0.989
MA0101.1 0.0993
MA0102.2 0.893
MA0103.1 0.0371
MA0104.2 0.767
MA0105.1 0.0178
MA0106.1 0.158
MA0107.1 0.0916
MA0108.2 7.16136e-4
MA0111.1 0.857
MA0112.2 5.68311e-5
MA0113.1 0.286
MA0114.1 3.13334e-5
MA0115.1 4.64768e-4
MA0116.1 0.0392
MA0117.1 0.894
MA0119.1 0.169
MA0122.1 0.972
MA0124.1 0.729
MA0125.1 0.13
MA0131.1 0.767
MA0135.1 0.435
MA0136.1 5.06838e-9
MA0137.2 0.139
MA0138.2 0.557
MA0139.1 0.221
MA0140.1 5.09718e-4
MA0141.1 1.98965e-4
MA0142.1 0.221
MA0143.1 0.114
MA0144.1 0.0624
MA0145.1 0.0542
MA0146.1 0.041
MA0147.1 0.876
MA0148.1 1.20069e-6
MA0149.1 0.0515
MA0150.1 0.0273
MA0152.1 0.261
MA0153.1 9.34583e-13
MA0154.1 0.017
MA0155.1 0.412
MA0156.1 4.80416e-5
MA0157.1 0.0346
MA0159.1 3.36566e-4
MA0160.1 0.00578
MA0162.1 0.267
MA0163.1 2.29065e-4
MA0164.1 0.926
MA0258.1 0.00188
MA0259.1 0.557



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: CNhs11228

Novel motif P-value
1 0.161
10 0.12
100 0.727
101 0.975
102 0.852
103 0.103
104 0.957
105 0.188
106 0.0118
107 0.0551
108 0.853
109 0.00533
11 0.0465
110 0.0643
111 0.0236
112 0.0053
113 0.776
114 0.127
115 0.591
116 0.352
117 0.0404
118 0.438
119 0.11
12 0.914
120 0.665
121 0.368
122 0.899
123 0.355
124 0.356
125 0.338
126 0.0615
127 0.0828
128 0.0217
129 0.0638
13 8.14349e-5
130 0.754
131 0.679
132 0.937
133 0.816
134 0.379
135 0.875
136 0.104
137 0.645
138 0.847
139 0.181
14 0.603
140 0.0699
141 0.151
142 0.154
143 0.283
144 0.721
145 0.0214
146 0.414
147 0.918
148 0.508
149 0.0618
15 0.147
150 0.14
151 0.413
152 0.0596
153 0.681
154 0.957
155 0.572
156 0.0112
157 0.454
158 0.201
159 0.96
160 0.196
161 0.0773
162 0.996
163 0.232
164 0.0435
165 0.0105
166 0.782
167 0.621
168 0.275
169 0.00595
17 0.0268
18 0.696
19 0.0749
2 0.667
20 0.463
21 0.49
22 0.108
23 0.323
24 0.035
25 0.566
26 3.53023e-4
27 0.738
28 0.447
29 0.0901
3 0.0505
30 0.807
31 0.706
32 0.289
33 0.222
34 0.621
35 0.915
36 0.484
37 0.0166
38 0.374
39 0.219
4 0.296
40 0.21
41 0.364
42 0.215
43 0.121
44 0.239
45 0.549
46 0.136
47 0.136
48 0.118
49 0.148
5 0.118
50 0.304
51 0.625
52 0.137
53 0.918
54 0.583
55 0.578
56 0.316
57 0.683
58 0.253
59 0.0329
6 0.974
60 0.0214
61 0.18
62 0.139
63 0.126
64 0.6
65 0.215
66 0.923
67 0.478
68 0.894
69 0.348
7 0.0321
70 0.0125
71 0.0174
72 0.433
73 0.0264
74 0.521
75 0.0936
76 0.942
77 0.197
78 0.00791
79 0.468
8 0.106
80 0.945
81 0.487
82 0.104
83 0.0778
84 0.854
85 0.0399
86 0.185
87 0.0626
88 0.209
89 0.292
9 0.383
90 0.161
91 0.177
92 0.141
93 0.0381
94 0.521
95 0.0478
96 0.203
97 0.976
98 0.522
99 0.244



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: CNhs11228


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)
0001954 (Ammon's horn)
0000956 (cerebral cortex)
0000479 (tissue)
0004121 (ectoderm-derived structure)
0000064 (organ part)
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)
0003528 (brain grey matter)
0002791 (regional part of telencephalon)
0000467 (anatomical system)
0002619 (regional part of cerebral cortex)
0001062 (anatomical entity)
0000480 (anatomical group)
0002616 (regional part of brain)
0002780 (regional part of forebrain)
0002020 (gray matter)
0003022 (lobe parts of cerebral cortex)
0010317 (germ layer / neural crest derived structure)
0001017 (central nervous system)
0002421 (hippocampal formation)
0001016 (nervous system)
0001869 (cerebral hemisphere)
0001893 (telencephalon)
0001890 (forebrain)
0000203 (pallium)
0000349 (limbic system)
0002600 (limbic lobe)

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)
0011391 (mouse hippocampus- 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)